TriticeaeExpDB

• Analyze Gene Expression
• Explore Gene Details & BioProjects

Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJDB8633	A gene expression map of the developing wheat leaf	Cellular and transcriptomic analyses reveal two-staged chloroplast biogenesis underpinning photosynthesis build-up in the wheat leaf	Illumina HiSeq 4000	To understand the biogenesis of photosynthetic organelles in developmental gradient of the monocotyledon leaf, we provide the first detailed and comprehensive gene expression map of the developing leaf of wheat.	Leaf
PRJDB8961	Introgression of chromosomal segments conferring early heading time from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars	Introgression of chromosomal segments conferring early heading date from wheat diploid progenitor, Aegilops tauschii Coss., into Japanese elite wheat cultivars.	Illumina MiSeq	We backcrossed two early heading lines of synthetic hexaploid wheat with four Japanese elite cultivars to develop the early heading lines of bread wheat. In total, nine early heading lines, which showed two to eight days earlier heading time than their parental cultivars in the field conditions, were selected and established from the selfed progenies of the two- or three-times backcrossed populations. RNA sequencing-based genotyping was performed to detect single nucleotide polymorphisms between the selected lines and their parental wheat cultivars, which revealed the chromosomal regions transmitted from the parental synthetic wheat to the selected lines	Leaf
PRJEB29855	RNAseq data for hexaploid wheat Paragon	Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat	Illumina HiSeq 2500	RNAseq data were prepared from 5 tissues of hexaploid wheat (Triticum aestivum) Paragon cultivar: leaf (14dd) * rep3, root (14dd) * rep3, developing grain (10dd) * rep3, developing grain (27dd) * rep3, pooled developing grain (5,10, 15,20,27,30dd) * rep1; and seedling (4dd) * rep3.Pooled developing grain was used to collect all the grain genes for genome annotation and not used for gene expression	Leaf, root, grain, seedling
PRJEB36244	Identification of genes involved in pollen development in wheat	Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses	Illumina HiSeq 2500	RNASeq of stamens and pistils around the time of meiosis of wheat flowers.	Stamens and pistils
PRJEB38081	RNA-seq of developing grain tissues (12 days post-anthesis) of red (R-D1b) and white (R-D1a) near-isogenic lines of wheat cv. Holdfast.	Proanthocyanidin biosynthesis in the developing wheat seed coat investigated by chemical and RNA-Seq analysis	Illumina Genome Analyzer IIx	Proanthocyanidin (PA) is a polymeric flavonoid found in the seed coat of many plant species, including wheat, and is responsible for the red grain colour of most wheat cultivars. White wheat cultivars that lack PA have null mutations in all three homoeologues of the gene encoding the R myb transcription factor. Previous work has shown that R control several genes in the PA biosynthetic pathway. The aim of this experiment was to identify other components of the PA pathway of wheat controlled by R through comparison of transcript levels in tissues of developing grain of red and white near-isogenic lines of the cultivar Holdfast. Note: RNA-seq reads from the Red samples in this experiment have previously been submitted to ENA under the accession number E-MTAB-3103	Grains
PRJEB43230	Identification of Rf genes in hexaploid wheat (Triticum aestivum L.) by RNA-seq.	Identification of Rf Genes in Hexaploid Wheat (Triticumaestivum L.) by RNA-Seq and Paralog Analyses	Illumina HiSeq 4000	Plants of two non-restorer varieties of hexaploid winter wheat (Astoria, Grana) and two restorers ones (Patres and Primépi) were used to identify effective Rf (fertility restorer) genes by next generation sequencing on whole transcriptomes (RNA-seq).	Anthers
PRJEB50830	Using TILLING lines and RNA-seq to investigate genes that control wheat inflorescence development.	MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat	Illumina NovaSeq 6000	We sought to identify genes that control spikelet development by screening the Cadenza bread wheat TILLING population for lines that display a modified form of inflorescence architecture known as paired spikelets. Here, we used exome capture sequence analysis to identify candidate mutations the promote the modified form of inflorescence architecture in two lines, and RNA-seq transcriptome experiments to enhance our understanding of the underlying genetic pathways. This research identified a homeobox domain transcription factor that controls inflorescence architecture in wheat.	Inflorescence
PRJEB5135	Analysis of the bread wheat grain transcriptome reveals complex genome interplay in a hexaploid cereal.	Genome interplay in the grain transcriptome of hexaploid bread wheat	Illumina HiSeq 2000	Allohexaploid bread wheat (Triticum aestivum, L.) provides ~ 20% of calories consumed by humans. Hitherto lack of genome sequence for the three homoelogous and highly similar bread wheat genomes (A, B and, D) impeded expression analysis of the grain transcriptome. We used novel genome information to analyze the cell type specific expression of homeologous genes in the developing wheat grain	Grains
PRJEB55858	RNA-seq of wheat lodicules in four varieties at pre-flowering and early flowering stages	-	Illumina HiSeq 4000	RNA-seq of wheat lodicules in two higly-chasmogamous (HCH) (Piko and Poezja) and two low-chasmogamy (LCH) (Euforia and KWS Dacanto) varieties at two developmental stages - pre-flowering and early flowering.	Lodicules
PRJEB7795	Tissue layers from developing wheat grain at 12 days post-anthesis	-	Illumina Genome Analyzer IIx	Inner pericarp, outer pericarp and endosperm layers from developing grain of bread wheat cv. Holdfast at 12 days post-anthesis.	Inner pericarp, outer pericarp and endosperm layers
PRJNA167943	Gene expression in the developing aleurone and starchy endosperm of wheat	Analysis of the expression of transcription factors and other genes associated with aleurone layer development in wheat endosperm	Illumina Genome Analyzer IIx	Examines the transcript profile of aleurone and starchy endoperm tissues at 6,9 and 14DPA. A minimum of 5 individual seeds from 3 separate spikes from three individual plants were pooled for each tissue preparation	Seeds
PRJNA213168	mRNA-Seq for homoeologous gene expression analysis in hexaploid bread wheat	Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat	Illumina Genome Analyzer IIx	Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoalleles, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ‘nullisomic-tetrasomic’ lines) with next generation deep sequencing of gene transcripts (RNA-seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative homoeoallelic contribution to gene expression. We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 40% of wheat genes are expressed from all three distinct homoeoalleles. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeoallele. The remaining ~60% of wheat genes are expressed from either one or two homoeoalleles only, through a combination of extensive transcriptional silencing and homoeoallele loss. We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoalleles to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution	Leaf and root
PRJNA214739	Triticum aestivum strain:Chinese Spring (bread wheat)	-	Illumina Genome Analyzer II	Transcriptome data for Triticum aestivum young root and shoot samples	Root and shoot
PRJNA217717	Triticum aestivum strain:cultivar (bread wheat)	Evaluation of Assembly Strategies Using RNA-Seq Data Associated with Grain Development of Wheat (Triticum aestivum L.)	Illumina Genome Analyzer II	Wheat yield is correlated significantly with grain size which is established during morphological stage. In present study, morphological stage of developing wheat grain were analyzed by RNA-seq.This research will help us to understand the mechnism underlying of grain development. This is the first study on gene expression profiling of morphological stage of developing wheat grain and the results may aid the identification of pathways and genes associated with seed development in wheat.	Grains
PRJNA297977	Triticum aestivum cultivar:Svilena (bread wheat)	Analysis of wheat microspore embryogenesis induction by transcriptome and small RNA sequencing using the highly responsive cultivar “Svilena”	Illumina HiSeq 2000	We performed mRNA and sRNA transcriptome sequencing of three stages from wheat microspore embryogenesis induction to generate the first sequencing based resource of mRNA and sRNA expression of microspore embryogensis induction.	Anther in vitro culture
PRJNA307237	Triticum aestivum cultivar:Chinese spring (bread wheat)	Transcriptome Analysis of Early Senescence in the Post-Anthesis Flag Leaf of Wheat (Triticum aestivum L.)	Illumina HiSeq 2500	Flag leaf is of paramount importance in determining the grain yield ability of wheat. Compared with other leaves, flag leaf contributed the most photosynthates (41-43%) to the grain. And Leaf senescence is essential for wheat productivity as well. As leaf senesces, nutrients are relocated to the sinks, such as nitrogen, metals, etc. Up to 75% of the reduced nitrogen in leaves is located in chloroplasts. However, the relationship between flag leaf photosynthesis, the timing of senescence, and grain filling has not been clear yet. To aid a better molecular understanding of the post-anthesis flag leaf and also provide an invaluable resource for identification of genes that involved in senescence, the transcriptome of post-anthesis flag leaf was studied over an irregular time course	Flag leaf
PRJNA308628	Triticum aestivum (bread wheat)	Transcriptome Analysis of Purple Pericarps in Common Wheat (Triticum aestivum L.)	Illumina HiSeq 2000	This study comparative transcriptome analysis of purple and white pericarp was carried out using next-generation sequencing technology.	Pericarp
PRJNA318885	riticum aestivum cultivar:BS366 (bread wheat)	-	Illumina HiSeq 2000	The goal of this project is to identify wheat transcriptome of BS366 using de novo assembly of NextGen sequences.	Anthers
PRJNA318961	Triticum aestivum cultivar:CP806 (bread wheat)	-	Illumina HiSeq 2000	The goal of this project is to idengtify wheat transcriptomes using de novo assembly of NextGen sequences.	Anthers
PRJNA318963	Triticum aestivum cultivar:JM8 (bread wheat)	-	Illumina HiSeq 2000	The goal of this project is to idengtify wheat transcriptomes using de novo assembly of NextGen sequences.	Anthers
PRJNA322418	Triticum aestivum Transcriptome or Gene expression	Genomic Imprinting Was Evolutionarily Conserved during Wheat Polyploidization	Illumina HiSeq 2500	Transcriptome of hexaploid wheat, tetroploid wheat and Aegilops tauschii endosperm, used for gene imprinting analysis	Endosperm
PRJNA325489	Genome-wide mRNA Transcriptional Profiling Reveals Regulatory Network for Coordinated Early Wheat Spike Development	A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat	Illumina HiSeq 2000	Wheat panicle development is a coordinated process of proliferation and differentiation with distinctive phase and architecture changes. However, the multiple genes involved networks controlling this process remain enigmatic. Here, we characterized and dissected common wheat panicles in the stages of vegetative stage before elongation, elongation, single ridge, double ridge, glume primodium differentiation and floret differentiation, respectively, followed by RNA-seq and bioinformatics analysis to study genome-wide mRNA transcriptome profiling in wheat early spike development. High gene expression correlations between any two stages (R2>0.97) and only 4000 Differentially Expressed Genes (DEGs) out of 49624 expressed transcripts in all stages indicated that wheat early panicle development is just controlled by an small proportion of important genes. Three subgenomes (A, B and D) contribute equally to this process. K-means clustering analysis revealed the dynamic expression patterns of DEGs and Hierarchical Clustering analysis demonstrated that single bridge stage and double bridge stage are most important for wheat panicle development. Interestingly, 306 transcription factors (TFs) with various functions from different families were identified and the spatial-temporal expression patterns of some were verified by quantitative PCR or in situ hybridization. At early stages, repressing flowering TFs combined with AP2/ERF TFs and cytokinin promote inflorescence meristem development and repress meristem differentiation. At single ridge and double ridge stages, highly expressed stress-response TFs balance the interaction between stress response and development. During reproductive stages, crosstalk between auxin and cytokinin coordinate the meristem proliferation and differentiation, and promoting flowering TFs with polarity establishment TFs and MADS-box TFs promote floral meristem generation and floral organ identity and development. This dataset provided an ideal resource for wheat panicle developmental research. Our study uncovered the regulatory network for coordinated wheat early spike development and would eventually contribute to the improvement of grain number and crop yield. Overall design: mRNA profiles of early wheat spike in six stages	Spikes
PRJNA341486	small RNA and RNA profiling in Triticum turgidum and Triticum aestivum	-	Illumina HiSeq 2500	Identification of key genes for wax production	Leaf sheath
PRJNA344856	RAN-seq of wheat cv. Fukuhomugi and A. cristatum accession Z559 Transcriptome	RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat	Illumina HiSeq 2500	Dissection of interspecific variation and development of single-nucleotide polymorphism markers between Agropyron cristatum and wheat using transcriptome sequencing	Leaves and young spikes
PRJNA348655	Triticum aestivum Transcriptome or Gene expression	Transcriptome Association Identifies Regulators of Wheat Spike Architecture.	Illumina HiSeq 2500	Improving grain yield is an aim during crop domestication, and also a major goal of crop breeding. Spike complexity determines the number of seeds per spike, and is a major strategy to improve yield potential. Whereas a large number of inflorescence regulators have been identified in other plant species, we have limited understanding of wheat spike development. In this work, we tried to identified genes or gene regulatory networks, underlying spike architecture, by correlating trait variation with quantitative gene expression variation.	Spikes
PRJNA353135	Triticum aestivum cultivar:Zhoumai 18 (bread wheat)	De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.)	Illumina HiSeq 2500	ME3/ME6/ME15: Callus from mature embryo for in vitro culture at 3/6/15 days. IME3/IME6/IME15: Callus from immature embryo for in vitro culture at 3/6/15 days.	Callus
PRJNA379374	Triticum aestivum breed:wheat breeding | cultivar:KTM3315A (bread wheat)	Identification and validation of TCONS_00093333 for regulating fertility conversion of thermo-sensitive cytoplasmic male-sterility wheat with Aegilops kotschyi cytoplasm	Illumina HiSeq 2000	KTM3315A is a thermo-sensitive cytoplasmic male sterile/fertile wheat, which is male sterile under normal conditions of autumn sowing, wheares its fertility restored under the conditions of spring sowing or temperature higher than 20℃. Take the anthers of the late uninucleate, the binucleate, the trinucleate stages as the sequencing material, and analyze the differentially expressed genes to find the key genes and molecular mechanism of fertility conversion	Anthers
PRJNA383677	Raw sequence reads of transcriptome for wheat inflorescence development	Transcriptome Profiling of Wheat Inflorescence Development from Spikelet Initiation to Floral Patterning Identified Stage-Specific Regulatory Genes	Illumina HiSeq 2000	Transcriptome profiling of wheat inflorescence development from spikelet initiation to floral patterning identified stage-specific regulatory genes	Inflorescence
PRJNA385600	RNAseq in a population of wheat landraces	-	Illumina HiSeq 2500	RNAseq data from ~200 wheat lines collected from different places of the world	Leaf
PRJNA386580	Triticum aestivum (bread wheat)	ThMYC4E, candidate Blue aleurone 1 gene controlling the associated trait in Triticum aestivum	Illumina MiSeq	The transcriptome analysis of blue grain and white grain wheat was employed for isolating the Ba1 controlling the blue aleurone trait.	Aleurone
PRJNA392390	Triticum aestivum Transcriptome or Gene expression	The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat	Illumina Genome Analyzer II	Developing wheat seed Transcriptome data at 14 and at 30 days post anthesis of a diverse set of wheat genotypes	Seeds
PRJNA393734	Triticum aestivum (bread wheat)	Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field.	Illumina HiSeq 2500	To explore transcriptional regulations in common wheat cultivars Norstar (NO), Manitou (MA), and the near-isogenic lines (NIL) spring Norstar (SN) and winter Manitou (WM) during seasonal cold acclimation. Overall design: Total RNA were extracted from crowns of wheat NIL lines, up to five time points, for each line, in each year	Crown
PRJNA397654	Tissue-specific expression and phylogeny of ammonium and nitrate transporter genes in wheat	Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat	Illumina HiSeq 2500	Plants uptake nitrogen (N) in two main forms: ammonium (NH4+) and nitrate (NO3-). Several ammonium transporter (AMT) and nitrate transporter (NRT) genes are deployed in uptake and transport of N-compound molecules (NH4+ & NO3-) from the soil into the roots and then to other plant organs. Wheat coding sequences obtained from ENSEMBL were BLAST-searched against known AMT and NRT sequences of Arabidopsis, barley, maize, rice, and wheat to retrieve homologous gene sequences in wheat. Phylogenetic relationship among these wheat genes were established using Bayesian models. Results showed distinct classification of sequences with significant homology to NRT1, NRT2, and NRT3 (NAR2) wheat sequences. Members of same gene families (NPF, NRT, NAR) also resolved into close groups. To study the expression patterns of these genes, RNA-seq was carried out on whole transcriptome of 21-days old seedlings of five spring wheat lines grown in controlled environment. Eight AMT and 52 NRT genes were differentially expressed between root and shoot tissues. Several other genes did not express neither in root nor in shoot. Seventy-five percent of differentially expressed wAMT genes and 69% of differentially expressed wNRT genes were observed in at least two out of the five wheat lines. Homeologous genes, characterized by sequence homology, revealed that their counterparts exhibited different expression patterns. Gene ontology classification of the genes showed that most were involved in several cellular and intracellular processes such as binding, catalytic activity, receptor and transporter activities as well as in metabolic processes	Root and shoot
PRJNA398700	Triticum aestivum Transcriptome or Gene expression	Transcriptome analysis of wheat seedling and spike tissues in the hybrid Jingmai 8 uncovered genes involved in heterosis	Illumina HiSeq 2000	transcriptome analysis of heterosis in wheat seedling and spike	Seedling and spike
PRJNA406980	Subgenome Interplay Shapes Genomic Variations and Transcriptomic Changes during Wheat Hexaploidization Events	-	Illumina HiSeq 2500	Genomic variations and transcriptomic changes extensively occur in newly formed polyploids to reconcile immediate challenges caused by divergent subgenomes in one nucleus. To comprehensively investigate sequence elimination and expression alteration in wheat hexaploidization, here we performed whole exome capture experiments coupled with high throughput sequencing analysis by exploiting three sets of newly synthesized wheat species. We observed that the whole wheat chromosomes were subjected to extensive genomic elimination partially regulated by sequence homology in response to hexaploidization. But homeologous subgenomes exhibited distinct features that DNA sequences were preferentially eliminated on DD genome compared with AA and BB genome. In addition, a higher proportion of eliminated sequences occurred in exonic regions than in intergenic regions on DD genome, whereas a significant enrichment was observed in the repeat-rich intergenic regions for AA and BB genome, exhibiting a contrast distribution pattern compared to the gene density. Furthermore, we detected 488 overlapped genes with sequence elimination on DD genome but few on the other two genomes across three nascent hexaploid wheats. Interestingly, GO enrichment analysis showed genes with sequence elimination were enriched in distinct functional pathways between subgenomes. Transcriptome analysis indicates polyploidization enhanced gene expression differentiation between root and leaf and led to rapid and extensive gene expression changes in synthetic hexaploid wheat. AA and BB genome exhibited synergistic expression profiling which was distinct from DD genome, and interestingly, expression bias was observed for a proportion of homeologs in synthetic hexaploid wheat. Strikingly, only 3.3-23.6% genes with sequence elimination exhibited expression changes in synthetic hexaploid wheat compared with their respective progenitors, indicating genomic variation is not the major cause resulting in the transcirptomic changes during wheat polyploidization events, whereas epigenetic modifications might play an important role in regulating expression profiling alterations	Leaf and root
PRJNA407398	Transcriptome analysis reveals potential mechanisms for different grain size between natural and resynthesized allohexaploid wheats with near-identical AABB genomes	Transcriptome analysis reveals potential mechanisms for different grain size between natural and resynthesized allohexaploid wheats with near-identical AABB genomes	Illumina HiSeq 2500	Significant differences in grain size and weight between TAA10 and XX329 were observed at the early stages of development, which could be mainly attributed to the higher growth rate of the pericarp and endosperm cells in XX329 compared to TAA10. Furthermore, comparative transcriptome analysis identified 8891 of 69711 unigenes (12.75%) were differentially expressed genes between grains at 6 days after pollination (DAP) of TAA10 and XX329, including 5314 up-regulated and 3577 down-regulated genes in XX329 compared to TAA10. The MapMan functional annotation and enrichment analysis revealed that the differentially expressed genes were significantly enriched in categories of cell wall, carbohydrate and hormone metabolism. Notably, consistent with the up-regulation of sucrose synthase genes in resynthesized relative to natural allohexaploid wheat, the resynthesized allohexaploid wheat showed higher contents of glucose and fructose in 6-DAP grains than those of the natural allohexaploid wheat.	Whole seed
PRJNA412872	Genomics of alien gene transfer in wheat	Transcriptome reprogramming due to the introduction of a barley telosome into bread wheat affects more barley genes than wheat	Illumina HiSeq 2000	How barley 7HL alien genes are transcribed in the wheat host genetic background, and reciprocally how wheat host genes are impacted by additional alien-homeologous gene copies	Leaf
PRJNA436817	Chinese Spring RNAseq data-set	Shifting the limits in wheat research and breeding using a fully annotated reference genome	Illumina HiSeq 2000	Stage specific RNA sequencing paired sequence reads to study gene expressions related with plant development and flowering stages	"Ovary, rachis,
spike"
PRJNA448363	Comparative Transcriptomic analysis between Low-and High-Zinc and Iron accumulating Wheat (Triticum aestivum L.) Genotypes reveals the Metabolic Changes	Comparative transcriptomic profiling of High- and Low- grain Zinc and Iron containing Indian wheat genotypes	Illumina HiSeq 2500	Main objective of the project to increase Zinc (Zn) and Iron (Fe) concentration in the wheat seeds, which can be helpful to reduce the globally spread malnutrition problem. In current work, 4 High-Zn & Fe-accumulating wheat genotypes (HZFWGs) and 3 Low-Zn & Fe accumulating wheat genotypes (LZFWGs) were grown in homogeneous soil plots with essential nutrients and growth conditions. Twenty-one pots were filled with 30 kg homogeneous soil for growing 7 genotypes into 3 replications. This experiment was conducted during November to December 2014-15 and 2015-16	Leaves(Zn, Fe)
PRJNA454376	Triticum aestivum (bread wheat)	Comparative transcriptome profiling of multi-ovary wheat under heterogeneous cytoplasm suppression	Illumina HiSeq 4000	The differential expression of genes in the reciprocal crosses made between multi-ovary wheat and heterogeneous cytoplasm wheat.	Spikes
PRJNA476679	A map of bread wheat genome variation revealed the sources and patterns of genetic diversity	Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat	Illumina HiSeq X Ten	We report a comprehensive genomic constitution of cultivated wheat by analyzing 93 resequencing accessions from divergent breeds and locations.	Leaf
PRJNA477934	RNA seq data from tetraploid wheat, hexaploid wheat and reciprocally crossed endosperm	-	Illumina HiSeq 2500	Genomic imbalance affects seed development and mass accumulation in wheat interspecific crosses with different ploidies	Seeds
PRJNA485741	Insights into transcriptional characteristics and homoeolog expression bias of embryo and endosperm in developing grain through mRNA-Seq and Iso-Seq (bread wheat)	Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq	Illumina HiSeq 4000	To analyse the regulation of transcripts in grain embryo and endosperm during development, we performed RNA-Seq for wheat from 14 and 25 day post anthesis (DPA). And long-read sequencing for mixed whole grains from 14 and 25 DPA was employed to obtain full-length transcripts. A series of differentially expressed genes and tissues-specific genes of embryo and endosperm were identified. Moreover, 4351, 4641, 4516 and 4453 genes with A, B and D homoeoloci were detected in the four tissues. These provide specific gene pools of embryo and endosperm and homoeolog expression bias model in a large scale, which provides new insights into the molecular physiology of wheat. Overall design: Wheat (Triticum aestivum L.) cultivar Zhou 8425B were field cultivated. Embryo and endosperm (including episperm and pericarp) at 14 and 25 day post anthesis (DPA) were collected respectively for three biological replicates and immediately frozen in liquid nitrogen. They were then stored at -80°C following RNA extraction. Totals RNAs were extracted from each tissue sample using Plant Total RNA Purification Kit (GMbiolab co., Ltd. Taichung, Taiwan) according to the manufacturer’s protocol. Finally, the twelve RNA librarie sequencing based on Illumina HiSeq 4000 platform by paired-end experiments.	Embryo or endosperm
PRJNA491844	Transcriptome of cleistogamous wheat and its wild type wheat	Transcriptome analysis suggests mechanisms for a novel flowering type: Cleistogamous wheat	Illumina HiSeq 2000	We attempted to provide insight into genes changes associated with the cleistogamous phenotype in wheat, specifically exploring lodicule expanding mechanisms.	Spikes
PRJNA497810	Triticum aestivum cultivar:Bobwhite (bread wheat)	Identification of Transcription Factors Regulating Senescence in Wheat through Gene Regulatory Network Modelling	Illumina HiSeq 2500	The aim of the study was to investigate gene expression during a timecourse of flag leaf senescence . The timecourse largely focused on early (pre-visual) senescence, with only the latest timepoints (23 and 26 days) showing yellowing of the leaf. Triticum aestivum cv. Bobwhite was grown in a controlled environment room and the flag leaf was harvested at ten timepoints (3, 7, 10, 13, 15, 17, 21, 23, and 26 days post anthesis) which coincided with the period of grain development.	Flag leaf
PRJNA499014	Distinct chromatin signitures of promoters, enhancers and transposons in allohexaploid wheat (bread wheat)	The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements.	Illumina HiSeq 3000	Bread wheat is allohexaploid with 16 Gb genome, which has large intergenic region with abundant TEs and regulatory sequences . Our results give insight into the connections between chromatin modifications and transcriptional regulatory activity and provide the first systematic epigenomic map for functional annotation of the allohexaploid wheat genome. Overall design: We integrated seven major chromatin marks, DNA methylome and open chromatin, along with transcriptomic data in allohexaploid wheat to systematically characterize distinct chromatin archetectures surrounding regulatory elements including promoters, enhancers and transposons.	Seeds
PRJNA503549	Differential gene expression between durum and bread wheat during grain filling	Transcriptome data of cultivated tetraploid and hexaploid wheat variety during grain development	Illumina HiSeq 2000	Biofortification	Grains
PRJNA506031	Transcriptome sequencing of strong, middle and weak gluten strength wheat (bread wheat)	-	Illumina HiSeq 4000	Here is reported the first study of transcriptome analyses using the Illumina HiSeq 4000 platform for three kinds of wheat (G represents Strong gluten wheat, Z represents middle gluten wheat,R represents weak gluten wheat). The variation of wheat varieties with different gluten content is mainly shown in the content of gluten, flour is divided into high gluten powder ( > 30%), medium gluten powder (26%-30%) and low gluten powder ( < 20%), according to the wet gluten content. In total, over 102.6 Gb clean reads were produced and 114, 621 unigenes were assembled; more than 59,085 unigenes had at least one significant match to an existing gene model. Differentially expressed gene analysis identified 2339 and 2600 unigenes which were expressed higher or lower among strong gluten, middle gluten and weak gluten wheat. After functional annotation and classification, three dominant pathways including protein isomerase, antioxidase activity and energy metabolism, and 410 unigenes related to gluten strength polymerization of wheat were discovered. In strong-gluten wheat, low molecular weight subunit content is higher than weak-gluten wheat, and the activity of cysteine synthase and isomerase is increased, which may promote the cross-linking of low molecular weight protein to high molecular weight protein. Meanwhile, POD enzyme strengthens gluten network and CAT enzyme affects gluten polymerization, along with higher ATPase activity, which will provides energy for protein polymerization reaction in comparison of strong-gluten wheat and weak-gluten wheat. The accuracy of these RNA-seq data was validated by qRT-PCR analysis. These data will extend our knowledge of quality characteristics of wheat and provide a theoretical foundation for molecular mechanism research of wheat. Overall design: Different gluten strength wheat mRNA profiles was generated by RNA-seq, with three biological repeats, using Illumina 4000 platform	Seeds
PRJNA524238	wheat seed transcriptome sequence	Transcriptome analysis reveals important candidate genes involved in grain-size formation at the stage of grain enlargement in common wheat cultivar “Bainong 4199”	Illumina HiSeq 2500	The present database will help us understand the molecular mechanisms underlying early grain development and provide the foundation for increasing grain-size and yield in wheat breeding programs	Grains
PRJNA525250	Global transcriptome analysis uncovers the gene co-expression regulation network and key genes involved in grain development of wheat (Triticum aestivum L.)	Global transcriptome analysis uncovers the gene co-expression regulation network and key genes involved in grain development of wheat (Triticum aestivum L.)	Illumina HiSeq 2500	Wheat grain development is a robust biological process that largely determines grain quality and yield. In this study, we investigate the grain transcriptome of winter wheat cv. Xiaoyan-6 at four developmental stages (5, 10, 15 and 20 days post-anthesis), using high throughout RNA sequencing (RNA-Seq). We identified 427 grain specific transcription factors (TFs) and 1,653 differentially expressed TFs during grain development as well as a grain co-expression regulation network (GrainNet) of the TFs and their predicted co-expressed genes. Our study identified ten putative key TFs and the predicted regulatory genes of these key TF genes in wheat grain development of Xiaoyan-6. The analysis was given a firm basis through the study of additional wheat tissues, including root, stem, leaf, flag leaf, grain, spikes (from wheat plants at booting or heading stages) to provide a dataset of 92,478 high-confidence protein-coding genes that were mostly evenly distributed between subgenomes, but unevenly distributed across each of the chromosomes or each of the seven homeologous groups. Within this larger framework the transcriptomes we identified 4,659 grain specific genes (SEGs) and 26,500 differentially expressed genes (DEGs) throughout grain development stages tested. The SEGs identified mainly associated with regulation and signaling-related biological processes, the DEGs were mainly involved in cellular component organization or biogenesis and nutrient reservoir activity during grain development of Xiaoyan-6. The study establishes new targets for modifying genes related to grain development and yield, to fine-tune expression in different varieties and environments.	Grains
PRJNA530064	wheat 18 samples RNA-seq	Energy metabolism involved in fertility of the wheat TCMS line YS3038	HiSeq X Ten	To study the fertility mechanism of a TCMS line	Anthers
PRJNA532455	The Evolution of Gene Expression in Polyploid Wheats and Their Diploid Ancestors during Embryogenesis	The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development	Illumina HiSeq 2500	we present an atlas of global gene expression as well as the evolutionary divergence covering embryo, endosperm and seed coat development in wheats and their diploid ancestors, providing insights into the evolution of gene expression in embryogenesis and grain development of wheat species. Overall design: We investigate the dynamics and evolution of gene expression throughout seven stages of embryo development (including the two cell, pre-embryo, transition, leaf early, leaf middle, leaf late and mature embryo), two stages of endosperm (transition stage endosperm and leaf late stage endosperm), and one pericarp stage (leaf early stage pericarp) across five wheat and ancestral grass species (AC -hexaploid, SF-tetraploid, DV-A genome diploid, SP-B genome diploid and TA-D genome diploid), two replicates for each stage.	Embryo
PRJNA534411	Agropyron cristatum and Triticum aestivum Raw sequence reads	Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line	Illumina HiSeq 2500	Full-length transcriptome sequences of Agropyron cristatum facilitates the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line	Leaves, stems, roots and caryopses
PRJNA543139	Triticum aestivum (bread wheat)	-	Illumina HiSeq 2500	A population of 72 wheat accessions with varying germination rates was sequenced using RNA Seq. Single nucleotide polymorphisms (SNPs) were detected with a focus placed on those associated with deleterious changes for the purpose of inferring genetic variability	2 cm of stem and leaf from root collar
PRJNA544398	Triticum aestivum Transcriptome or Gene expression	Transcriptome analysis reveals the mechanism by which spraying diethyl aminoethyl hexanoate after anthesis regulates wheat grain filling	Illumina HiSeq 2000	To investigate the effects of spraying DA-6 after anthesis on wheat grain filling, RNA-seq was used to analyze the transcriptomes of samples (leaves, stems and seeds) at 24 days after anthesis.	DA-6
PRJNA546471	Triticum aestivum (bread wheat)	-	Illumina HiSeq X Ten	Wheat transcriptome	Flag leaf
PRJNA551129	Transcriptome changes in wheat roots caused by preceding plant species and soil disturbance	Transcriptome Analysis of Wheat Roots Reveals a Differential Regulation of Stress Responses Related to Arbuscular Mycorrhizal Fungi and Soil Disturbance	Illumina HiSeq 4000	This study shows that the preceding plant species and soil disturbance have an impact on the transcriptome of wheat roots, probably associated to the arbuscular mycorrhizal fungi communities existent in the roots and to the integrity of the extraradical mycelium network in the soil.	Arbuscular mycorrhizal colonization
PRJNA551725	Triticum aestivum cultivar:Guomai 301 (bread wheat)	Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301	Illumina HiSeq X Ten	To find gene expression profiles of tiller primordia, stem tips and young spikes for Guomai 301 (Triticum aestivum), we carried out the transcriptome.	Tiller primordia, stem tips and young spikes
PRJNA552801	Transcriptome analyses of different region tissue of wheat grain endosperm (bread wheat)	Transcriptomic and Metabolomics Analysis of Different Endosperm Region under Nitrogen Treatments	Illumina HiSeq 2500	The different parts of wheat grain endosperm at 25 days after anthesis were collected. Transcriptome analysis were conducted to investigate the differentially expressed transcript between inner and puter parts of endosperm. The study provide some useful information for understanding the protein gradient distribution in endosperm. Overall design: mRNA profiles of 25-day after anthesis grain enposperm inner part and outer parts were generated by deep sequencing, in triplicate, using Illumina	Grain endosperm
PRJNA552872	Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_RNAseq) (bread wheat)	Wheat chromatin architecture is organized in genome territories and transcription factories	NextSeq 500	Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat. Overall design: 3 RNA-seq libraries were sequenced	Shoots
PRJNA553311	Transcriptome Sequencing of Different Ploidy Wheat	Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat	Illumina HiSeq X Ten	Alternative splicing changes during domestication and polyploidization were revealed by transcriptome sequencing of wheat materials with different ploidy.	Leaf and root
PRJNA578098	Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression (bread wheat)	Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression	Illumina HiSeq 3000	Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely-cultivated allohexaploid wheat variety carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants. Overall design: We probed the whole-genome chromosomal interactions using HiC along with DNA metholome and transcriptomic data to systematically characterize the 3D structure of bread wheat cultivar AK58	Leaf
PRJNA593367	Transcriptomic analysis of low gluten RNAi bread wheat lines	New transcriptomic insights in two RNAi wheat lines with the gliadins strongly down-regulated by two endosperm specific promoters	Illumina Genome Analyzer IIx	A differential gene expression analysis of twowheat lines with low gluten content was performed to understand the effect of gliadin silencing on other biological processes.	Seeds
PRJNA596597	Draw data of of wheat in response to pistillody of stamen	Comparative transcriptome analysis indicates conversion of stamens into pistil-like structures in male sterile wheat (Triticum aestivum L.) with Aegilops crassa cytoplasm	Illumina HiSeq 2500	Comparative transcriptome analysis of wheat in response to pistillody of stamen provides insights into candidate genes and biosynthesis pathways	Stamens
PRJNA596859	Transcriptome data for Zang1817 genome annotation	Origin and adaptation to high altitude of Tibetan semi-wild wheat	HiSeq X Ten	To aid genome annotation and perform the transcriptome analysis, we generated the RNA-seq data for 4 different tissues. including leaf, root, stem and spike	Leaf, root, stem and spike
PRJNA603450	Whole transcriptome sequencing of Triticum aestivum cv. Cadenza	Comparative Genomics and Functional Studies of Wheat BED-NLR Loci	Illumina HiSeq 2000	Whole transcriptome sequencing of cv. Cadenza RNA-sequencing	3-leaf stage
PRJNA607628	A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy	A transcriptomic view of the ability of nascent hexaploid wheat to tolerate aneuploidy	Illumina HiSeq 2000	In contrast to most animal species, polyploid plant species are quite tolerant of aneuploidy. Here, the global transcriptome of four aneuploid derivatives of a synthetic hexaploid wheat line was acquired, with the goal of characterizing the relationship between gene copy number and transcript abundance. For most of the genes mapped to the chromosome involved in aneuploidy, the abundance of transcripts reflected the gene copy number. Aneuploidy had a greater effect on the strength of transcription of genes mapped to the chromosome present in a noneuploid dose than on that of genes mapped elsewhere in the genome. Overall, changing the copy number of one member of a homeologous set had little effect on the abundance of transcripts generated from the set of homeologs as a whole, consistent with the tolerance of aneuploidy exhibited by allopolyploids, whether in the form of a chromosomal deficit (monosomy) or chromosomal excess (trisomy). Our findings shed new light on the genetic regulation of homeoallele transcription and contribute to a deeper understanding of allopolyploid genome evolution, with implications for the breeding of polyploid crops.	Spikes
PRJNA609457	H3K27me2 and H3K27me3 ChIP-seq in wheat evolution	Intra-Varietal Diversity and Its Contribution to Wheat Evolution, Domestication, and Improvement in Wheat	HiSeq X Ten	Bread wheat is a widely cultivated allohexaploid arise via two recent polyploidization events. Growing evidence suggests histone modifications are involved in response to genomic shock and adaption to adverse environments during formation of polyploid plants. However, the roles of histone modifications in wheat evolution remain elusive. We analyzed profiles of H3K27me2 and H3K27me3 during polyploidization and hybridization of wheat using hexaploid bread and its tetraploid and diploid relatives. H3K27me2 levels positively correlated with the ploidy levels and the increased H3K27me2 may contributed to repress massively amplified transposons to maintain genome stability during wheat evolution. H3K27me2 is involved in silencing euchromatic TEs and the distribution of H3K27me2 is mutually exclusive with another repressive mark H3K9me2. Regions of H3K27me2 canyons were highly related with formation of DNA double-strand breaks in genomes of wheat, maize and Arabidopsis, revealing a novel histone modification contributing to recombination regulation. Our results provided comprehensive view of H3K27me2 and H3K27me3 distribution during wheat evolution and proposed potential roles of H3K27me2 on genome stability and genetic recombination, which may contribute to accelerate crop breeding	Seeding leaves
PRJNA624178	RNA sequencing of wild and domesticated wheat genotypes	Comparative transcriptomic and metabolic analysis of wild and domesticated wheat genotypes reveals differences in chemical and physical defense responses against aphids.	Illumina HiSeq 4000	Comparative transcriptomic analysis of Triticum turgidum ssp. durum cv. Svevo, Triticum turgidum ssp. dicoccoides (accession Zavitan) and Triticum aestivum cv. Chinese Spring for elucidation of defense mechanisms against aphids.	Leaf
PRJNA625320	Molecular changes in wheat improvement	Evidence for the Accumulation of Nonsynonymous Mutations and Favorable Pleiotropic Alleles During Wheat Breeding	Illumina HiSeq 2500	This study investigated the DNA changes that occurred during the development of the Stettler bread wheat cultivar from a key ancestor, Red Fife	Leaf
PRJNA636099	sRNA and RNA sequencing profile of barley and wheat anther	Premeiotic, 24-Nucleotide Reproductive PhasiRNAs Are Abundant in Anthers of Wheat and Barley But Not Rice and Maize Sébastien Bélanger, Suresh Pokh	NextSeq 550	Two classes of pre-meiotic (21-nt) and meiotic (24-nt) phasiRNAs and their patterns of accumulation, have been described in maize and rice anthers. Their precise function remains unclear but some studies have shown that they support male fertility. Their important role in anthers underpins our current study to characterize phasiRNAs in wheat and barley anthers. We staged anthers at every 0.2 mm of development for one wheat and two barley varieties. We identified pre-meiotic (0.2 mm, 0.4 mm and 0.6 mm), meiotic (0.8 mm, 1.0 mm and 1.4 mm) and post-meiotic (1.8 mm) anthers for which we then investigated accumulation patterns of RNAs, including reproductive phasiRNAs	Anthers
PRJNA638000	The whole transcriptome sequencing of germinating and non-germinating seeds in wheat	Regulatory Network of Preharvest Sprouting Resistance Revealed by Integrative Analysis of mRNA, Noncoding RNA, and DNA Methylation in Wheat	Illumina HiSeq 4000	Sequencing data includes comparative transcriptomes of germinated and non-germinated seeds, long non-coding RNA, and small RNA sequencing data	seed grain
PRJNA640732	Triticum aestivum (bread wheat)	Wheat FRIZZY PANICLE activates VERNALIZATION1-A and HOMEOBOX4-A to regulate spike development in wheat	Illumina HiSeq 2000	RNA-seq of wheat cultivar YM44	spike
PRJNA663737	Aegilops tauschii Genome sequencing and assembly	Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement	Illumina NovaSeq 6000	Sequencing and assembly Aegilops tauschii. Provide genetic resouce for wheat breeding.	Seed, Pericarp
PRJNA664618	Identification of the genes involved in the S1-mediated regulatory network in hexaploid wheat	Multiple origins of Indian dwarf wheat by mutations targeting the TREE domain of a GSK3-like kinase for drought tolerance, phosphate uptake, and grain quality	Illumina NovaSeq 6000	The project was to identify the genes involved in the S1-mediated regulatory network in hexaploid wheat. Wheat S1 gene encodes a GSK3-like protein homologous to Arabidopsis BIN2.	Inflorescence, root
PRJNA668815	RNA-seq of wheat early and late headign date	Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date	Illumina HiSeq 4000	transcriptome of wheat	Apical,leaf
PRJNA675907	Molecular cloning of Rf1 and Rf3 restorer genes in wheat	The genetic basis of cytoplasmic male sterility and fertility restoration in wheat	Illumina NovaSeq 6000	RNA-seq data from anthers at three developmental stages from male-sterile and male-fertile wheat genotypes (Fielder*CMS, R0932E carrying Rf1, R0946E carrying Rf3, R0934F carrying both Rf1 and Rf3)	Anthers
PRJNA693003	W7984 x Opata M85 fine-mapping chromosome 5AS structural variation	Positional-based cloning ‘fail-safe’ approach is overpowered by wheat chromosome structural variation	Illumina NovaSeq 6000	In this study, we sought to positionally clone the causal genetic variant of a thousand grain weight, TGW, quantitative trait loci, QTL, on wheat chromosome 5AL. We developed a heterogenous inbred family, HIF, of more than 5,000 plants for enhanced genotypic resolution and fine-mapped the QTL to a ten Mbp region.	Spikes
PRJNA701317	wheat PHS RNA-seq	Identification of QTLs and a Candidate Gene for Reducing Pre-Harvest Sprouting in Aegilops tauschii–Triticum aestivum Chromosome Segment Substitution Lines	Illumina NovaSeq 6000	wheat PHS RNA-seq	Seed(PHS)
PRJNA705851	RNA-seq of wheat	-	Illumina NovaSeq 6000	transcriptome of wheat	Tiller bases
PRJNA718695	Genome-wide studies of spike development in wheat	Genome-wide profiling of long noncoding RNAs involved in wheat spike development	Illumina HiSeq 4000	This study mainly focus on genome-wide transcriptional dynamics of lncRNAs and coding genes during wheat spike development process	Spikes
PRJNA734863	RNA-seq data of the seeds at development stage from wheat cultivars of Zhengmai366 and Zhengmai004	Promoter DNA hypermethylation of TaGli-γ-2.1 positively regulates gluten strength in bread wheat	Illumina HiSeq 2000	In order to mini the related genes for gluten strength, Zhengmai366 (strong gluten strength wheat) and Zhengmai004 (weak gluten strength wheat) were used as materials for RNA sequencing. The seeds at five different development stages (7, 14, 21, 28 and 35 day after pollination) were collected, respectively. Then, the seeds taking from the same cultivar were mixed for RNA sequencing. Illumina HiSeq 2000 system was used and sequenced in paired-end mode	Seeds
PRJNA749586	RNA-Seq of Triticum aestivum inflorescence development	High expression of VRT2 increases the number of rudimentary basal spikelets in wheat	Illumina NovaSeq 6000	The aim of this study was to investigate differences in gene expression across the wheat spike. To achieve this, individual wheat spikes (cv Paragon) were dissected into apical, central, and basal sections (1:1:1 size ratio). For each section from a single spike, an individual RNA-Seq library was generated and then sequenced. Plants were grown under control conditions and samples were collected at two consecutive developmental stages, Double Ridge (DR) and Glume Primordia (GP)	Spikes
PRJNA772972	RNA -Seq of flag leaves of the mid-flowering stage from Jinmai84 and Jinmai47	Lipidomic, Transcriptomic, and BSA-660K Single Nucleotide Polymorphisms Profiling Reveal Characteristics of the Cuticular Wax in Wheat	Illumina HiSeq 2000	Flag leaves were removed and flash frozen in liquid nitrogen. Total RNA was isolated from whole siliques using a method described by Suzuki et al. (2004). TruSeq RNA sequencing libraries were constructed following the standard preparation guide	Fresh flag leaves
PRJNA777016	grain_RNA-SEQ	Comparison of the Agronomic, Cytological, Grain Protein Characteristics, as Well as Transcriptomic Profile of Two Wheat Lines Derived From Wild Emmer	BGISEQ-500	Triticum aestivum RNA-Seq reads	Grains
PRJNA780107	RNA-seq data for early grain development of Chinese Spring	Transcriptome Analysis of Developing Wheat Grains at Rapid Expanding Phase Reveals Dynamic Gene Expression Patterns	HiSeq X Ten	RNA-seq data for early grain development of Chinese Spring; Whole grains at 0,2,4,6,8,10 days after pollination	Grains
PRJNA788400	Genome-Wide Investigation and Functional Analysis of RNA Editing Sites in Wheat	Genome-wide investigation and functional analysis of RNA editing sites in wheat	NextSeq 500	The goals of this study were to compare the transcriptome of six genotypes of wheat grown under the normal conditions by RNA-Seq and to study the root architecture in drought sensitive and tolerant genotypes. Overall design: Roots mRNA profiles of 35 days old six genotypes of wheat.	Seeds
PRJNA792995	Transcriptomes analysis of grains of two wheat cultivars with different antioxidant activity	-	Illumina NovaSeq 6000	The goals of this study are to compare transcriptome profiling (RNA-seq) between two wheat cultivars with different antioxidant actvity and to clarify the differences of these two wheat cultivars. Overall design: Examination of grains sampled from 2 different wheat culitvars at 20 days after anthesis and 30 day after anthesis	Grains
PRJNA815667	Integrated Transcriptome and Metabolome Identified Novel Candidate Genes Regulating Anthocyanin Biosynthesis in Colored-Grain Wheat (Triticum aestivum L.) (bread wheat)	Metabolome and transcriptome analyses of anthocyanin biosynthesis reveal key metabolites and candidate genes in purple wheat (Triticum aestivum L.)	Illumina NovaSeq 6000	Purpose: The present study aimed to investigate the anthocyanin components and identify relevant regulatory genes in purple wheat grain by carrying out transcriptome analyses. Methods: The seeds of purple grain wheat and white grain wheat were collected 30 days after flowering, and three biological replicates were set. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. Then synthesizing the fragmented RNA into cDNA through the action of reverse transcriptase, and finally obtaining acDNA library. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol. Results: A total of 10440 diferentially expressed genes were signifcantly enriched by RNA sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed signifcantly enriched flavonoid biosynthesis and anthocyanin biosynthesis in CW_S versus W_S. And the ANS and UFGT genes were predicted as core genes in anthocyanin biosynthesis. Conclusions: Our study represents the detailed analysis of wheat grain transcriptomes, with biologic replicates, generated by RNA-seq technology. Through this study, we speculated that ANS and UFGT genes are the core genes of anthocyanin biosynthesis.The significant differences of these genes affect the synthesis of anthocyanins in wheat grains, and thus affect the grain color of wheat. Overall design: The mRNA profiles of white grain wheat (W_S) and purple grain wheat (CW_S) grains 30 days after flowering.	Grains
PRJNA834580	RNA-seq of developing wheat spike	A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement	Illumina NovaSeq 6000	The total RNA from wheat spikes was extracted using TRIzol reagent. Paired-end RNA-seq libraries were prepared with TruSeq RNA Sample Preparation Kit v2 and sequenced on NovaSeq6000	Spikes
PRJNA863398	Differential gene expression analysis of bread wheat cultivars using RNA-seq	Association of Root Hair Length and Density with Yield-Related Traits and Expression Patterns of TaRSL4 Underpinning Root Hair Length in Spring Wheat	BGISEQ-500	Using RNA-seq approach, the project aims at unveiling the genes in bread wheat that are differentially expressed in roots and leaves of bread wheat. The varying transcript levels of differentially expressed genes (DEGs) can offer insights into various biological and cellular processes that are affected by conditions of interest.	Leaf and roots of 14 days old seedlings
PRJNA886978	Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [RNA-seq]	Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development	Illumina NovaSeq 6000	It is reported that the CRE variants are associated with many important agronomic traits. In this study, we unravelling the transcriptional network underlying wheat grain development by combing ATAC-seq (Assay for Transposase Accessible Chromatin sequencing) and RNA-seq with samples from a series of time points.	Grains
PRJNA899349	seeds RNA-seq	An elite γ-gliadin allele improves end-use quality in wheat	Illumina NovaSeq 6000	we assessed the expression level of the gliadin genes in Fielder by transcriptome deep sequencing (RNA-seq) using total RNA extracted from whole seeds at 4 days after pollination (DAP) and from endosperm of seeds collected at 10, 15, 20, and 25 DAP.	Seeds
PRJNA919175	Mapping quantitative trait loci and developing their KASP markers for Pre-harvest Sprouting resistance of Henan wheat varieties in China (bread wheat)	Mapping quantitative trait loci and developing their KASP markers for pre-harvest sprouting resistance of Henan wheat varieties in China	Illumina NovaSeq 6000	Introduction: Pre-harvest Sprouting (PHS) seriously affects wheat quality and yield. However, to date there have been limited reports. It is of great urgency to breed resistance varieties via quantitative trait nucleotides (QTNs) or genes for PHS resistance in white-grained wheat. Methods: 629 Chinese wheat varieties, including 373 local wheat varieties from 70 years ago and 256 improved wheat varieties were phenotyped for spike sprouting (SS) in two environments and genotyped by wheat 660K microarray. These phenotypes were used to associate with 314,548 SNP markers for identifying QTNs for PHS resistance using several multi-locus genome-wide association study (GWAS) methods. Their candidate genes were verified by RNA-seq, and the validated candidate genes were further exploited in wheat breeding. Results: As a result, variation coefficients of 50% and 47% for PHS in 629 wheat varieties, respectively, in 2020-2021 and 2021-2022 indicated large phenotypic variation, in particular, 38 white grain varieties appeared at least medium resistance, such as Baipimai, Fengchan 3, and Jimai 20. In GWAS, 22 significant QTNs, with the sizes of 0.06% ~ 38.11%, for PHS resistance were stably identified by multiple multi-locus methods in two environments, e.g., AX-95124645 (chr3D:571.35Mb), with the sizes of 36.390% and 45.850% in 2020-2021 and 2021-2022, respectively, was detected by several multi-locus methods in two environments. As compared with previous studies, the AX-95124645 was used to develop Kompetitive Allele-Specific PCR marker QSS.TAF9-3D (chr3D:569.17Mb~573.55Mb) for the first time, especially, it is available in white-grain wheat varieties. Around this locus, nine genes were significantly differentially expressed, and two of them (TraesCS3D01G466100 and TraesCS3D01G468500) were found by GO annotation to be related to PHS resistance and determined as candidate genes. Discussion: The QTN and two new candidate genes related to PHS resistance were identified in this study. The QTN can be used to effectively identify the PHS resistance materials, especially, all the white-grained varieties with QSS.TAF9-3D-TT haplotype are resistant to spike sprouting. Thus, this study provides candidate genes, materials, and methodological basis for breeding wheat PHS resistance in the future. Overall design: Spike of wheat wax ripe stage Time: 0 hour, 48hour and 96 hour represents the time the sample was processed at a temperature of 22 plus or minus 1 degrees C and a relative humidity of 95% plus or minus 5%.	15 cm below the spike
PRJNA976038	wheat anther RNA-seq	BRI1 EMS SUPPRESSOR1 genes regulate abiotic stress and anther development in wheat (Triticum aestivum L.)	Illumina HiSeq 4000	transcriptome of wheat anthers at specific developmental stages under different fertility conditions	Anthers

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Biological Characteristics	Notes
PRJEB12358	RNA-seq of coding RNA of wheat heads from 3, 6, 12, 24, 36, and 48 hours after inoculation of fungal pathogen Fusarium graminearum or mock inoculation	Suppressed recombination and unique candidate genes in the divergent haplotype encoding Fhb1, a major Fusarium head blight resistance locus in wheat	Illumina HiSeq 2000	Near isogenic wheat lines, differing in the presence of both or none of the FHB-resistance QTL Fhb1 and Qfhs.ifa-5A, have been sequenced using Illumina HiSeq2000 under disease pressure (3, 6, 12, 24, 36, 48 hai) as well as with mock-inoculation, to discern transcriptional differences induced by Fusarium graminearum. The NILs are BC5F2 lines generated from the Mexican Spring wheat line CM-82036, the resistance QTL donor line, as recurrent background and the susceptible German Spring wheat line Remus as the donor of the susceptible QTL alleles	Stress	Inoculation of fungal pathogen Fusarium graminearum or mock inoculation
PRJEB13569	Field Pathogenomics of Wheat Blast	Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae	Illumina HiSeq 2500	Wheat blast is caused by a fungus that belongs to Magnaporthe oryzae species. We isolated RNA from wheat leaf blades harvested from the infected wheat fields of Bangladesh in March, 2016, and obtained sequence data using RNA-seq and Illumina sequencing technology. Our field-pathogenomics approach identified M. oryzae in symptomatic samples. Data generated from this project will be freely available to public.	Stress	Wheat blast
PRJEB22854	RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 15 days (D15) and 20 days (D20) shading treatment after pollination, against 15 DAP, 20 DAP untreated controls. The purple-grain wheat were grown under natural field conditions at Shandong Agricultural University Experimental Station (36169 N, 117169 E), Taian, China during Octubor, 2015 to June, 2016	-	Illumina HiSeq 2000	Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. But little is known about molecular mechanism of anthocyanin biosynthesis. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced four pericarp cDNA libraries, D15 (15 DAP), D20 (20 DAP) of shading treatment, and L15 (15 DAP), L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000. After quality control, raw reads are filtered into clean reads which will be aligned to the reference sequences. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio, and proceed with downstream analysis including gene and isoform expression, deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection. Further, we also perform deep analysis based on different expression genes, including Gene Ontology (GO) enrichment analysis, Pathway enrichment analysis, cluster analysis, and finding transcriptor factor	Stress	Shading treatment
PRJEB23056	Pamp Triggered Immune Response in wheat leafs.	The transcriptional landscape of polyploid wheat	Illumina HiSeq 2500	Hexaploid bread wheat, variety Chinese Spring, was treated with flg22 or chitin. Transcriptomes were sequenced before, 30 minutes and 180 minutes after treatment.	Stress	Treated with flg22 or chitin
PRJEB23118	Differential gene expression studies for identifying genes imparting heat stress tolerance in wheat during grain filling.	-	Illumina HiSeq 4000	Heat stress is one of the major abiotic stress factor that affects wheat yield. Especially, heat stress during grain filling affects grain yield besides reduced grain quality. So, in our present study, three genotypes with varied levels of tolerance to heat stress were chosen. They were subjected to heat stress at two stages for three days viz., early (11-14days-post-anthesis) and late (27-30dpa) grain filling independently under controlled conditions. At 14 and 30dpa, the spikes were harvested from control and stress conditions from all the three genotypes, grains were isolated and pulverized. Hence pulverized tissues are used for RNA extraction and further for transcriptome sequencing using HiSeq 4000. Data were analyzed to identify the genes involved in imparting heat stress tolerance	Stress	Heat
PRJEB24582	RNA-seq of pericarp of purple-grain wheat Luozhen No.1 of 20 days (D20) shading treatment after pollination, against 20 DAP untreated controls	-	Illumina HiSeq 2000	Purple-grain wheat are caused by anthocyanin accumulation in the seed coat. The anthocyanin biosynthesis and accumulation were affected by light in purple-grain wheat. The spikes of purple-grain wheat Luozhen No.1 were bagged with four-layer Kraft paper bags after pollination. To identify genes involved in the anthocyanin biosynthesis, we sequenced two pericarp cDNA libraries, D20 (20 DAP) of shading treatment, and L20 (20 DAP) of untreated control using an Illumina HiSeqTM 2000.	Stress	Shading treatment
PRJEB29046	Exploration of wheat and pathogen transcriptomes during tan spot infection	Exploration of wheat and pathogen transcriptomes during tan spot infection	Illumina HiSeq 2000	The fungus Pyrenophora tritici-repentis is the causal agent of tan spot, a major disease of wheat (Triticum aestivum). Here, we used RNA sequencing to generate transcriptional datasets for both the host and pathogen during infection and during in vitro pathogen growth stages. Data description: To capture gene expression during wheat infection with P. tritici-repentis isolate M4, RNA datasets were generated for wheat inoculations with P. tritici-repentis (infection) and a mock (control) 3 and 4 days post-infection. The P. tritici-repentis isolate M4 was also RNA sequenced to capture gene expression in vitro at two different growth stages: 7-day old vegetative mycelia and 9-day old sporulating mycelia. In total 6 RNA datasets are available to aid in the validation of predicted genes of P. tritici-repentis and wheat. The datasets generated offer an insight into the transcriptomic profile of the host-pathogen interaction and can be used to investigate the expression of a subset of transcripts or targeted genes prior to designing cost-intensive RNA sequencing experiments, that would be best further explored with replication and a time series analysis.	Stress	Pyrenophora tritici-repentis
PRJEB31122	Asparagine levels in wheat in response to sulphur	Contrasting gene expression patterns in grain of high and low asparagine wheat genotypes in response to sulphur supply	Illumina HiSeq 4000	RNA-seq data was acquired for the embryo and endosperm of two related genotypes of bread wheat, Spark and SR3, growing under conditions of sulphur sufficiency and deficiency, and sampled at 14 and 21 days post anthesis (dpa).	Stress	Sulphur
PRJEB35451	Effect of heat stress on developing wheat grain	High post-anthesis temperature effects on bread wheat (Triticum aestivum L.) grain transcriptome during early grain-filling	Illumina HiSeq 2500	effect of post anthesis heat stress on transcriptome of developing wheat grain	Stress	Heat
PRJEB36444	Identification of wheat genes required for pathogen ingress	The branched-chain amino acid aminotransferase TaBCAT1 modulates amino acid metabolism and positively regulates wheat rust susceptibility	Illumina HiSeq 2500	We used RNA-seq analysis of Pst-infected wheat varieties with variable levels of susceptibility to uncover novel plant genes that are essential for pathogen ingress	Stress	Puccinia striiformis f. sp. tritici
PRJEB40948	Circadian RNA-seq time series data for wheat	Interpreting machine learning models to investigate circadian regulation and facilitate exploration of clock function	Illumina HiSeq 4000	For the wheat variety Cadenza seedlings were grown under 12:12 light:dark cycles at 22C for 14 days before transfer to constant light. After 24 hours under constant conditions, whole aerial tissue samples were taken every 2 hours for 3 days starting at perceived dawn (ZT=0). RNA-seq information was generated	Stress	The circadian clock
PRJEB41456	Transcriptome analysis in the old Brazilian wheat variety Toropi in response to infection with Puccinia triticina, the causal pathogen of leaf rust	Transcriptome Analysis of the Durable Leaf Rust Resistance in the Wheat Variety Toropi	Illumina HiSeq 2000	We undertook a time course analysis of gene expression between mock (non)-inoculated and pathogen (Puccinia triticinia)-infected wheat samples using RNA sequencing (RNA-Seq).	Stress	Puccinia triticina
PRJEB44859	Characterization of dynamic regulatory gene and protein networks in wheat root upon perceiving drought stress through comparative transcriptomics survey	Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey	HiSeq X Ten	A well-developed root system benefit host plants by optimizing water absorption and nutrient uptake and thereby increases plant productivity. In this study we have characterized the root transcriptome using RNA-seq and subsequential functional analysis in a set of drought tolerant or susceptible genotypes.	Stress	Drought
PRJEB5341	CWR1.1	Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes	AB SOLiD System 3.0	Plant growth promoting bacteria (PGPB) might be an alternative to increase nitrogenous use efficiency (NUE) in important crops such wheat. Azospirillum brasilense is one of the most promising PGPB and wheat roots colonized by Azospirillum brasilense is a good model to investigate the molecular basis of plant-PGPB interaction including improvement in plant-NUE promoted by PGPB. An RNA-seq transcriptional analysis of Triticum aestivum roots was carried out in two independent samples (biological replicates) of each treatment (PGPB-colonized or non-inoculated), yielding a total of 4 sequencing libraries, which were designated CWR1 and CWR2 libraries (colonized roots) and N-IWR1 and N-IWR2 (non-inoculated roots)	Stress	Azospirillum brasilense
PRJEB54622	RNA-seq in the root and basal nodes of nitrogen-stressed Triticum aestivum var Graham (wheat) treated and untreated with a biostimulant	-	Illumina NovaSeq 6000	three biological replicates were included per treatment. RNA-seq was conducted in total RNA extracted from 3 basal node samples pooled together per biological replicate. In this study, the basal node is defined as the 0.5 cm of the main shoot base, which includes the apical meristem, lateral buds, leaf meristems etc.	Stress	Nitrogen-stressed/microalgae extract based biostimulant
PRJEB54900	RNA-seq in the basal nodes of nitrogen- and phosphorus-stressed Triticum aestivum var Cadenza (wheat) plants.	-	Illumina NovaSeq 6000	The aim of this study was to examine the transcriptional changes that govern low nitrogen (N) and low phosphorus (P) responses in basal nodes and may be associated with tiller suppression under nutrient-limiting conditions.	Stress	Nitrogen- and phosphorus-stressed
PRJEB8762	A genome-wide methylation study of hexaploid wheat	A genome-wide survey of DNA methylation in hexaploid wheat	Illumina HiSeq 2500	DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome specific methylation shows more variation.	Temperature
PRJNA1000650	Triticum aestivum Raw sequence reads	Regulation of hormone pathways in wheat infested by Blumeria graminis f. sp. tritici	Illumina NovaSeq 6000	Transcriptome sequencing was performed on wheat leaves infested with powdery mildew. RNA-seq of wheat and powdery mildew were performed, respectively.	Stress	Powdery mildew infection
PRJNA1006331	RNA-seq of incompatible and compatible interactions between wheat and Pst	-	HiSeq X Ten	Integrated metabolomic and transcriptomic analysis of wheat leaves infected with Puccinia striiformis f. sp. tritici revealed a new perspective for elucidation of wheat stripe rust resistance based on metabolic dynamics.	Stress	Pst Infection
PRJNA1015138	Comparative transcriptome analysis in bread wheat (Triticum aestivum L.) under drought stress	-	Illumina HiSeq 2000	The aim of this study was to identify drought stress-related genes in Triticum aestivum in their responses to different drought stress conditions. The most promising drought stress tolerant and non-tolerant wheat varieties were selected based on the physiological data from our screening. In this research Atay, Gerek and Mufitbey varieties were used. RNA-Seq was performed using tolerant and non-tolerant wheat cultivars to identify differentially expressed transcripts under different drought stress conditions.	Stress	Drought
PRJNA168479	Triticum aestivum (bread wheat)	-	Illumina HiSeq 1000	Korean Wheat	Stress	Temperature
PRJNA171754	Triticum aestivum strain:HD2985, HD2329 (bread wheat)	Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)	454 GS FLX+	The study was conducted in order to find out the differential change in the transcript of tolerant and susceptible wheat cultivar under heat stress and to decipher the mechanism of thermotolerance in wheat by identifying novel genes and transcription factors involved in the pathways. Wheat cultivar HD2985 (thermotolerant) and HD2329 (thermosusceptible) were exposed to heat stress of 42 degree for 4h at pollination stage and samples were collected from both control and heat shock treated plants for further characterization.	Stress	Heat
PRJNA196595	Interaction transcriptome of host wheat and hemibiotrophic fungal pathogen Septoria tritici during disease transition Transcriptome or Gene expression	Transcriptional Reprogramming of Wheat and the Hemibiotrophic Pathogen Septoria tritici during Two Phases of the Compatible Interaction	Illumina HiSeq 2000	Molecular mechanisms underlying the interplay between fungal pathogenicity and host responses at specific growth phases and the factors triggering disease transition.	Stress	Septoria tritici
PRJNA200921	Triticum aestivum (bread wheat)	-	Illumina HiSeq 2000	analysis of differentially expressed genes and in the wheat callus infected by Agrobacterium tumefaciens.	Stress	Agrobacterium tumefaciens
PRJNA243835	Triticum aestivum strain:N9134 Transcriptome or Gene expression	Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew	Illumina HiSeq 2000	Transcriptome Divergence and Overlap for Wheat in Response to Stripe rust and Powdery Mildew Pathogen Stress	Stress	Stripe rust and powdery mildew pathogen stress
PRJNA253535	Wheat (Triticum aestivum L.) transcriptome profiling	Understanding the Biochemical Basis of Temperature-Induced Lipid Pathway Adjustments in Plants	Illumina HiSeq 2500	Transcript changes in response to low temperature Overall design: Total RNA for RNA-seq analysis were extracted from wheat leaf tissues with three biological replicates for each growth condition.	Stress	Temperature
PRJNA257938	Triticum aestivum strain:TAM107 Transcriptome or Gene expression	Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (Triticum aestivum L.)	Illumina HiSeq 2000	wheat transcriptome study	Stress	Drought and heat
PRJNA270262	Triticum aestivum subsp. yunnanense cultivar:HD2985 and HD2329	Characterization of putative calcium-dependent protein kinase-1 (TaCPK-1) gene: hubs in signalling and tolerance network of wheat under terminal heat	Illumina MiSeq	The project has been undertaken to elucidate the mechanism associated with heat stress tolerance in developing wheat, to remodel the starch biosynthesis pathway and to study the effect of terminal heat stress on yield of wheat. Goal: To decipher the thermotolerance mechanism of wheat during grain-filling stage. Relevance: Climate change has severe effect on the growth and yield of heat sensitive crops like wheat which provides 12% of the carbohydrate and 20% of the calorie in the diet. The grain-filling stage is critical and even slight variation in temperature affect the quality and quantity of the grains. The present investigation will provide the information for novel stress associated genes and proteins as well as some of the new members of starch biosynthesis pathway. It will also help us in elucidating the tolerance mechanism of starch biosynthesis pathway, so that the information can be used for the development of climate smart wheat crop	Stress	Heat
PRJNA271511	Triticum aestivum (bread wheat)	De Novo Assembly and Transcriptome Analysis of Wheat with Male Sterility Induced by the Chemical Hybridizing Agent SQ-1	Illumina HiSeq 2500	The aim of this study was to seek out the key genes and important metabolic pathways associated with wheat PMS	Stress	Induced by the Chemical Hybridizing Agent SQ-1
PRJNA289545	Expression profiling of wheat heads from spring wheat Chinese Spring (CS) and CS-7EL (CS with additional chromosome arm 7EL from Thinopyrum elongatum), after inoculation with either water (mock inoculation) or Fusarium graminearum	Genomic sequencing of Thinopyrum elongatum chromosome arm 7EL, carrying fusarium head blight resistance, and characterization of its impact on the transcriptome of the introgressed line CS-7EL	Illumina HiSeq 2500	The ditelocentric addition line CS-7EL of the spring wheat (Triticum aestivum) cultivar Chinese Spring (CS) contains the long arm of the chromosome 7E from Thinopyrum elongatum (CS-7EL), which confers high resistance to fusarium head blight. It is of great interest to breeders to integrate the resistance locus (loci) from Th. elongatum into commercial wheat varieties. The objectives of this study were to identify candidate genes expressed from the 7EL chromosome of CS-7EL, to develop 7EL-specific molecular markers, and to validate their usefulness to characterize recombination between one of the group 7 chromosomes of wheat and Th. elongatum. High-throughput sequencing of Fusarium graminearum-infected and control CS and CS-7EL cDNA libraries was performed using RNA-Seq. A stepwise bioinformatics strategy was applied to assemble the sequences obtained from RNA-Seq and to create a conservative list of candidate genes expressed from the foreign chromosome 7EL. PCR primer pairs were designed and tested for 135 candidate genes. A total of 48 expressed molecular markers specific for the chromosome 7EL were successfully developed. Screening of progenies from two BC1F2 families from the cross CS-7E(7D)×2*CSph1b showed that these markers are useful to characterize recombination events between the chromosomes 7D from wheat and 7E from Th. elongatum. Overall design: Expression profiling of inoculated rachis from CS and CS-7EL heads sampled at 4 days after inoculation. Inoculation of all developed spikelets on each head at mid-anthesis was done with either water or F. graminearum strain DAOM 180378. Three biological replicates were done for each treatment, and 10 to 12 heads were inoculated per biological replicate	Stress	Inoculation with either water (mock inoculation) or Fusarium graminearum
PRJNA293629	Triticum aestivum Transcriptome or Gene expression	Survey of High Throughput RNA-Seq Data Reveals Potential Roles for lncRNAs during Development and Stress Response in Bread Wheat	Illumina HiSeq 2500	transcriptome response of two wheat cultivers to salt stress	Stress	Salt
PRJNA297822	Triticum aestivum cultivar:Chara Transcriptome or Gene expression	The Fusarium crown rot pathogen Fusarium pseudograminearum triggers a suite of transcriptional and metabolic changes in bread wheat (Triticum aestivum L.)	Illumina HiSeq 2000	Bread wheat (Triticum aestivum L.) is an allopolyploid species that contains three ancestral genomes. Therefore, potentially three homoeologous copies exist for any given gene in the wheat genome. Whether different homoeologs are differentially expressed (homoeolog expression bias) in response to biotic and abiotic stresses in wheat is poorly understood. In this study, we used an RNA-seq approach to analyze homoeolog-specific global gene expression patterns during infection by the fungal pathogen Fusarium pseudograminearum, which causes crown rot disease. We substantially increased the number of known homoeologous gene sets in wheat. Our analyses revealed patterns of differential expression among homoeologs under both control and infection conditions, indicating homoeolog expression bias underpins a large proportion of the wheat transcriptome. We found that B and D subgenomes disproportionately contributed to differentially expressed genes during plant defense. Furthermore, we observed that the degree of responsiveness to pathogen infection varied among homoeologous genes and we use the term “homoeolog induction bias” to refer to this phenomenon. Further understanding how homoeolog expression and induction bias impacts biotic stress responses will assist the improvement of biotic stress tolerance in elite wheat cultivars.	Stress	Infection by the fungal pathogen Fusarium pseudograminearum
PRJNA306536	Triticum aestivum Transcriptome or Gene expression	Relationships between some transcription factors and concordantly expressed drought stress-related genes in bread wheat	Illumina HiSeq 2000	genotypes, Giza 168 (or GZ168) as the tolerant cultivar and Gemmiza 10 (or GM10)	Stress	Drought
PRJNA307989	Triticum aestivum	Exogenous Abscisic Acid and Gibberellic Acid Elicit Opposing Effects on Fusarium graminearum Infection in Wheat	Illumina HiSeq 2500	Examining the effects of F. graminearum infection on FHB susceptible wheat cultivar 'fielder'.	Stress	F. graminearum, ABA, GA
PRJNA314426	Triticum aestivum (bread wheat)	Drought-responsive WRKY transcription factor genes TaWRKY1 and TaWRKY33 from wheat confer drought and/or heat resistance in Arabidopsis	Illumina HiSeq 2000	wheat de novo transcriptome sequencing project	Stress	Drought
PRJNA316081	Triticum aestivum (bread wheat)	Tuning water-use efficiency and drought tolerance in wheat using abscisic acid receptors	Illumina HiSeq 2500	Water availability is a key determinant of terrestrial plant productivity. Many climate models predict that water stress will increasingly challenge agricultural yields and exacerbate projected food deficits. To ensure food security and increase agricultural efficiency, crop water productivity must be increased. Research over past decades has established that the phytohormone abscisic acid (ABA) is a central regulator of water use and directly regulates stomatal opening and transpiration. In this study, we investigated whether the water productivity of wheat could be improved by increasing its ABA sensitivity. We show that overexpression of a wheat ABA receptor increases wheat ABA sensitivity, which significantly lowers a plant’s lifetime water consumption. Physiological analyses demonstrated that this water-saving trait is a consequence of reduced transpiration and a concomitant increase in photosynthetic activity, which together boost grain production per liter of water and protect productivity during water deficit. Our findings provide a general strategy for increasing water productivity that should be applicable to other crops because of the high conservation of the ABA signaling pathway. Overall design: One representative transgenic line (TaPYLox) and its background non-transgenic cultivar (Null; cv. Fielder) were subjected to the analysis. The transcriptome was analyzed using three biological replicates of RNA samples from leaves of 40-day-old plants after exposure to one of three stress conditions. The three treatments were as follows: WWC, corresponding to normal conditions (soil water potential [SWP] > -110 kPa); ABA, namely, incubation for 24 h after spraying with 25 μM ABA; and drought, involving incubation for 24 h after withholding water to maintain SWP < -390 kPa. Each total RNA was isolated using the RNeasy® Plant Mini Kit (Qiagen) and evaluated for quality and quantity with an Agilent 2100 Bioanalyzer (Agilent Technologies) and the Agilent RNA 6000 Nano Kit (Agilent Technologies). Library preparation was performed according to the TruSeq RNA Sample Preparation v2 guide (Illumina). Sequencing on an Illumina HiSeq® 2500 system generated an average of 91.3 M paired-end reads (2 × 101 nt) per library.	Stress	ABA
PRJNA316919	Triticum aestivum (bread wheat)	Transcriptome analysis of genes related to resistance against powdery mildew in wheat-Thinopyrum alien addition disomic line germplasm SN6306	Illumina HiSeq 2000	Transcriptome analysis of genes related to the powdery mildew resistance of wheat-Thinopyrum alien addition disomic line germplasm SN6306	Stress	Powdery mildew infection
PRJNA327013	Comparative transcriptomics of Zymoseptoria tritici isolates	The expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici	Illumina HiSeq 2500	RNAseq of wheat leaves (cultivar drifter) infected with different strains of Zymoseptoria tritici	Stress	Zymoseptoria tritici
PRJNA327829	Triticum aestivum cultivar:Glenlea and Salamouni (bread wheat)	-	Illumina HiSeq 2000	We used Illumina RNAseq to compared the leaf transcriptomes before and after Pyrenophora tritici-repentis inoculation and before and after infiltration of its host selective toxin PtrTox A in two wheat genotypes ‘Glenlea’ susceptible and ‘Salamouni’ resistant.	Stress	Ptr inoculation
PRJNA328385	Transcriptome Profiling of Wheat Near Isogenic Line Carrying Lr57 Under Compatible and Incompatible interactions	Comparative Temporal Transcriptome Profiling of Wheat near Isogenic Line Carrying Lr57 under Compatible and Incompatible Interactions	Illumina HiSeq 2000	Leaf rust caused by Puccinia triticina (Pt) is one of the most important diseases of bread wheat globally. Next generation sequencing technologies has made feasible the study of the complete transcriptome of the host as well as pathogen through RNA sequencing (RNAseq) allowing expression analysis of the host genes in response to pathogen attack. Differential expression in a near isogenic line carrying leaf rust resistance gene Lr57 and recipient genotype upon challenge with the Pt isolate 77-5 is being reported in the present study. RNA samples were collected at five different time points 0, 12, 24, 48 and 72 hours post inoculation (HPI) following inoculation with Pt 77-5.	Stress	Puccinia triticina infection
PRJNA340343	Triticum aestivum cultivar:kharchia Transcriptome or Gene expression	Shedding light on response of Triticum aestivum cv. Kharchia Local roots to long-term salinity stress through transcriptome profiling	Illumina HiSeq 2500	Triticum aestivum L. an important cereal food crop providing basic staple food for major civilization of world. Even though it is moderately salt tolerant, there are reports of crop yield losses under salinity stress. Triticum aestivum cultivar Kharchia local, a salt tolerant wheat landrace, native to saline- sodic soils of Rajasthan, developed through a selection from farmer’s field. Investigating the mechanisms and pathways involved in salinity-tolerance of wheat could facilitate better understanding of the molecular basis of salinity response and therefore enable the effective use of genetic and genomic approaches to improve salinity tolerance in major cultivated crops	Stress	Salt(CK)
PRJNA340344	Triticum aestivum breed:bread wheat | cultivar:kharchia local Transcriptome or Gene expression	Shedding light on response of Triticum aestivum cv. Kharchia Local roots to long-term salinity stress through transcriptome profiling	Illumina HiSeq 2500	Triticum aestivum L. an important cereal food crop providing basic staple food for major civilization of world. Even though it is moderately salt tolerant, there are reports of crop yield losses under salinity stress. Triticum aestivum cultivar Kharchia local, a salt tolerant wheat landrace, native to saline- sodic soils of Rajasthan, developed through a selection from farmer’s field. Investigating the mechanisms and pathways involved in salinity-tolerance of wheat could facilitate better understanding of the molecular basis of salinity response and therefore enable the effective use of genetic and genomic approaches to improve salinity tolerance in major cultivated crops	Stress	Salt(treated)
PRJNA342474	Identification of circular RNAs and their targets in leaves of Triticum aestivum L. under dehydration stress	Identification of Circular RNAs and Their Targets in Leaves of Triticum aestivum L. under Dehydration Stress	Illumina HiSeq 2000	circRNA sequencing for 2 samples Overall design: Examing 2 conditions	Stress	Dehydration stress
PRJNA355905	Triticum aestivum (bread wheat)	-	Illumina HiSeq 2500	The drought and salt tolerant transgenic wheat overexpressing the transcription factor GmDREB1 was selected to investigate unintended pleiotropic effects using RNA-sequence analysis. As a control, we compared the transcriptome alteration of transgenic plants with wild-type plants treated with salt stress	Stress	Salt
PRJNA358808	Triticum aestivum cultivar:Zubkov and Atay 85 (bread wheat)	-	Illumina HiSeq 4000	Two cultivars (resistant and susceptible) stress treatment (drought, heat, and drought + heat) leaf, root and grain tissues	Stress	Drought, heat
PRJNA369686	Transcriptomic analysis of RNA-seq in drought-stressed hexaploid wheat var. Chinese Spring	Gene co-expression network analysis to identify critical modules and candidate genes of drought-resistance in wheat	Illumina HiSeq 2000	The data were RNA-seq from hexaploid wheat Tritium estivate, var Chinese Spring. Three tissues, roots, crown and leaves from 19 days old young seedlings (3-4 leaves stages) are used for RNA-seq after specific drought treatment (7 days drought , 36 hours after water potential below withering point) and before treatment. There are 10 plants in each treatment . Three experimental replicates were conducted. Two technical replicate for Illumina sequencing were done from two library of same RNAs. RNA-Seq reads are 100 bp Pair-end. Contact Xuewen Wang xwwang@uga.edu or Katrien Devos kdevos@uga.edu. The experiment was done in University of Georgia	Stress	Drought
PRJNA378325	Triticum aestivum (bread wheat)	"Transcriptome analysis of drought‑responsive genes regulated
by hydrogen sulfde in wheat (Triticum aestivum L.) leaves"	https://link.springer.com/article/10.1007/s00438-017-1330-4	Illumina HiSeq 4000	Stress	Drought
PRJNA379663	Transcriptome sequencing of T.aestivum replicates	Identification, characterization and expression analysis of lineage-specific genes within Triticeae	Illumina HiSeq 4000	Transcriptome profiling of salt-stressed and control wheat calluses of Kazakhstanskaya variety for identification of differential expressed genes during induction of somatic embryogenesis.	Stress	Salt
PRJNA380841	Triticum aestivum cultivar:Luyuan502 (bread wheat)	Transcriptomics Analyses Reveal Wheat Responses to Drought Stress during Reproductive Stages under Field Conditions	Illumina HiSeq 2500	we performed a transcriptomic analysis of a drought-tolerant wheat variety subjected to drought stress at various growth stages.	Stress	Drought
PRJNA387101	Large scale transcriptome analysis of high-temperature seedling-plant resistance to Puccinia striiformis f. sp. tritici in wheat revealed a non-race-specific resistance	CAFU: a Galaxy framework for exploring unmapped RNA-Seq data	Illumina HiSeq 2000	Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive disease of wheat worldwide. Previous studies showed that the resistance of wheat cv. XY 6 against Pst belongs to high-temperature seedling-plant (HTSP) resistance which is non-race specific and durable. But its underlying mechanism is complex and not fully understood.	Stress	Pst infection
PRJNA387602	Early events during the interaction between wheat and cereal cyst nematode as revealed by transcriptomic analysis	Transcriptional responses of wheat and the cereal cyst nematode Heterodera avenae during their early contact stage	Illumina HiSeq 4000	Cereal cyst nematode (Heterodera avenae) can be attracted by wheat roots before infestation, while largely is unknown underlying this phenomenon. Here, we examined the transcriptional responses of both wheat roots and nematodes during the attraction stage by mRNA sequencing analysis (with and without reference genome, respectively). We found that consistent with their respective mobility, the immobile host wheat root only had 93 DEGs (27 up-regulated and 66 down-regulated), while the mobile plant parasitic nematode H. avenae reacted much more actively with 879 DEGs (867 up-regulated and 12 down-regulated). Among the DEGs, a number of wheat DEGs (most down-regulated) were involved in biotic stress pathways, while several putative effector genes (up-regulated) were found in the nematode DEGs.	Stress	Heterodera avenae
PRJNA389404	Bread wheat RNA Seq	-	Illumina HiSeq 2000	The total RNA extracted from leaf tissues of control and salt-treated samples was sequenced using the Illumina technology.	Stress	Salt
PRJNA391049	Triticum aestivum cultivar:PBW343 (bread wheat)	Molecular characterization of Indian pathotypes of Puccinia striiformis f. sp. tritici and multigene phylogenetic analysis to establish inter- and intraspecific relationships	Illumina HiSeq 2500	The whole transcriptome sequencing of wheat will provide a profile of changes occurring in wheat genotype PBW343 after inoculation with Puccinia striiformis f. sp. tritici pathotypes 38S102 and 46S119	Stress	Pst Infection
PRJNA391522	The zinc-finger ubiquitin E3 ligase TaSAP5 regulates drought stress responses by promoting the degradation of DREB2A-INTERACTING PROTEIN in wheat	The E3 Ligase TaSAP5 Alters Drought Stress Responses by Promoting the Degradation of DRIP Proteins	Illumina HiSeq 2500	Wheat TaSAP5 gene is inducible by drought, and TaSAP5 overexpression in Arabidopsis and wheat seedlings increased their drought tolerance as measured by survival rate and grain yield under severe drought stress. TaSAP5 interacts with and ubiquitinated AtDRIP1, AtDRIP2, and TaDRIP, leading to their subsequent degradation through the 26S proteasome pathway. Consistently, TaSAP5 overexpression enhances DRIP degradation and increases level of DREB2A protein and of its downstream targets. These results suggest that TaSAP5 acts to link drought with DREB2A accumulation and illustrate the molecular mechanisms involved in this process.	Stress	Drought
PRJNA392366	Triticum aestivum cultivar:HD 29 and WH 542 Transcriptome or Gene expression	Transcriptome Analysis of Wheat–Tilletia indica Interaction Provides Defense and Pathogenesis-Related Genes	NextSeq 500	Comparative transcriptome analysis between resistant (HD29) and susceptible (WH542) cultivars of wheat inoculated with Tilletia indica RAKB_UP_1	Stress	Tilletia indica
PRJNA392368	Triticum aestivum cultivar:yangmai 16 (bread wheat)	Nitric Oxide and Hydrogen Peroxide Mediate Wounding-Induced Freezing Tolerance through Modifications in Photosystem and Antioxidant System in Wheat	Illumina HiSeq 2500	Transcriptional profiling of wheat plants due to the wounding and freezing treatment. Four treatments of systemic leaves: control (ck), 3 h after wounding (wo), 24 h after freezing (fr) and 3 h wounding + 24 h freezing (wo_fr) were collected for RNA sequencing analysis	Stress	Freezing and wounding
PRJNA395300	Triticum aestivum Leaf rust transcriptome data	Large-scale stage-specific regulation of gene expression during host–pathogen interactions in CSP44 bread wheat carrying APR gene Lr48	Illumina HiSeq 2000	The project aimed at studying the molecular basis of leaf rust resistance due to an Adult plant resistance gene (Lr48) in bread wheat. A selection line from Australian cultivar 'Condor' was found to carry adult plant resistance due to Lr48 gene, which is recessive in nature. The plants showed susceptibility untill boot stage to puccinia triticina race 77-5 while it displayed resistance symptoms as it enters the boot stage. The main objective was to identify transcripts from wheat host and fungal pathogen that were involved in rust infection.	Stress	Puccinia triticina infection
PRJNA401295	Triticum aestivum and Blumeria graminis f. sp. tritici Raw sequence reads	LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat	Illumina HiSeq 2000	To study molecular mechanisms of host resistance and the pathogenesis of wheat powdery mildew, leaf tissues of both Pm40-expressing L658 and the Pm40-deficient sister line L958 were harvested at 0, 6, 12, 24, 48 and 72 hours post-inoculation (hpi) with Blumeria graminis f.sp.tritici and then subjected to RNA sequencing (RNA-seq).	Stress	Powdery mildew infection
PRJNA408322	Transcriptome of cold-acclimated 1BL.1RS wheat-rye translocation line and its near-isoline	-	Illumina HiSeq 2500	Investigation of gene expressions of 1BL.1RS wheat-rye translocation line and its near-isoline under cold treatment.	Stress	Cold(CK)
PRJNA412622	Flag leaf field drought responses in Chinese Spring	Hotspots in the genomic architecture of field drought responses in wheat as breeding targets	NextSeq 500	Wheat transcriptome study in two levels of field drought.	Stress	Drought
PRJNA415716	Transcriptome analyses of three Zymoseptoria tritici isolates during infection of Triticum aestivum	Highly flexible infection programs in a specialized wheat pathogen	Illumina HiSeq 2500	We collected infected wheat leaf material at up to nine time points per Z. tritici isolate and conducted confocal microscopy analyses to select samples for RNA extraction and transcriptome sequencing based on the morphological infection stage. Thereby, we generated stage-specific RNA-seq datasets corresponding to the four core infection stages allowing us to compare the isolate-specific expression profiles at the same developmental stage of infection. Our final dataset comprises four stage-specific transcriptomes per isolate with two biological replicates per sample. Comparative transcriptome analyses reveal that the expression phenotypes of the three isolates differ significantly. Overall design: Comparative analyses of stage-specific and isolate-specific expression profiles of three Z. tritici isolates	Stress	Three Zymoseptoria tritici isolates
PRJNA422010	Deciphering molecular mechanisms underlying salinity stress tolerance in Kharchia Local	"Genome-wide Analysis of a Plant AT-rich Sequence and Zinc-binding Protein
(PLATZ) in Triticum Aestivum"	https://cdn.techscience.cn/uploads/attached/file/20210330/20210330022007_48386.pdf	Illumina HiSeq 2000	Stress	Salt
PRJNA427159	Transcriptomics study of three Blumeria graminis formae speciales	Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen	Illumina HiSeq 2000	We analyzed the gene expression and especially the expression of effector candidate genes in wheat and rye powdery mildews. Overall design: mRNA of wheat, rye and triticale infected with 3 wheat, 2 rye and 2 triticale powdery mildew isolates, respectively. 3 biological replicates of each infection were collected 48 hours after infection	Stress	Powdery mildew infection
PRJNA435777	RNA-Seq of Wheat (Triticum aestivum)	Transcriptome analysis reveals interplay between hormones, ROS metabolism and cell wall biosynthesis for drought-induced root growth in wheat	Illumina HiSeq 1000	Total RNA libraries were prepared using isolated total RNA according to the protocol of Illumina TrueSeq RNA Library Preparation Kit (https://support.illumina.com/). The libraries were checked for the average size (300-700 bp) on Agilent DNA 1000 chip using Agilent 2100 Bioanalyzer. After obtaining the Qubit concentration for each of the respective libraries, cluster generation was performed using Illumina CBotinstrument and finally loaded onto Illumina HiSeq platform for paired-end sequencing	Stress	Drought
PRJNA436722	Triticum aestivum Transcriptome analysis	Shifting the limits in wheat research and breeding using a fully annotated reference genome.	Illumina HiSeq 2500	ChineseSpring leaf, root, and spike transcriptome data.	Stress	bisulfite treatment
PRJNA437523	Transcriptome analysis of wheat root	Comparative analysis of root transcriptome profiles between drought-tolerant and susceptible wheat genotypes in response to water stress	Illumina HiSeq 4000	Comparative analysis of root transcriptome profiles between two wheat genotypes in response to water stress	Stress	Water
PRJNA472095	Novel transcripts in transcriptome of Triticum aestivum L. cv. Guizi 1	Upregulated structural and regulatory genes involved in anthocyanin biosynthesis for coloration of purple grains during the middle and late grain-filling stages	Illumina HiSeq 4000	In order to explore the molecular mechanism of anthocyanin synthesis in purple wheat and the effect of stresses on the purple wheat, the transcriptomes were sequenced in different periods and under different stress treatments, compared with reference genomes, and some new transcripts were obtained.	Stress	Drought, wounding, hormone
PRJNA472714	herbivory-induced changes in the wheat transcriptome	Convergent evolution of a metabolic switch between aphid and caterpillar resistance in cereals	Illumina HiSeq 2500	The goal of this project is to identify genes that are up regulated or down regulated after caterpillar (Spodoptera littoralis) feeding in wheat.	Stress	Herbivory-induced response
PRJNA472848	Transcriptomics and QTL analysis to identifying candidate genes for yellow rust resistance in wheat	Differential Gene Expression Analysis of Wheat Breeding Lines Reveal Molecular Insights in Yellow Rust Resistance under Field Conditions	Illumina HiSeq 2500	A winter wheat bi-parental population of 109 lines segregating for yellow rust resistance was sown in the field in Svalöv, Sweden in the autumn of 2013. Scoring was done at the booting stage (Zadoks stage 41-49) in the spring of 2014 with a scale of 1 (high resistant) to 9 (highly susceptible). Leaf material was collected from penultimate leaves pooled from three-four plants from each line of the segregating population at the booting stage (Zadoks stage 41-49). Leaves were flash frozen in liquid nitrogen and stored at -180oC until further processing. Total RNA was extracted with RNeasy Plant Mini kit (Qiagen) including DNase treatment (RNase-free DNase set, Qiagen). Concentration and quality of the RNA was estimated in Experion™ Automated Electrophoresis System (Bio-Rad Laboratories, Hercules, USA). CDNA library construction and sequencing of 20 samples with 9 resistant and 11 susceptible lines for yellow rust were done at the SciLifeLab (Stockholm, Sweden). Sequencing was performed on Illumina Hiseq 2500 instrument by paired-end sequencing of 150bp length as per manufacturer’s instructions	Stress	Yellow rust
PRJNA476783	Triticum aestivum cultivar:HD 2967 (bread wheat)	Comparative transcriptome analysis of wheat in response to corn leaf aphid, Rhopalosiphum maidis F. infestation	NextSeq 500	Gene expression of wheat variety after aphid attack	Stress	Aphid
PRJNA483762	The global wheat gene expressional responses to fusaoctaxin A (bread wheat)	A linear nonribosomal octapeptide from Fusarium graminearum facilitates cell-to-cell invasion of wheat	Illumina NovaSeq 6000	Purpose: To assess global changes of wheat coleoptiles gene expression in response to fusaoctaxin A which is a linear, C-terminally-reduced and D-amino acid residue-rich octapeptide, as the product of the two non-ribosomal peptide synthetases encoded by Fusarium graminearum fg3_54 cluster. Methods: For RNA seq of wheat coleoptiles, three biological replicates of mock-inoculated coleoptiles, wild-type PH-1 inoculated coleoptiles (3 dpi), ∆fg3_54 inoculated coleoptiles (3 dpi), after 3 hours fusaoctaxin A-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin A-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced. Results: For each sample, 33-95 M RNA-seq clean reads were obtained mapped to the Triticum aestivum Chinesespring genome sequence.Our results of RNA sequencing indicated fusaoctaxin does not induce PR gene expression, but suppress plant immunity and chloroplastc activity. Conclusions: Fusaoctaxin A represents an unprecedented virulence factor which can manipulate chloroplast and suppress host immunity. Overall design: Three biological replicates of mock-inoculated coleoptiles, wild-type PH-1 inoculated coleoptiles (3 dpi), ∆fg3_54 inoculated coleoptiles (3 dpi), after 3 hours fusaoctaxin A-treated coleoptiles, after 3 hours control (0.5% Tween-20) treated coleoptiles, after 24 hours fusaoctaxin A-treated coleoptiles and after 24 hours control (0.5% Tween-20) treated coleoptiles were sequenced using Illumina NovaSeq 6000 Sequencing System	Stress	Fusaoctaxin A
PRJNA484520	Integrated transcriptome and hormone profiling highlight the role of multiple phytohormone pathways in wheat resistance against fusarium head blight (bread wheat)	Integrated transcriptome and hormone profiling highlight the role of multiple phytohormone pathways in wheat resistance against fusarium head blight	Illumina HiSeq 2500	Multiple molecular tools and assays were deployed to compare the resistant variety Sumai3 with three regionally adapted Canadian cultivars, Stettler, Muchmore and FL62R1. Macroscopic and microscopic disease evaluation established the relative level of Type II FHB resistance of the four varieties and revealed that the F. graminearum (Fg) infection process displayed substantial temporal differences among organs. The rachis was found to play a critical role in preventing Fg spread within spikes. Large-scale, organ-specific RNA-seq at different times after Fg infection demonstrated that diverse defense mechanisms were expressed faster and more intensely in the spikelet of resistant varieties. The roles of plant hormones during the interaction of wheat with Fg was inferred based on the transcriptomic data obtained and the quantification of the major plant hormones. Salicylic acid and jasmonic acid were found to play predominantly positive roles in FHB resistance, whereas auxin and ABA were associated with susceptibility, and ethylene appeared to play a dual role during the interaction with Fg. Overall design: The four genotypes were subjected to challenge by the pathogenic fungus Fusarium graminearum or with 10 μl ddH2O as a mock treatment. Samples inoculated with Fg were taken at 1, 2, 3 days post inoculation (dpi) from spikelets and 2, 3, 4 dpi from rachis. Samples treated with water were harvested at 2 days post treatment from spikelets and rachis	Stress	Inoculated with F. graminearum
PRJNA485739	The wheat roots sequencing	Comparative Transcriptome Profiling of Gaeumannomyces graminis var. tritici in Wheat Roots in the Absence and Presence of Biocontrol Bacillus velezensis CC09	Illumina HiSeq 4000	Unraveling the mechanism of PGPR mediated enhanced resistance and fitness of wheat under biotic stress of pathogen	Stress	Bacillus velezensis CC09 (Bv),Gaeumannomyces graminis var. tritici(Ggt)
PRJNA487922	Triticum aestivum cultivar:Arg Transcriptome or Gene expression	Transcriptome analysis of bread wheat leaves in response to salt stress	Illumina HiSeq 2500	The leaf transcriptome profiling of the salt-stress response in bread wheat	Stress	Salt
PRJNA487923	Triticum aestivum_Raw sequence reads_Root	Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar	Illumina HiSeq 2500	The root transcriptome profiling of the salt-stress response in bread wheat	Stress	Salt
PRJNA490015	Transcriptomics of MRCV-infected wheat	Mal de Río Cuarto virus infection causes hormone imbalance and sugar accumulation in wheat leaves	Illumina HiSeq 3000	Wheat leaves infected with Mal de Río Cuarto Virus (MRCV, Fijivirus, Reoviridae) and wheat leaves from mock-inoculated plants	Stress	Mal de Río Cuarto Virus
PRJNA506702	Molecular signal communication in soil during arbuscular mycorrhizal formation changes the transcriptome profiles in wheat (Triticum aestivum L.) roots (bread wheat)	Molecular signal communication during arbuscular mycorrhizal formation induces significant transcriptional reprogramming of wheat (Triticum aestivum) roots	Illumina Genome Analyzer	We aimed to test the hypothesis that the transcriptional profile of wheat roots can be changed by the AM symbiotic signals, even though there is no physical contact with AM fungi. A total of 2,360 differentially expressed genes (DEGs), including 1,888 up-regulated DEGs and 472 down-regulated DEGs were found. Among them, 59 were highly induced DEGs (gene expression fold changed > 500), and 121 genes only expressed in the NM treatment. The DGEs covered all the 21 chromosomes of wheat genome, and were dominantly distributed on the 2A, 2B, 2D, 3B, 5B and 5D chromosomes. Most of the DEGs located at membrane, and functioned in catalytic activity, transferase activity and binding. 63 orthologues of the previously reported genes wich play important roles during AM symbiosis in model plants were found. Overall design: 6 samples for the two treatments, and three biological replicates for each treatment	Stress	Arbuscular mycorrhizal
PRJNA509214	Characterization of QTL and eQTL linked with early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan -1 x Nyubai doubled-haploid wheat population at two days post inoculation (bread wheat)	Characterization of QTL and eQTL controlling early Fusarium graminearum infection and deoxynivalenol levels in a Wuhan 1 x Nyubai doubled haploid wheat population.	Illumina HiSeq 2500	In this study, early infection by F. graminearum was characterized in a doubled-haploid population derived from the cross of the moderately FHB resistant wheat genotypes Wuhan 1 and Nyubai. Three significant QTL were identified: 1AL was associated with reduced deoxynivalenol levels, and 4BS and 5A were associated with reduced F. graminearum levels at 2 days after infection. The early resistance alleles for 1AL and 4BS were inherited from Wuhan 1, and those for the 5A QTL were inherited from Nyubai. The LOD support interval for the 5A QTL was in the same region as FHB5, a QTL previously associated with field resistance to FHB. Cis and trans eQTL were identified using RNA sequencing data from infected head samples. In total, 240 cis eQTL and 17,401 trans eQTL were identified within LOD support intervals for the three QTL. Hotspots for trans eQTL were identified within LOD support intervals for the 1AL and 4BS QTL. Differential gene expression analysis revealed twenty genes with cis eQTL within one of the 3 QTL support intervals, that had higher expression associated with FHB early resistance, and 17 genes with higher expression associated with FHB early susceptibility. Among those, genes with a cis eQTL peak coinciding with QTL peaks were enriched in functions related to signaling and protein-protein interaction, including NBS-LRR, BAH, LRR/F-box and TPR domain-containing proteins. Several genes located within one of the three QTL support intervals also had a trans eQTL with a peak at the same position as QTL peaks on other chromosomes, suggesting interactions between the QTL. Overall design: In this study, we have analyzed RNA-seq and genotype (SRR, SNP) data in two parent genotypes with moderate resistance to F. graminearum and 81 DH lines obtained by crossing the two parents at 2 dpi.	Stress	Fg inoculation
PRJNA512537	Pratylenchus/Wheat Root Interaction	Cereal Root Interactions with Soilborne Pathogens—From Trait to Gene and Back	Illumina HiSeq 2000	These sequences represent transcripts expressed in roots of a susceptible Triticum aestivum (hexaploid wheat) cultivar after challenge with the root lesion nematodes Pratylenchus neglectus and/or P. thornei. The objective was to identify nematode-inducible promoters for future studies on root defense.	Stress	Pratylenchus neglectus and/or P. thornei
PRJNA514418	Mutation of a histidine-rich calcium-binding protein gene in wheat confers resistance to Fusarium head blight	Mutation of a histidine-rich calcium-binding-protein gene in wheat confers resistance to Fusarium head blight	Illumina HiSeq 2500	We isolated the major-effect wheat QTL, Qfhs.njau-3B, that confers head blight resistance and showed that it is the same as the previously designated Fhb1. Fhb1 results from a rare deletion involving the 3’ exon of the histidine-rich calcium-binding protein gene on chromosome 3BS. Both wheat and Arabidopsis transformed with the Fhb1 sequence showed enhanced resistance to F. graminearum infection. The translation products of this gene’s homologs among plants are well conserved and might be essential to plant growth and development. Fhb1 could be useful not only for curbing FHB diseases in grain crops but also for improving other plants vulnerable to Fusarium spp	Stress	Fusarium head blight
PRJNA515393	wheat under 7Li treatment Transcriptome	Comparative transcriptome analysis of two common wheat varieties induced by 7Li-ion beam irradiation reveals mutation hotspot regions and associated pathways	HiSeq X Ten	Transcriptome profiling of two common wheat varieties induced by different doses of 7Li-ion beam irradiations	Stress	Li-ion beam irradiation
PRJNA516785	Transcriptome sequencing of Triticum aestivum seedling after iron overdose and deficiency	-	Illumina HiSeq 1500	Wheat seedlings were subjected to iron overdose and deficiency in hydroponic condition, separately. Total RNA was isolated and used for high throughput transcriptome sequencing using Illumina platform	Stress	Iron overdose and deficiency in hydroponic condition
PRJNA521521	Root transcriptome of the contrasting wheat genotypes under water deficit	Root transcriptome profiling of contrasting wheat genotypes provides an insight to their adaptive strategies to water deficit	HiSeq X Ten	Water deficit limits plant growth and productivity in wheat. This study attempted comparative transcriptome profiling of the tolerant (Abura) and susceptible (AUS12671) genotypes under PEG-simulated water stress via genome-wide RNA-seq technology to understand the dynamics of tolerance mechanism	Stress	Water deficit
PRJNA522013	RNA-seq analysis of the interaction of Fusarium graminearum and wheat heads	Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses	Illumina HiSeq 2500	Wheat heads of cultivar norm from 24, 48, and 72h post-inoculation of fungal pathogen Fusarium graminearum as well as from mock-inoculation (0h) were sequenced using Illumina Hiseq2500 PE150 by strand-specific RNA-seq. Only inoculated spikelets of the head were sampled. Three biological replicates were done for each time point.	Stress	Fusarium graminearum
PRJNA522933	Transcriptom study on wheat under water stress	-	HiSeq X Ten	We study on the response mechanisms of wheat under water stress by using transcriptomics and metabonomics	Stress	Water
PRJNA523855	Triticum aestivum cultivar:Sumai3 and Pasteur Raw sequence reads	Identification of Candidate R Genes in Wheat, Sumai-3 and Pasteur Against Fusarium Head Blight Based on Transcriptomics, Metabolomics, and Single Nucleotide Polymorphism	Illumina HiSeq 4000	Transcriptomics approach to identify the FHB response resistance genes in Sumai3 and Pasteur upon pathogen and mock inoculation	Stress	Fusarium graminearum
PRJNA523972	Brassinosteroid regulates root development with highly redundant genes in hexaploid wheat	Brassinosteroid Regulates Root Development with Highly Redundant Genes in Hexaploid Wheat	Illumina HiSeq 2500	Transcriptional changes were investigated in the roots taken from the 3-day-old wheat seedlings treated with Sterile water (CK), 50 nM EpiBL (BR1), 1 μM EpiBL (BR2) and 1 μM BRZ treatment for additional 12 days .	Stress	Epibrassinolide,brassinozole
PRJNA526019	Transcriptome of wheat	Identification of conserved genes involved in nitrogen metabolic activities in wheat	Illumina HiSeq 2000	Identification of conserved genes involved in nitrogen metabolic activities in wheat	Stress	Nitrogen
PRJNA527827	Identify genes involved in ER stress in wheat using RNA sequencing (bread wheat)	Transcriptome and physiological analyses for revealing genes involved in wheat response to endoplasmic reticulum stress	Illumina HiSeq 4000	We used dithiothreitol (DTT) and tauroursodeoxycholic acid (TUDCA) to induce or suppress ER stress in wheat cells, respectively, with the aim to reveal the molecular background of ER stress responses using RNA sequencing. Transcriptomic analysis revealed that 8204 genes were differentially expressed in three treatment groups. Among these genes, 158 photosynthesis-related genes, 42 antioxidant enzyme genes, 318 plant hormone-related genes and 457 transcription factors (TFs) might play vital roles in regulating wheat response to ER stress. Overall design: Experiments were established with three treatments: control (C), DTT (D), and DTT+TUDCA (T). Three independent biological replicates were performed, and a total of nine leaf samples were performed by RNA sequencing	Stress	Dithiothreitol and tauroursodeoxycholic acid
PRJNA528563	wheat leaves and roots transcriptome	Morphological and Transcriptome Analysis of Wheat Seedlings Response to Low Nitrogen Stress	Illumina MiSeq	RNA-seq data in wheat seedlings leaves and roots under low nitrogen stress	Stress	Low nitrogen
PRJNA529036	Integrative analysis of hexaploid wheat roots identifies signature components during changing regimes of iron and phosphate starvation	Integrative analysis of hexaploid wheat roots identifies signature components during iron starvation	NextSeq 500	The effect of Fe deprivation was investigated at transcriptomic level in hexaploid wheat. A genome-wide gene expression reprogramming was observed with a total of 5854 genes showing differential expression in roots of wheat subjected to Fe-starved medium. Subsequent analysis revealed a predominance of strategy-II mode of Fe uptake, with induced genome bias contribution from the A and B genomes. In general, the predominance of genes encoding for nicotianamine synthase, yellow stripe like transporters, metal transporters, ABC transporters and zinc-induced facilitator-like protein was noticed. Interestingly, Fe starvation causes a significant temporal increase of glutathione-S-transferase, which indicates the important role of glutathione in the response to Fe starvation in wheat roots. Taken together, our result provides new insight on wheat response to Fe starvation and lays foundation to design strategies to improve Fe nutrition in crops	Stress	Fe, phosphorus
PRJNA529321	Transcriptome analysis of two contrasting wheat genotypes during grain development under nitrogen optimum and stress condition	Genome-Wide Identification, Characterization, and Expression Analysis of Four Subgroup Members of the GH13 Family in Wheat (Triticum aestivum L.)	Illumina HiSeq 2500	Two contrasting bread wheat (hexaploid) genotypes were grown under optimum as well as low dose of Nitrogen. Grains were sampled at 4 stages of development (2, 3, 4 and 5 weeks after anthesis). RNA from each samples were extracted separately and pooled by mixing equimolar concentration. Experiment was replicated thrice. Total 12 libraries were prepared for sequencing	Stress	Nitrogen
PRJNA529884	Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis (bread wheat)	Transcriptome responses in wheat roots to colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis	Illumina Genome Analyzer	6 samples for the two treatments, and three biological replicates for each treatment	Stress	arbuscular mycorrhizal
PRJNA529906	Wheat Pyrenophora tritici-repentis Interaction	Disease Resistance in Wheat and Its Relatives	Illumina HiSeq 3000	Expression data for wheat exposed to either Pyrenophora tritici-repentis Race 2 spores (inoculated) or directly infiltrated with Ptr ToxA isolate. Treatments include: (P) inoculated with Ptr Race 2 spores, (C1) inoculated with water, (T) infiltrated with Ptr ToxA, or (C2) infiltrated with water. Timepoints include 0, 8, and 16 hours. Wheat cultivars Glenlea (susceptible) and Salamouni (resistant) were used.	Stress	Arbuscular mycorrhizal colonization
PRJNA541994	Triticum aestivum cultivar:Qingmai 6 (bread wheat)	Complementary analyses of the transcriptome and iTRAQ proteome revealed mechanism of ethylene dependent salt response in bread wheat (Triticum aestivum L.)	Illumina HiSeq 2500	RNA-seq for ethylene regulated salt tolerance genes in wheat	Stress	Salt, ethylene
PRJNA542779	QTL mapping and transcriptome analysis to identify wheat resistance genes for Septoria tritici blotch disease	-	Illumina HiSeq 2500	Growing a resistant cultivar is considered as the best strategy for STB disease management as it is effective, environmentally friendly and reduces the cost of production. The pathogen population causing STB is highly dynamic overcoming resistance genes and fungicide effects rapidly. Several quantitative trait loci (QTL) for STB resistance were identified in wheat but due to the dynamic pathogen population it is necessary to continuously identify new resistance genes/QTLand determine the underlying resistance mechanism. In this work, we integrated QTL mapping and transcriptome profiling to identify candidate genes underlying QTL associated with STB resistance in bread wheat at the seedling stage. The results revealed four QTL on chromosome arms 3DL, 2BL, 1BS and 3AS that contribute to STB resistance. Among these, two QTL on 3DL and 2BL were mapped for chlorosis, necrosis and pycnidia and the other two on 1BS and 3AS were only associated with necrosis and pycnidia. Among the four identified QTL, candidate genes were only identified in three QTL (1BS, 2BL and 3DL). In total, 238 differentially expressed genes (DEGs) were localized on 1BS, 16 DEGs on 2BL and 80 DEGs on 3DL QTL region, of which, several DEGs related to F-box protein, NBS-LRR disease resistance genes and receptor-like protein kinase were most over-represented. The results emphasise the importance of integrating QTL and transcriptome analysis to accelerate the identification of key genes underlying the traits of interest	Stress	Septoria Tritici Blotch
PRJNA545277	Triticum aestivum: GBS and transcriptome	-	Illumina HiSeq 3000	Genotyping-by-sequencing (GBS) of an Oklahoma winter wheat DH population (Duster x Billings) and RNAseq of selected DH individuals under well-watered and drought conditions.	Stress	Drought
PRJNA546228	wheat	A cosmopolitan fungal pathogen of dicots adopts an endophytic lifestyle on cereal crops and protects them from major fungal diseases	Illumina HiSeq 2500	wheat rna sequence	Stress	S. sclerotiorum treatment
PRJNA549144	Triticum aestivum (bread wheat)	Regulatory changes in TaSNAC8-6A are associated with drought tolerance in wheat seedlings	Illumina HiSeq 2500	TaSNAC8-6A is associated with drought tolerance in wheat seedlings	Stress	Drought
PRJNA550982	Male Sterile Wheat	Blocked synthesis of sporopollenin and jasmonic acid leads to pollen wall defects and anther indehiscence in genic male sterile wheat line 4110S at high temperatures	Illumina HiScanSQ	Blocked Synthesis of Sporopollenin and Jasmonic Acid Leads to Pollen Wall Defects and Anther Indehiscence in Genic Male Sterile Wheat Line 4110S at High Temperatures	Stress	Heat
PRJNA555667	Triticum aestivum (bread wheat)	Comparative transcriptome analyses for metribuzin tolerance provide insights into key genes and mechanisms restoring photosynthetic efficiency in bread wheat (Triticum aestivum L.)	Illumina NovaSeq 6000	Transcriptome sequence for metribuzin tolerance in wheat (Triticum aestivum L.	Stress	Herbicide treatment
PRJNA556084	Triticum aestivum (bread wheat)	Transcriptome analysis of activated charcoal-induced growth promotion of wheat seedlings in tissue culture	Illumina HiSeq 2500	purpose:the difference in gene expression of 10 d old wheat seedlings cultured on two media types (with and without AC) was analyzed by transcriptome sequencing technology, which laid a foundation for further study of gene expression and the mechanism used by AC to promote the development of immature wheat embryos. Genes that promote wheat growth were analyzed and excavated to provide a theoretical basis for breeding high-yielding wheat varieties	Stress	Activated charcoal
PRJNA559183	Spermidine promote the sucrose content in inferior grain and by this improve the grain filling in inferior grain of wheat (bread wheat)	Spermidine Increases the Sucrose Content in Inferior Grain of Wheat and Thereby Promotes Its Grain Filling	Illumina HiSeq 2500	Exogenous spermidine promotes starch sugar metabolism in wheat grains, thereby promoting grain filling Overall design: Analysis of the role of spermidine in grain filling from the perspective of endogenous and exogenous sources	Stress	Spermidine
PRJNA564622	Rye Sequence Data	Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential	Illumina HiSeq 2500	A reference quality assembly of the rye genome along with annotated gene features, miRNAs, and repetitive elements is used to investigate Triticeae evolution, focusing on the influence of transposable elements (TEs) and gross structural variations (CVs) to determine genome architectural features.	Stress	Temperature
PRJNA573996	Adaptive strategy of allohexaploid wheat to long-term salinity Stress	Adaptive strategy of allohexaploid wheat to long-term salinity stress	Illumina NovaSeq 6000	Most investigations of crop salinity tolerance are conducted on the basis of short-term stress condition within one growth stage. Understanding of crop response mechanisms to the long-term salinity stress (LSS) will be more valuable for improvement of crop salinity tolerance than that of short-term stress. Hence, we treated allohexaploid wheat seeds with a LSS condition cross germination and seedling stages for 30 days. To elucidate comprehensive gene expression and physiological response strategies of allohexaploid wheat to LSS, we analyzed the chloroplast ultrastructure, anatomy, plant hormones, organic compatible solutes, inorganic ions, and transcriptomic profiling of the stressed plants. The global transcriptomic profiling and biochemical measurements showed that energy partitioning between general metabolism maintenance and stress response may be crucial for survival of allohexaploid wheat under LSS. Under LSS, wheat might shift energy form general maintenance to stress response thr allohexaploid ough enhancing ABA pathways, and suppressing GA and JA pathways in leaf. We further distinguished the expression status of A, B, and D homoeologs of any gene traid, and surveyed effects of LSS on the homoeolog expression bias for salinity tolerant triads. We found LSS has similar effect on expression of three homoeologs (A, B, and D) for most salinity tolerant triads. However, in some salinity tolerant triads, LSS imposed different effects on expression of three homoeologs. We searched three key salinity responsive elements (ABREs, DRE1, dehydration responsive element) in promoter regions of A, B, D homoeologs of all 149 salinity tolerance triads. Only 48 salinity tolerant triads contain ARBEs or DRE1 in their promoter. Of these 48 salinity tolerant triads, only in four salinity tolerant triads three homoeologs showed same salinity responsive element composition, in other 44 salinity tolerant triads three homoeologs contained different salinity responsive element elements in their promoter regions. We propose that, for these salinity tolerant triads, expression of three homoeologs may be modulated by different mechanisms. The Cis-acting element divergence among three homoeologs may incur their different responses to LSS.	Stress	Salt
PRJNA575568	Wheat roots sequencing with/without Bacillus altitudinis WR10 under Cu stress	Endophytic Bacillus altitudinis WR10 alleviates Cu toxicity in wheat by augmenting reactive oxygen species scavenging and phenylpropanoid biosynthesis	Illumina HiSeq 4000	We report that an endophytic PGPB, Bacillus altitudinis WR10 alleviates Cu toxicity in wheat and explore the mechanisms via transcriptome sequencing. Our findings indicate that the alleviating effect are related to differentially expressed genes involved in reactive oxygen species (ROS) and glutathione (GSH) metabolism and phenylpropanoid biosynthesis	Stress	Cu
PRJNA575739	Triticum aestivum cultivar:Duster (bread wheat)	-	Illumina HiSeq 3000	Individuals sequenced under well-watered and drought conditions	Stress	Drought
PRJNA577523	BIOCOMES RNASeq	Deciphering the modes of action of Golubevia sp., an antagonist against the causal agent of powdery mildew in wheat, using an mRNA-based systems approach	Illumina HiSeq 2500	RNASeq based analysis on the mode of action of Golubevia sp. isolates against powdery mildew in wheat.	Stress	Golubevia sp & Blumeria graminis fp. tritici
PRJNA591384	Carbohydrates and plant hormones regulate alkali tolerance of hexaploid wheat plant (Triticum aestivum)	Carbohydrate and plant hormone regulate the alkali stress response of hexaploid wheat (Triticum aestivum L.)	Illumina NovaSeq 6000	In the present study, we subjected wheat plants to alkali stress treatment for 30 days. RNAseq of leaf and roots was conducted.	Stress	Alkali
PRJNA592401	Triticum aestivum cultivar:Zhoumai 18 (bread wheat)	Isoform Sequencing Provides Insight Into Freezing Response of Common Wheat (Triticum aestivum L.)	Illumina MiSeq	The objective of the study is to reveal the freezing tolerance mechanisms of wheat using the emerging single-molecule real-time (SMRT) sequencing technology PacBio Sequel.	Stress	Freezing
PRJNA595435	TaSNAC3-4A expression contributes to drought tolerance in wheat	Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat	Illumina HiSeq 2500	Our findings provide important insights into the genetic basis for natural variation in wheat drought tolerance, as well as new targets for both genetic engineering and selection to improve this trait.	Stress	Drought
PRJNA595999	Epigenetic control of fusarium head blight disease	Epigenetic regulation of gene expression improves Fusarium head blight resistance in durum wheat	Illumina HiSeq 2500	The objective of the project was to find a novel source of fusarium head blight disease resistance in durum wheat, which is susceptible to fusarium infection. Additionally, durum wheat has less genetic variation for this trait which makes it difficult to achieve resistance through breeding.	Stress	Fusarium graminearum
PRJNA601623	Triticum aestivum cultivar:Jimai22 (bread wheat)	Seed dressing with mefenpyr-diethyl as a safener for mesosulfuron-methyl application in wheat: The evaluation and mechanisms	HiSeq X Ten	Transcriptome of wheat leaves and shoot treated with or without mesosulfuron-methyl and/or mefenpyr-diethyl	Stress	Mesosulfuron-methyl and/or mefenpyr-diethyl
PRJNA604012	Transcriptomic and anatomic profiling reveal germination process of different wheat varieties in response to waterlogging stress (bread wheat)	Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress	Illumina NovaSeq 6000	At the same time, Illumina sequencing technology was used to determine the transcriptome of these three wheat varieties during germination	Stress	Waterlogging
PRJNA604047	Zymoseptoria tritici; Triticum aestivum	The identification of a transposon affecting the asexual reproduction of the wheat pathogen Zymoseptoria tritici	NextSeq 500	This study used long-read sequencing technology (either PacBio SMRT or Oxford Nanopore) to resequence 3 Zymoseptoria tritici isolates and generated near-complete genome assemblies for them. This project also includes RNAseq data of wheat leaves (cultivar WW2449) infected with the 3 strains of Zymoseptoria tritici and RNAseq data of the a single Zymoseptoria tritici strain under in vitro conditions	Stress	Zymoseptoria tritici
PRJNA605071	wheat silicon treatment (bread wheat)	Transcriptome analysis reveals differentially expressed MYB transcription factors associated with silicon response in wheat	Illumina Genome Analyzer	we performed RNA-seq technology to identify differentially expressed genes (DEGs) in seedlings under silicon stress of wheat	Stress	Silicon treatment
PRJNA605909	Triticum aestivum cultivar:Sonora 64; Vinata; CRP1660; DBW 17 (bread wheat)	Identifying transcripts associated with efficient transport and accumulation of Fe and Zn in hexaploid wheat (T. aestivum L.)	Illumina HiSeq 4000	We performed transcriptome analysis of 4 Indian heaxaploid wheat genotypes i.e Sonora 64; Vinata; CRP1660; DBW 17 differing in their total grain Fe/Zn content. Seed;lings were grown for 21 days in sand culture followed by applying Fe/Zn withdrawal (Control (C), Treatment 1(0% Fe and Zn) for 9 days. Thirty days old seedlings were harvested for RNA isolation and sequencing to capture the transcripts associated with efficient uptake, and utilization of Fe/Zn from root to the grain.	Stress	Fe/Zn
PRJNA613349	Transcriptome analysis reveals key defense related differentially expressed genes in response to stripe rust on wheat	Identification of QTLs/Defense Genes Effective at Seedling Stage Against Prevailing Races of Wheat Stripe Rust in India	Illumina HiSeq 4000	at 12, 48 and 72 hr post-inoculation (HPI). The collected samples were immediately placed in RNA later and stored at -20 degree C until use. The RNA from leaf samples were extracted using Qiagen RNeasy Mini kit (QiagenInc, USA). Samples were IIumina sequenced on a single HiSeq 4000 machines yielding at least 895M 150bp paired-end reads per sample. Each sample represents one experimental condition (pathogen/mock; time points; genotype).	Stress	P. striiformis tritici
PRJNA628157	Nonuniform Salt Distribution in the Root Zone Alleviates Salt Damage in Wheat	Non-uniform salt distribution in the root zone alleviates salt damage in wheat	Illumina NovaSeq 6000	Furrow sowing could significantly decrease salt damage to wheat. However, the underlying molecular mechanism is not well known. A split-root system was applied to simulate non-uniform root zone salinity in this study. Hydroponic results showed that wheat seedlings under non-uniform salt stress may take a salt avoidance method to ensure growth. RNA sequencing analysis showed that 1648 and 3245 differentially expressed genes were identified in the 0/150 and 75/75 salt treatments, respectively, with an intersection of 690. GO terms which represent normal growth were specifically enriched by up-regulated genes in the 0/150 treatment or down-regulated genes in the 75/75 treatment, while terms which represent phytoremediation were specifically enriched by up-regulated genes in the 75/75 treatment or down-regulated genes in the 0/150 treatment. Besides, differentially expressed genes between the 0/150 and 75/75 treatments known as marker genes for salt tolerance and transcription factors all showed a significantly higher expression level in the 75/75 treatment. All these suggest that a uniform salt treatment causes wheat to initiate a more complex salt-tolerance mechanism to confront salt stress. In addition, 11 genes annotated to peroxidase were more highly expressed in the 0/150 treatment, and the enzyme activity showed the same trend. This indicates that peroxidase may play some role in the better performance of wheat plants undergoing non-uniform salt stress. Lastly, pot culture experiment showed that wheat plants under non-uniform salt stress attained higher yields, further indicating that inducing unequal salt distribution in the soil could provide significant improvements in wheat cultivation	Stress	Salt
PRJNA629995	Wheat Lr47-mediated resistance RNA-seq	Genome-Wide Expression Profiling of Genes Associated with the Lr47-Mediated Wheat Resistance to Leaf Rust (Puccinia triticina)	Illumina HiSeq 4000	Genome-wide expression profiling of genes associated with the Lr47-mediated wheat resistance to Puccinia triticina.	Stress	Puccinia triticina
PRJNA630059	Effect of water deficit and cold stress on Triticum aestivum cv. Saratovskaya 29 and cv. Yanetzkis Probat	Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress	NextSeq 500	Leaf tissue transcriptomes for Triticum aestivum cv. Saratovskaya 29 (S29) and cv. Yanetzkis Probat (YP) grown under abiotic stress conditions (water deficiency and +4C cold (4h and 24h)) obtained using Illumina based MACE technology of sequencing	Stress	Water deficiency and cold
PRJNA630776	RNA sequencing - Fusarium Head Blight 5dpi AAC Tenacious and Roblin	Histology and RNA Sequencing Provide Insights Into Fusarium Head Blight Resistance in AAC Tenacious	Illumina HiSeq 2500	RNA sequencing of AAC Tenacious and Roblin in response to Fusarium Head Blight	Stress	Fusarium head blight
PRJNA632706	Triticum aestivum cultivar:Chinese Spring (bread wheat)	Comparative Analysis of the Glutathione S-Transferase Gene Family of Four Triticeae Species and Transcriptome Analysis of GST Genes in Common Wheat Responding to Salt Stress	Illumina HiSeq 2500	To investigate the expression patterns of GST genes in wheat under salt stress, a common wheat cultivar (Chinese Spring) was planted in a growth chamber under a photoperiod of 16 h/8 h (light/dark). The seedlings were subjected to salt treatment at concentrations of 0, 100, 200, and 300 mM NaCl at the one week stage.	Stress	Salt
PRJNA636099	Transcriptome comparison for wheat stripe rust fungus during the infeciton of wheat and barberry	Distinct Transcriptomic Reprogramming in the Wheat Stripe Rust Fungus During the Initial Infection of Wheat and Barberry	Illumina HiSeq 4000	To clarify the different mechanisms deployed by wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) urediospores and basidiosopres during the infection of wheat and barberry, transcriptomes of both interactions were compared. Two Pst isolates, CYR32 and V26, were inoculated on wheat and barberry leaves. Then wheat leaf samples at 2 dpi and barberry leaf samples at 4 dpi were collected. Since the fungal RNA at the early stage of infection represents only a small fraction of the total RNA from infected leaves, we constructed normalized cDNA library to increase the proportion of pathogen RNA that enabled us to detect expressed fungal genes more readily. Data from normalized library were used for qualitative comparison of expressed genes of two Pst isolates in wheat and barberry. Meanwhile, barberry leaf samples from 3 and 4 dpi as well as wheat leaf samples from 1 and 2 dpi were collected, and non-normalized libraries were constructed for quantitative analysis of transcriptional levels for Pst genes during the early stage of infection of two hosts.	Stress	Puccinia striiformis f. sp. tritici
PRJNA638505	molecular mechanism of post-mowing of forage wheat	RNA Sequencing Reveals Dynamic Carbohydrate Metabolism and Phytohormone Signaling Accompanying Post-mowing Regeneration of Forage Winter Wheat (Triticum aestivum L.)	Illumina HiSeq 4000	This study was designed to reveal the molecular mechanism of post-mowing of forage wheat	Stress	Mowing
PRJNA649099	Local Saudi wheat cultivar (Triticum aestivum L.)	Physiological and molecular responses to water-stress in local Saudi wheat cultivars	Illumina HiSeq 2500	Identification of mechanisms and genes involved in drought resistance in some local Saudi wheat cultivars.	Stress	Drought
PRJNA649300	Multi-omics Analyses Reveal Molecular Mechanisms of Potassium Deprivation Adaption in Wheat (Triticum aestivum L.) (bread wheat)	Multi-Omics Analyses Reveal the Molecular Mechanisms Underlying the Adaptation of Wheat (Triticum aestivum L.) to Potassium Deprivation	Illumina HiSeq 4000	This study evaluated the level of genetic variation among 543 wheat associations differing in K-deficiency tolerance at seedling and adult plant stages. Two of the 543 wheat associations, i.e. KN9204 and BN207, were identified as extreme K-deficiency tolerant and sensitive cultivars, respectively. We further conducted transcriptomic and metabolomics analyses using the roots of KN9204 and BN207 under normal or K-deficient conditions.Integrated analysis of gene expression and metabolite profiles revealed that dramatically more genes including those involved in ion homeostasis, cellular reactive oxygen species (ROS) homeostasis and glutamine synthetase pathways were induced in KN9204 as compared with BN207 under K-deficient conditions, which might indicate their unique roles in regulating plant K-starvation tolerance. These findings provided a better understanding of molecular responses of root adaptive strategies to K deprivation in wheat. Overall design: Root mRNA profiles of Kenong 9204 and Bainong 207 treated with normal potassium and low potassium for 14 days	Stress	K-deficient
PRJNA656427	Wheat treated with zymoseptoria tritici in resistant and susceptible cultivars	Insights into the resistance of a synthetically-derived wheat to Septoria tritici blotch disease: less is more	Illumina HiSeq 4000	Wheat cultivars Stigg (STB resistant) and Longbow (STB susceptible) were treated with an aggressive Irish Isolate of zymoseptoria tritici (Cork Cordiale 4), and RNA was sequenced at 6, 24, 48 and 96 hours post inoculation.	Stress	Septoria Tritici Blotch
PRJNA658641	RNA-seq for Korean wheat cultivar under pre-harvest sprouting	Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)	Illumina HiSeq 2500	Studies for differentially expressed genes under artificial pre-harvest sprouting and ABA treatments in Korean wheat cultivars	Stress	ABA，PHS
PRJNA659916	RNA-seq Analysis Reveals Different Drought Tolerance Mechanisms in Two Broadly Adapted Wheat Cultivars ‘TAM 111’ and ‘TAM 112’ (bread wheat)	RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'	RNA-Seq	Wheat cultivars ‘TAM 111’ and ‘TAM 112’ have been dominantly grown in the Southern U.S. Great Plains for many years due to their excellent, yet variable, drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. Of the 122,017 gene sequences assembled, 2,254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1,532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1,670 at heading and grain-filling stages, respectively. The two cultivars have 1,214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each may have a specific mechanism to cope with drought. Annotation of all 2,254 genes with dry-wet expression difference found 1,855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. Comparing gene expressions involved in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation found TAM 112 have more specific dry-wet DEGs than TAM 111 with most of them up-regulated, indicating that TAM 112 is more active than TAM 111 in response to drought. In addition, 399 dry-wet DEGs with unknown functions included 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases. These may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Overall design: Compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions	Stress	Drought
PRJNA663325	Factors affecting the rapid changes of protein under short-term heat stress (bread wheat)	Factors affecting the rapid changes of protein under short-term heat stress	Illumina HiSeq 4000	The protein content determines the cell state. The variation in protein abundance is crucial when organisms are in the early stages of heat stress, but the reasons affecting their changes are still unknown. We quantified 47,535 mRNAs and 3,742 proteins in filling grain of wheat under two thermal environments. The impact of mRNA abundance and sequence features implicated in protein translation and degradation on protein expression were evaluated by regression analysis. Transcription, codon usage and amino acid frequency mainly affect protein expression, and their combined contribution explains 58.2% and 66.4% of protein abundance variation in two types of heat stresses. Of which, transcription contributes more to the protein expression under severe heat stress (31%) than to mild stress (6%). Codon usage plays a stable and powerful role in protein expression under heat stress, even surpassing transcription. What’s more, the usage of AAG is a key factor regulating rapid protein expression under heat stress. This study revealed the main factors affecting the changes of protein abundance in the early stage of heat stress, and explained the mystery that plants can express protein rapidly under heat stress. Overall design: The reflection of wheat grains at the filling stage under two heat stresses	Stress	Heat
PRJNA664832	Black point	Transcriptome-based analysis of resistance mechanism to black point caused by Bipolaris sorokiniana in wheat	Illumina HiSeq 2500	Resistance to black point	Stress	Inoculated with B. sorokiniana
PRJNA667481	Wheat response to combined starvation of iron and phosphate	Physiological and molecular responses to combinatorial iron and phosphate deficiencies in hexaploid wheat seedlings	Illumina NovaSeq 6000	This dataset is a part of the study for analyzing the cross-talk between iron and phosphate homeostasis in wheat.	Stress	Iron and phosphate
PRJNA671695	Transcriptomic Analysis of Wheat Seedling Responses to the Systemic Acquired Resistance Inducer N-Hydroxypipecolic Acid (bread wheat)	Transcriptomic Analysis of Wheat Seedling Responses to the Systemic Acquired Resistance Inducer N-Hydroxypipecolic Acid	Illumina NovaSeq 6000	This experiment is to assess global changes of wheat gene expression in response to N-hydroxypipecolic acid (NHP), which is an inducer of plant systemic accquired resistance. Six plates (24 seeds per plate) of wheat (Triticum aestivum) cultivar Zhongyuan 98-68 were planted under 25ºC incubator. After three days, three plates of seedlings were treated with 1 μL 1 mM NHP per seedling, called as NHP-rep 1,2,3. The other three were treated with water and used as the control group (called as water-rep 1,2,3). The coleoptiles were collected after one day after the treatment. Each plate serves as a biological replicate for its treatment group for RNA sequencing. Overall design: Three biological replicates of four-day-old wheat seedling at one day post water treatment were named water-rep 1, 2, 3, used as control. Three biological replicates of four-day-old wheat seedling at one day post NHP treatment (1 μL 1mM NHP per seedling) were named NHP-rep 1, 2, 3. Total RNA extracted from water-rep 1, 2, 3 and NHP-rep 1, 2, 3 were used for library preparation. The RNA sequencing was performed at Sinotech Genomics. The libraries for sequencing were prepared using SureSelect Strand-Specific RNA Component kit. RNA sequencing was performed using an Illumina NovaSeq 6000 machine to obtain 150 nt paired-end reads.	Stress	N-hydroxypipecolic acid
PRJNA674985	ThatcherLr14a Puccinia triticina infection	A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat	Illumina NovaSeq 6000	Triticum aestivum line ThatcherLr14a (and Thatcher) was infected with Puccinia triticina, avirulent, virulent to Lr14a, and mock treated.	Stress	Puccinia triticina
PRJNA680330	Iron Deficiency Triggered Transcriptome Changes in Bread Wheat (bread wheat)	Iron deficiency triggered transcriptome changes in bread wheat.	Illumina HiSeq 2000	Iron (Fe) plays a pivotal role in several metabolic and biosynthetic pathways essential for plant growth. Fe deficiency in plants severely affects the overall crop yield. Despite several studies on iron deficiency responses in different plant species, these mechanisms remain unclear in the allohexaploid wheat, which is the most widely cultivated commercial crop. In order to gain a comprehensive insight into molecular responses of bread wheat when exposed to iron deficiency, we studied transcriptomic changes in the roots and flag leaves of wheat plants subjected to iron-deficient and iron-sufficient conditions during early grain filling. Overall design: Triticum aestivum cv. Bobwhite S26 seeds were germinated on wet filter paper for 7 days and then transferred to the hydroponic system in the greenhouse conditions (22˚C/18˚C with 16-hour-light/8-hour-dark cycle, 60% relative humidity). All the seedlings were first maintained in iron-sufficient hydroponic solution for 7 days and then half of the plants were transferred to iron-deficient hydroponic solutions (iron-sufficient condition: 100.0 μM Fe; iron-deficient condition: 10.0 μM Fe). Roots and flag leaves were collected at 8-10 days post anthesis (DPA), i.e., around the commencement of grain filling. Three biological replicates were collected for each sample. Twelve samples were collected in total	Stress	Fe
PRJNA685218	wheat sequencing	-	NextSeq 500	Lr19-mediated response to P. triticinia in wheat.	Stress	P. triticina
PRJNA686485	Transcriptome of wheat (Triticum aestivum L.) leaf and root	Nanotoxicological effects and transcriptome mechanisms of wheat (Triticum aestivum L.) under stress of polystyrene nanoplastics	Illumina HiSeq 2500c	Wheat leaf and root RNA-seq data for polystyrene nanoplastics root-exposure	Stress	Polystyrene nanoplastics
PRJNA689352	RNA-sequencing of root in wheat with / without Bacillus sp. WR12 in the presence or absence of Fe deficiency	Bacillus sp. WR12 alleviates iron deficiency in wheat via enhancing siderophore- and phenol-mediated iron acquisition in roots	Illumina NovaSeq 6000	The study aimed to investigate the mechanisms of WR12 alleviating Fe deficiency in wheat.	Stress	Fe
PRJNA699868	Next-Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes Mechanism for Autophagy Inhibition Enhanced Salt Stress Sensitivity of Wheat Seedling	Comparative transcriptomic and metabolic profiling provides insight into the mechanism by which the autophagy inhibitor 3-MA enhances salt stress sensitivity in wheat seedlings	Illumina HiSeq 2000	Purpose: To characterize the functional implication of autophagy in the wheat response to stress, the key genes contributing in mediated salt tolerance of wheat seedlings through 3-MA were identified in normal or salt stress conditions in the presence or absence of added 3-MA by the transcriptome profiles. Methods: Four days after NaCl and 3-MA treatment, the roots and the third leaves were collected respectively with every 10 of them being mixed as one biological replicate for each treatment. Every treatment had four biological replicates. The wheat root and leaves mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results: The RNA-Seq data had high quality and reliable results were obtained from the transcriptome assembly. A high correlation between biological replicates was observed for all treatments, which indicated that the four biological replicates were reliable in this study. Based on the principal component analysis (PCA), a clear separation between the NaCl-treated group and controls could be observed. The Q30 percentage (sequences with sequencing error rate lower than 0.1%) was over 94%, and the average GC content of the RNA-seq reads was 55.46%. After removing the adaptor and low-quality sequence, each library received 68310810-83844286 clean reads. These clean reads were mapped to the reference genome with match ratios in the range of 93.6%-95.9%, and 120744 genes predicted from the genome were found to be expressed (with FPKM > 0), including 25180 annotated genes in wheat genome. 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings. Conclusions: 3-MA treatment shifted the transcriptome a salt-stressed wheat seedling. The up-regulated DEGs and DEMs were increased, and the down-regulated DEGs and DEMs were decreased in 3-MA-added plants under NaCl stress condition. The study may help us understand the mechanism for 3-MA mediated salt tolerance and provide a theoretical basis for autophagy regulated salt response in wheat seedlings. Overall design: Four days after NaCl and 3-MA treatment, the mRNA profiles of the roots and the third leaves.	Stress	Salt
PRJNA707202	Triticum aestivum (bread wheat)	Impacts of Nitrogen Deficiency on Wheat (Triticum aestivum L.) Grain During the Medium Filling Stage: Transcriptomic and Metabolomic Comparisons	HiSeq X Ten	Impacts of nitrogen deficiency on wheat (Triticum aestivum L.) grain during the medium filling stage	Stress	N-deficient
PRJNA718488	Plant sample from Triticum aestivum	Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens	Illumina HiSeq 2500	The goal of the study was to investigate the transcriptomic response of susceptible wheat cultivars to leaf rust (Puccinia triticina) and powdery mildew (Blumeria graminis f.sp. tritici) mixed infection, and to identify possible pathogen effector targets in the host. Five different wheat cultivars (three resistant and two suceptible ones) were infected in the field with a mixture of rust and mildew isolates. Flag leaves from infected and uninfected wheat plants were collected at late infection stage for RNA-Seq.	Stress	Leaf rust and powdery mildew mixed infection
PRJNA719174	Impact and mechanism of sulphur-deficiency on modern wheat farming nitrogen-related sustainability and gliadin content	Impact and mechanism of sulphur-deficiency on modern wheat farming nitrogen-related sustainability and gliadin content	HiSeq X Ten	Impact and mechanism of sulphur-deficiency on modern wheat farming nitrogen-related sustainability and gliadin content	Stress	Sulphur
PRJNA737275	transcriptome of wheat	Characterization and functional analyses of wheat TaPR1 genes in response to stripe rust fungal infection	HiSeq X Ten	Study on the Transcriptome of Wheat Stripe Rust	Stress	Pst-CYR34
PRJNA746965	2017 Drought RNA-seq of Oklahoma Winter Wheat	-	Illumina HiSeq 3000	Oklahoma Winter Wheat Raw Sequencing Reads.	Stress	Drought
PRJNA750734	T.aestivum cv Chineese Spring diurnal RNA-seq	Functional characterization of genes with daily expression patterns in common wheat	NextSeq 550	Common wheat cultivar Chinese Spring plants were grown for 21 days after germination in a climatic chamber. with short days (9 h of light, 20 C). Three replicate samples were harvested at 0, 3, 9, and 16 hour time points over 24 h starting at the beginning of the light period. The material was collected in the dark until the light was turned on (0 h), after 3 hours of the light on (3 h), before the light was turned off (9 h) and in the middle of the night (16 h)	Stress	The circadian clock
PRJNA765290	Characterizing wheat defense mechanisms against wheat curl mite infestation	Wheat transcriptomic responses to extended feeding by wheat curl mites	Illumina NovaSeq 6000	(containing a WCM resistance gene) and Settler (WCM susceptible) at 10 days post infestation. Our transcriptomic profiling of wheat cultivars provides important clues on factors that contribute to wheat defense against WCM.	Stress	WCM Infestation
PRJNA773507	TAMFT-3A & 3B2 homeologs are associated with wheat (Triticum aestivum) preharvest sprouting.	-	Illumina HiSeq X	Investigate the homeologs of the Mother of Flowering Time (MFT) gene in a double haploid population of winter wheat cultivar Loma (PI680576) and Warhorse (PI670157) for their effect on preharvest sprouting (PHS). Loma and Warhorse have different alleles of MFT on the A genome and the 2nd copy on the B genome, or B2. DHL population was grown in the field at the Post Farm in Bozeman Montana, and PHS was evaluated in misting chambers. RNA was extracted from DHL population seeds for RNA Seq evaluation of expression. PHS effects wheat negatively when rains occur after grain maturity, before harvest. Sprouted wheat loses its agronomic value and is often rejected at grain elevators. This study seeks to characterize genes that effect PHS and develop germplasm that is resistant to the phenomenon	Stress	PHS
PRJNA786911	Transcriptomic responses of common wheat segregating for Wsm2 locus to wheat streak mosaic virus (WSMV) and mock infection	Genomic and Molecular Characterization of Wheat Streak Mosaic Virus Resistance Locus 2 (Wsm2) in Common Wheat (Triticum aestivum L.)	Illumina HiSeq 2000	To understand transcriptomic responses of WSMV resistant (contains Wsm2 locus or Wsm2+) and susceptible wheat (absent Wsm2 locus or Wsm2-) to WSMV and mock treated conditions and identify possible causative genes underlying Wsm2 locus, we performed a RNA-seq study for differentially expressed genes (DEGs) and de novo transcriptome assembly analysis. Overall design: Illumina HiSeq 2000 were performed on RNA-seq libraries from four biological replicates of two genotypes (selected double haploids from Snowmass and Antero population contains or absent for Wsm2 locus, annotated as Wsm2+ and Wsm2-) under mock treated condition (Buffer) and WSMV treated (WSMV) condition. Raw reads were filtered to remove adaptor and low-quality reads, and then mapped to wheat reference genome IWGSC ReSeq v1.0. Expression was tabulated with Featurecounts and pairwise comparisons were performed on raw reads with DESeq2. De novo assembly of all cleaned reads were performed with Trinity software	Stress	T-WSMV inoculation
PRJNA798111	RNA-seq wheat yellow spot infection zones	Spatiotemporal patterns of wheat response to Pyrenophora tritici-repentis in asymptomatic regions revealed by transcriptomic and X-ray fluorescence microscopy analyses	Illumina NovaSeq 6000	Pyrenophora tritici repentis (Ptr) is a necrotrophic fungal pathogen and causal agent of yellow spot, a significant disease in wheat. Plant transcriptome changes that happen in response to fungal pathogens in the asymptomatic region surrounding a lesion have not been studied. Also, the dynamics of recovery of the impacted asymptomatic region post-fungicide treatment is largely unknown. Here, we present RNA-seq data encompassing asymptomatic zones surrounding necrotrophic lesion sites obtained for Ptr sensitive and resistant wheat cultivars during infection by Ptr.	Stress	Ptr Inoculation
PRJNA804652	RNA-seq of EsMYB90 transgenetic wheat under salt treatment	Eutrema EsMYB90 Gene Improves Growth and Antioxidant Capacity of Transgenic Wheat Under Salinity Stress	Illumina NovaSeq 6000	RNA-seq of EsMYB90 transgenetic wheat under salt treatment	Stress	Salt
PRJNA811517	HVA1 doubled haploid transgenic wheat RNA-seq data	Overexpression of HVA1 Enhances Drought and Heat Stress Tolerance in Triticum aestivum Doubled Haploid Plants	Illumina HiSeq 4000	RNA-seq data of the HVA1 overexpression doubled haploid transgenic wheat plants under drought and heat stress treatments at vegetative and reproductive stages	Stress	Drought and heat
PRJNA826345	Circular RNAs in common wheat during Fusarium head blight disease	Transcriptome Profiles of Circular RNAs in Common Wheat during Fusarium Head Blight Disease	HiSeq X Ten	We collected control (CK) and 1, 3, and 5 days post Fusarium graminearum inoculation (dpi) samples, and used RNA-seq to determine circRNA content.	Stress	Fg Inoculation
PRJNA835521	Triticum aestivum Raw sequence reads	Wheat Escapes Low Light Stress by Altering Pollination Types	Illumina NovaSeq 6000	To find key genes accounting for the opening of wheat florets after low light stress, spikes at young microspore stage and grain filling stage were collected for RNA-seq.	Stress	Light
PRJNA836737	Transcriptomics study of resistant and susceptible wheat lines to tan spot disease (Pyrenophora tritici-repentis)	-	Illumina NovaSeq 6000	Tan Spot (TS), causal agent Pyrenophora tritici-repentis (Ptr), is a major threat to wheat production due to the lack of resistant cultivars. In our previous work, we identified MAGIC population parental lines exhibiting TS resistance and susceptibility, namely Robigus and Hereward, respectively.	Stress	Ptr Inoculation
PRJNA842823	RNA-seq of Fusarium graminearum resistance in wheat	The Black Necrotic Lesion Enhanced Fusarium graminearum Resistance in Wheat	Illumina HiSeq 2000	Hypersensitive-response-like black necrotic lesion enhanced Fusarium graminearum resistance in wheat	Stress	Fg Inoculation
PRJNA843683	RNA-seq of TaPsIPK1-KO plant	"nactivation of a wheat protein kinase gene
confers broad-spectrum resistance to rust fungi"	https://www.cell.com/cell/pdf/S0092-8674(22)00779-6.pdf	Illumina NovaSeq 6000	Stress	Pst Infection
PRJNA851238	Triticum aestivum Raw sequence reads	Phytotoxicity Alleviation of Imazethapyr to Non-target Plant Wheat: Active Regulation Between Auxin and DIMBOA	Illumina HiSeq 2000	Normal RNA-seq of total RNA samples from leaf tissues of Triticum aestivum.	Stress	Auxin, herbicide
PRJNA867352	RNA-Seq transcriptome of wheat	Synergetic effect of water deficit and arbuscular mycorrhizal symbiosis on the expression of aquaporins in wheat (Triticum aestivum L.) roots: insights from NGS RNA-sequencing	NextSeq 500	RNA-Seq transcriptome profiling of wheat roots reveals improving effect of arbuscular mycorrhizal Glomus mosseae under water deficiency	Stress	Mycorrhizal inoculation and water deficit
PRJNA878612	Transcriptome analysis of infected wheat by two monosporidial lines and their dikaryon stage of Tilletia indica to understand host-pathogen interaction	-	Illumina HiSeq 2500	A transcriptome analysis was carried out on RNA-seq data obtained from a susceptible wheat cultivar (WL711) at 24 hours after inoculation (hai ), 48 hai and 7 days after inoculation (dai) of PSWKBGH-1, 2 and 3. The study aims at comparative analysis between the pathogenic dikaryon stage with its monosporidial lines at transcriptomic level to study the genes in all the three genomes and wheat genes affected due to their infection	Stress	Inoculation of PSWKBGH-1, 2 and 3
PRJNA881502	Triticum aestivum Raw sequence reads	Abscisic acid alleviates mercury toxicity in wheat (Triticum aestivum L.) by promoting cell wall formation	Illumina NovaSeq 6000	normal RNA-seq of Triticum aestivum L.	Stress	ABA, Hg
PRJNA901148	Transcriptome analysis of wheat at the meiosis stage reveals genes respond to cold stress	Transcriptomic profiling of wheat stem during meiosis in response to freezing stress	Illumina NovaSeq 6000	In this study, we investigated the response of a wheat cultivar Zhongmai8444 to freezing stress at the meiotic stage. Transcriptome profiles over a time course were subsequently generated by high-throughput sequencing. Our results revealed that the prolonged chilling temperature led to the significant reductions in plant height and seed setting rate. Cell wall thickening in the vascular tissue was also observed in the stems. RNA-seq analyses demonstrated the identification of 1010 up-regulated and 230 down-regulated genes shared in all time points of freezing treatment. Enrichment analysis revealed that gene activity related to hormone signal transduction and cell wall biosynthesis was significantly modulated under low temperature.	Stress	Cold
PRJNA913840	Triticum aestivum (bread wheat)	Identification of Key Modules and Candidate Genes for Powdery Mildew Resistance of Wheat-Agropyron cristatum Translocation Line WAT-2020-17-6 by WGCNA	Illumina NovaSeq 6000	normal RNA-seq of Triticum aestivum	Stress	Bgt inoculation
PRJNA935407	RNA-seq of wheat ABA stress sample	A transcriptomic study of PF06830 root cap proteins	Illumina NovaSeq 6000	Studies have shown there is a correlation between wheat drought tolerance ana ABA tolerance. we select JM47 (the wheat variety resistant to ABA stress )and ZM366(intolerance to ABA strsess) treated with water and ABA stress(15um/L ), Each tretment with 3 reception.We sequenced a total of 24 samples.After quality control,go enrichment analysis and cluster analysis were used to get the differential gene	Stress	ABA
PRJNA936261	Comparative Transcriptomic Profiling of Differentially Expressed Genes and Related Metabolic Pathways in a Saudi Wheat Cultivar (Najran) under Salinity Stress	Comparative transcriptomic profiling reveals differentially expressed genes and important related metabolic pathways in shoots and roots of a Saudi wheat cultivar (Najran) under salinity stress	Illumina NovaSeq 6000	Global profiling of wheat gene expression (Najran cultivar) was analysed under control and salt treatment in three biological replicates of root and shoot tissues.	Stress	Salt
PRJNA944729	Transcriptomic profile of wheat seed development under progressive drought conditions	Metabolic and transcriptomic profiling during wheat seed development under progressive drought conditions.	Illumina NovaSeq 6000	To investigate how progressive drought stress affected gene expression during seed development Overall design: Comparative gene expression profiling analysis of RNA-seq data for TaPYLox and the Null segregant	Stress	Drought
PRJNA950485	RNA-seq of wheat	Transcriptome Analysis of Roots from Wheat (Triticum aestivum L.) Varieties in Response to Drought Stress	Illumina NovaSeq 6000	CM42 and ZM366 were selected based on their obvious difference in root length under 15% PEG-6000 treatment and well watered condition (hydroponics) as a control.	Stress	Drought
PRJNA957734	Light-induced TaHY5-7A and TaBBX-3B physically interact to promote the expression of the anthocyanin regulatory gene TaPpm1 in purple pericarps of wheat	Light-Induced TaHY5-7A and TaBBX-3B Physically Interact to Promote PURPLE PERICARP-MYB 1 Expression in Purple-Grained Wheat	Illumina NovaSeq 6000	RNA-seq data of pericarp in purple grain wheat H76	Stress	Light
PRJNA996310	RNA seq of triticum aestivum-FLW30	Emphasizing the role of wheat circular RNA in defense response against stripe rust disease	Illumina HiSeq 4000	The seedlings, at the two-leaf stage or flag leaves (approximately 20 days after sowing), were inoculated using an automizer and then kept in darkness at 10 degree C for 16 hours of light and 8 hours of darkness to maintain high humidity. Leaf samples were collected at three different time points: 12, 48, and 72hours post-inoculation (HPI). The collected samples were immediately preserved in RNA later and stored at -20 degree C until further use. RNA extraction from the leaf samples was performed using the Qiagen RNeasy Mini kit (Qiagen Inc, USA).	Stress	46S119-inoculated

Mutant and Experimental Genetic Population

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB25119	RNAseq data for inflorescence tissue at white and green anther stage for mutant (Vrs1-N) and wildtype (Vrs1-Y) plants (4 replicates each).	Unleashing floret fertility in wheat through the mutation of a homeobox gene	Illumina HiSeq 4000	RNAseq data for inflorescence tissue at white and green anther stage for mutant (Vrs1-N) and wildtype (Vrs1-Y) plants (4 replicates each).	Mutant_Floret fertility
PRJEB33954	RNAseq from endosperm and pericarp of 3 wheat genotypes: Cadenza, triple stack of TaiRX9b knock-out alleles, null segregant control	Loss of TaIRX9b gene function in wheat decreases chain length and amount of arabinoxylan in grain but increases cross-linking	Illumina HiSeq 4000	Using mutagenised population of wheat cv Cadenza, we identified knock-out alleles fro the 3 homeologues of TaIRX9b and stacked them in one line. To look for effects of loss of TaiRX9b gene function on transcriptome we sequenced RNA from endosperm and pericarp from triple stack, null egregant control and unmutagenised Cadenza	Mutant_Xylan
PRJEB47173	Identification of the stem rust resistance gene Sr62 in Aegilops sharonensis by mutagenesis and transcriptome sequencing (MutRNA-Seq)	Reference genome-assisted identification of stem rust resistance gene Sr62 encoding a tandem kinase	Illumina HiSeq 4000	RNA sequencing data of Ae. sharonensis genotype 1644. Wild type plants and mutants showing loss of the Sr62 phenotype were subjected to Illumina RNA-seq. Libraries have been sequenced by Novogene Co., Ltd.Related projects: PRJEB40322, PRJEB40049	Mutant_The stem rust resistance gene Sr62
PRJNA1002999	TaCTR1 overexpression RNA-seq	Genome-wide evolutionary analysis of TKL_CTR1-DRK-2 gene family and functional characterization reveals that TaCTR1 positively regulates flowering time in wheat	Illumina HiSeq 2000	Transcriptomics analysis in TaCTR1 overexpression transgenic lines and wild type plants	Mutant_JWI and TaCTR1 overexpression transgenic lines
PRJNA239299	Triticum aestivum Transcriptome or Gene expression	Pistillody mutant reveals key insights into stamen and pistil development in wheat (Triticum aestivum L.)	Illumina HiSeq 2000	transcriptional profiling of pistillody stamen, pistil and stamen in wheat line HTS-1were studied by college of life science, China west normal university	Mutant_Pistillody
PRJNA263755	Triticum aestivum Transcriptome or Gene expression	Transcriptome and Allele Specificity Associated with a 3BL Locus for Fusarium Crown Rot Resistance in Bread Wheat	Illumina HiSeq 2000	Identify genes underlying the Fusarium crown rot resistance locus and find out if expressed genes associated with resistance to Fusarium crown rot were related to those observed by others for Fusarium head blight.	NIL_Inoculated with F. graminearum
PRJNA273659	Triticum aestivum Transcriptome or Gene expression	Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance	Illumina HiSeq 2000	The fungal pathogen Fusarium graminearum infects wheat spikes and causes Fusarium head blight (FHB). During infection the fungus produces a set of trichothecene mycotoxins (e.g. deoxynivalenol or DON) that increase the virulence of the fungus and result in reduced grain quality. The Fhb1 resistant allele confers type II resistance (reduced spread of symptoms on the spike) to F. graminearum infection. This study examined differentially expressed genes from a wheat near-isogenic line pair carrying resistant and susceptible alleles for the Fhb1 locus. The NIL pair for Fhb1 was derived from self pollinating a F7-derived line that was heterozygous for the Fhb1 region and identifying Fhb1+ (resistant) and Fhb1- (susceptible) lines. The wheat NIL pair 260-1-1-2 (Fhb1+) and 260-1-1-4 (Fhb1-) was used for this study. Spikelet and rachis tissue was sampled after inoculation with F. graminearum, DON, or water. For the F. graminearum-inoculated samples, wheat spikes were point inoculated with F. graminearum (10µl of 100,000 macroconidia per ml) in the four central spikelets and the inoculated spikelet and corresponding rachis were sampled at 96 hours after inoculation (hai). For the DON- and water-inoculated samples, wheat spikes were point inoculated with DON (2ug) and water on the four central spikelets, and the inoculated spikelets were sampled at 12 hai. The goal of this study was to identify plant and fungal genes that are differentially expressed between plants carrying the resistant and susceptible alleles for the Fhb1 locus	NIL_Disease resistance
PRJNA278920	Triticum aestivum Transcriptome or Gene expression	Transcriptomic analysis of wheat near-isogenic lines identifies PM19-A1 and A2 as candidates for a major dormancy QTL	Illumina HiSeq 2000	This study was to identify candidate genes underlying the 4AL QTL for grain dormancy in wheat. RNA was sequenced from pooled NILs segregating for the QTL. Identification of the PM19-A1 and A2 genes will enable the most efficient exploitation of this major source of dormancy for wheat breeding	NIL_Seed dormancy QTL
PRJNA351906	RNA sequencing of wheat Ms2 mutant among different tissues	Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species	Illumina HiSeq 2500	Ms2 isogenic lines, LM15 and LM15RMs2, were choosed for RNA sequencing. Plants were grown in the greenhouse with a 16h photoperiod and a daytime and nighttime temperature of 22°C and 15°C, respectively. At the S2 stage, when an auricle distance between the penultimate and flag leaf was between 3 to 5 cm, we collected four types of samples: fertile anthers (FA) of LM15, sterile anthers (SA) of LM15RMs2, pistils (P) of LM15 and LM15RMs2, and flag leaves (L) of LM15 and LM15RMs2.	Mutant_Male sterility
PRJNA355221	Triticum aestivum cultivar:Chinese spring (bread wheat)	A TRIM insertion in the promoter of Ms2 causes male sterility in wheat	Illumina HiSeq 2000	the transcriptome of wild type and ms2 mutant wheat	Mutant_Male-sterile
PRJNA362497	Triticum aestivum cultivar:Jimai5265 (bread wheat)	Physiological and transcriptomic analyses of a yellow-green mutant with high photosynthetic efficiency in wheat (Triticum aestivum L.)	Illumina HiSeq 2500	The purpose of this project is to find out the expression difference on transcription level between wild type (Jimai5265) and Jimai5265yg which is a chlorophyll-deficient mutant.	Mutant_yellow-green mutant
PRJNA374931	Triticum aestivum isolate:wheat shoot | cultivar:Jing 411 (bread wheat)	RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant	Illumina HiSeq 4000	RNAseq analysis reveals pathways and candidate genes associated with salinity tolerance in a spaceflight-induced wheat mutant	Mutant_Spaceflight-induced
PRJNA395401	Triticum aestivum (bread wheat)	Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat	Illumina HiSeq 2000	Rapid cloning of MS1 using next generation technology	Mutant_Male sterility(MS1)
PRJNA396738	Triticum aestivum Raw sequence reads	Ubiquitin-related genes are differentially expressed in isogenic lines contrasting for pericarp cell size and grain weight in hexaploid wheat	Illumina HiSeq 2500	In this study we performed RNA-sequencing on two NILs segregating for a major grain weight quantitative trait loci located on wheat chromosome arm 5AL. The QTL was identified in a doubled haploid population between the UK cultivars Charger and Badger. Badger offers the positive allele and Charger was used as the recurrent parent in NIL generation. 5A+ NILs have increased grain weight, grain length and pericarp cell size.	NIL_Grain
PRJNA396993	Triticum aestivum (bread wheat)	-	Illumina HiSeq 2000	Aneuploidy in hexaploid wheat induces dysregulated gene expression due to combined action of dosage effect, dosage compensation and transcriptional response, which brings about diverse phenotypes.	Mutant
PRJNA415853	Susceptible wheat cultivar infected with the wild type Puccinia graminis (isolate 99KS76A-1) and its mutants carrying knockout mutations in AvrSr35.	Variation in the AvrSr35 gene determines Sr35 resistance against wheat stem rust race Ug99	Illumina Genome Analyzer	The assess the effect of AvrSr35 knock-out on host-pathogen interaction in the compatible host, we have performed time-course analysis of leaf transcriptomes obtained by infecting susceptible wheat cultivar Fielder with the wild type Puccinia graminis f.sp. tritici (Pgt) isolate 99KS76A-1 and its three mutants, M1, M4 and M7, that carry loss-of-function mutations in the AvrSr35 gene	Mutant_Puccnina graminis
PRJNA417210	Triticum aestivum Transcriptome or Gene expression	Transcriptome sequencing reveals hotspot mutation regions and dwarfing mechanisms in wheat mutants induced by γ-ray irradiation and EMS	Illumina HiSeq 4000	Transcriptomic sequence variation and dwarfing mechanisms in dwarf wheat mutants derived from γ-rays irradiation and EMS mutagenesis	Mutant_Plant height
PRJNA436861	Triticum aestivum (bread wheat)	RNA-seq analysis of the peduncle development of Rht12 dwarf plants and primary mapping of Rht12 in common wheat	Illumina HiSeq 4000	The wheat peduncle samples at heading stages of the tall and dwarf lines derived from the cross of NC and KC were used for transcriptome sequencing to explore candidate genes involved in peduncle elongation.	Mutant_Rht12 dwarf plants
PRJNA485724	Xanthomonas translucens directly induces abscisic acid biosynthesis to enhance disease susceptibility in wheat	Xanthomonas translucens commandeers the host rate-limiting step in ABA biosynthesis for disease susceptibility	Illumina HiSeq 2000	Plants are vulnerable to disease through pathogen manipulation of phytohormone levels, which regulate development and defense pathways. Here, we show that the bacterial wheat pathogen Xanthomonas translucens pv. undulosa, through use of a type III transcription activation-like (TAL) effector, elevates expression of a host gene, TaNCED_5BS, encoding nine-cis-epoxycarotenoid dioxygenase which catalyzes the rate-limiting step in the biosynthesis of the phytohormone abscisic acid (ABA). The induction of TaNCED_5BS results in elevated ABA levels, reduced transpiration and water loss, and enhanced bacterial growth in leaves. Low virulence field strains of the pathogen lack the effector, and introduction of TaNCED_5BS cognate TAL effectors into a low-virulence field strain resulted in elevated TaNCED_5BS expression and enhanced virulence. The results support a hypothesis that X. translucens pv. undulosa strains gain virulence by directly targeting ABA biosynthesis and illustrate the adaptive versatility of TAL effector deployment, suggestive of the appearance of TAL effectors affecting the ABA pathway in other Xanthomonas-related diseases due to the conserved function of ABA function in plants	Mutant_Xanthomonas translucens
PRJNA485894	Fine mapping and clone TaCPA, which is regulate lamina joint development.	Wheat TaSPL8 Modulates Leaf Angle Through Auxin and Brassinosteroid Signaling	Illumina HiSeq 2500	For determining the differentially expressed genes in different Tacpa knock-out mutant.	Mutant_Leaf angle
PRJNA513351	Generation Sequencing Facilitates Quantitative Analysis of Wild Type and TaD27 Transcriptomes (bread wheat)	TaD27-B gene controls the tiller number in hexaploid wheat	Illumina HiSeq 2500	To further dissect the molecular basis of tiller generation, we performed an RNA-seq analysis of TaD27-RNAi axillary bud primordia at the three-week old. The axillary buds of wild type KN199 at the same development stage were used as the control. A total of 4,947 differentially expressed genes (DEGs) between the WT and TaD27-RNAi were identified using a fold-change of 2 and FDR<0.05. Among them, 4,124 genes were expressed at a low level, 823 genes were highly expressed in TaD27-RNAi compared to the WT. Overall design: Wheat mRNA profiles of 3-week old wild type (WT) and TaD27-RNAi were generated by deep sequencing, in triplicate, using Gene Denovo.	Mutant_The tiller number
PRJNA514367	The Impact of Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development under Field Conditions (bread wheat)	The Impact of the Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development Under Field Conditions	Illumina HiSeq 2500	The Reduced Height (Rht) genes formed the basis for the green revolution in wheat by decreasing plant height and increasing productive tillers. There are two current widely used Rht mutant alleles, Rht-B1b and Rht-D1b. Both reduce plant height by 20% and increase seed yield by 5-10%. They are also associated with decreased seed size and protein content. Here we tested the degree to which Rht-B1b impacts flag leaf photosynthetic rates and carbon and nitrogen partitioning to the flag leaf and grain during grain fill under field conditions using near isogenic lines (NILs) that were either standard height (Rht-B1a) or semi-dwarf (Rht-B1b). The results demonstrate that at anthesis, Rht-B1b reduces flag leaf photosynthetic rate per unit area by 18% and chlorophyll A content by 23%. Rht-B1b significantly reduced grain protein beginning at 14 days post anthesis with the greatest difference seen at 21 days post anthesis (DPA) (12%). Rht-B1b also significantly decreased individual seed weight beginning at 21 DPA and by 15.2% at 28 DPA. Global expression analysis using RNA extracted from developing leaves and stems demonstrated that genes associated with carbon and nitrogen metabolism are not substantially altered by Rht-B1b. From this study, we conclude that Rht-B1b reduces flag leaf photosynthetic rate at flowering while changes in grain composition begin shortly after anthesis. Overall design: Total RNA was collected from leaf and stem tissue from plants at 14 days past anthesis. Three samples were taken from plants carrying the semi-dwarfing allele Rht-B1b and three samples were taken from plants without the semi-dwarfing allele.	NIL_Rht-B1b Semi-Dwarfing Allele
PRJNA516027	Transcriptome analysis of Btr1-A transgenic wheat and control plants	Btr1-A Induces Grain Shattering and Affects Spike Morphology and Yield-Related Traits in Wheat	Illumina HiSeq 2000	To understand the mechanism underlying spike brittleness, we compared the transcriptome of the rachis node zone in transgenic wheat plants and non-transgenic control plants at flowering stage. A total of 1032 and 1939 genes were found to be up-regulated and down-regulated four-fold (FDR adjusted P < 0.005), respectively, in the transgenic plants compared with the control.	Mutant_Spike brittleness(Btr1-A)
PRJNA517367	Transcriptome of wheat with different heading time	Identification of the vernalization gene VRN-B1 responsible for heading date variation by QTL mapping using a RIL population in wheat	HiSeq X Ten	Bulked Segregant RNA-Seq (BSR-Seq) analysis for identification of early heading gene in wheat	Mutant_Heading time(VRN-B1)
PRJNA528595	Triticum aestivum Raw sequence reads	Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.)	Illumina HiSeq 2500	In this study we performed RNA-sequencing on three NIL pairs segregating for a major grain weight quantitative trait loci located on wheat chromosome arm 4AL using the whole grains at 10 days after pollination stage (DAP). The QTL was identified in a doubled haploid population between two Chinese hexaploid winter wheat varieties, Nongda3338 (ND3338) and Jingdong6 (JD6). JD6 offers the positive allele with increased thousand grain weight and ND3338 was used as the recurrent parent in NIL generation	NIL_Thousand-grain weight
PRJNA541573	Identification and functional characterization of the B1 awn inhibitor gene in Durum and Bread Wheat	Dominant inhibition of awn development by a putative zinc-finger transcriptional repressor expressed at the B1 locus in wheat	Illumina HiSeq 2500	"1) Identification of the B1 awn inhibitor gene from durum wheat by RNA sequencing of pooled awn and awnless floret-lemma samples
2) Functional characterization of the B1 gene through transcriptome analysis of transgenic B1 overexpression durum and bread wheat lines"	Mutant_Awns(B1)
PRJNA549107	Triticum aestivum (bread wheat)	Generation of new salt-tolerant wheat lines and transcriptomic exploration of the responsive genes to ethylene and salt stress	Illumina HiSeq 2500	salt releted genes in new cultivars of mutagenesis in bread wheat	Mutant_Salt
PRJNA551093	Whole Transcriptome Sequencing of Parent and Stable Mutants of Wheat for Elucidating the Tolerance Mechanism under Terminal Heat Stress	Insight into the mechanisms of terminal HS-tolerance in wheat mutant with improved nutritional quality through de novo transcriptome sequencing	Illumina HiSeq 4000	Wheat, being staple food grain crops, is highly sensitive to terminal heat stress. Even a slight fluctuation in temperature during critical stages - pollination and grain-filling - has been observed to affect the quantity and quality of the grains. Recent study showed depletion in the nutrient of wheat grains exposed to terminal heat stress. Here, Department of Atomic Energy (DAE), Bhabha Atomic Research Center (BARC), Mumbai developed mutants of wheat for heat stress tolerance using gamma irradiation. The mutants were evaluated for thermotolerance based on morphological, physiological, biochemical characterization and seed yield, and further stable mutants (M-4) along with parents were shared with IARI, New Delhi for further characterization. Forty mutants were further evaluated for thermotolerance using different molecular and biochemical markers for two generations. Based on the evaluation, wheat mutant- 3 was observed promising over the generation. In order to understand the mechanism of thermotolerance and to locate the heat-responsive SNIPs, whole transcriptome sequencing was carried out using the pooled samples (root, stem, leaves and spikes) of Stable Mutant -3 and Parent-3 under control and HS-treated conditions	Mutant_Terminal HS
PRJNA553833	Triticum aestivum cultivar:guomai301 (bread wheat)	Enhanced Senescence Process is the Major Factor Stopping Spike Differentiation of Wheat Mutant ptsd1	Illumina HiSeq X Ten	Transcriptomes and miRNomes of the wide type (WT) and mutant ptsd1 at the early wheat reproductive developmental stage.	Mutant_Spike differentiation(ptsd1)
PRJNA554312	Transcriptomic analysis of near isogenic lines on 3AL QTL for pre-harvest sprouting in wheat	Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance	Illumina HiSeq X Ten	This study generated transcriptome profiling of the two pairs of near-isogenic lines in different seed developing stages for pre-harvest sprouting resistant locus on 3AL via genome-wide RNA-seq technology.	NIL_Seeds
PRJNA578055	RNA-seq for a genic male sterile mutant NWMS1 in wheat (Triticum aestivum L.)	The Major Factors Causing the Microspore Abortion of Genic Male Sterile Mutant NWMS1 in Wheat (Triticum aestivum L.)	HiSeq X Ten	RNA-seq for mutant NWMS1 and Shengnong 1 , including the early anther development stage, pollen mother cell meiotic stage and binucleate microspore stage	Mutant_Male sterility(NWMS1)
PRJNA579285	Triticum aestivum (bread wheat)	Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat	Illumina NovaSeq 6000	An new 260M exon capture panel were apply for gene mapping via bulked segregant analysis. EMS mutant BC2F3 samples were bulked by to two different phenotype. Both RNA-seq and Exome capture sequencing were used to mapping the causal gene	Mutant_The yellow-green leaf mutant ygl1
PRJNA588134	ChIP-Seq and RNA-Seq analysis for leaf rust resistance in wheat	BS-Seq reveals major role of differential CHH methylation during leaf rust resistance in wheat (Triticum aestivum L.)	NextSeq 500	The main objective of the study was to identify the genomic regions associated to H3 histone methylation due to H3K4/K27me3 and to examine the relationship of the associated genes with differentially methylated genes (using MeDIP-Seq) and differentially expressed genes (using RNA-Seq analysis)	NIL_leaf rust resistance gene Lr28
PRJNA591385	Overexpression of ThMYC4E enhanced anthocyanin biosynthesis in common wheat	Overexpression of ThMYC4E Enhances Anthocyanin Biosynthesis in Common Wheat	Illumina HiSeq 2000	ThMYC4E, candidate gene controlling blue grain trait, was transferred to common wheat JW1. the RNA-Seq and qRT-PCR analysis showed the transcript level of the structural genes of anthocyanin biosynthesis were higher in transgenic wheat than WT, which indicated that ThMYC4E activated the anthocyanins biosynthesis in transgenic lines	Mutant_Anthocyanins(ThMYC4E)
PRJNA605937	Myb10-D confers PHS-3D resistance to pre-harvest sprouting by regulating NCED in ABA biosynthesis pathway of wheat	Myb10-D confers PHS-3D resistance to pre-harvest sprouting by regulating NCED in ABA biosynthesis pathway of wheat	Illumina NovaSeq 6000	The metadata includes 1) the resequencing data of Ae.tauschii AS60, T.turgidum AS2255, and synthetic wheat SHW-L1 obtained by a cross between AS60 and AS2255; 2) RNA-seq data of PHS susceptible wheat cultivar CM32, PHS resistant SHW-L1, wide type cultivar Fielder, and PHS-3D overexpression transgenic Fielder line OE58.	Mutant_Pre-harvest sprouting
PRJNA612424	Triticum aestivum cultivar:zhoumai 18 (bread wheat)	Cytological and molecular characterizations of a novel 2A nullisomic line derived from a widely-grown wheat cultivar Zhoumai 18 conferring male sterility	HiSeq X Ten	Transcriptomes of the novel natural mutant dwarf, multi-pistil and male sterility (dms).	Mutant_Male sterile(dms)
PRJNA626525	TaPYL is associated with drought tolerance in wheat seedlings	The wheat ABA receptor gene TaPYL1-1B contributes to drought tolerance and grain yield by increasing water-use efficiency	Illumina HiSeq 2500	Transcriptomic analysis of Ubi:TaPYL1-1B transgenic wheat	Mutant_Drought,ABA(TaPYL1-1B)
PRJNA629470	Pleiotropic function of TaSPL14 on plant architecture of wheat	Pleiotropic function of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE gene TaSPL14 in wheat plant architecture	Illumina NovaSeq 6000	The RNA sequencing for young spikes (20-30mm) of wild-type Fielder and mutant line taspl14-#13-4 with two biological replications.	Mutant_TaSPL14
PRJNA635231	Triticum aestivum (bread wheat)	Wheat FRIZZY PANICLE activates VERNALIZATION1-A and HOMEOBOX4-A to regulate spike development in wheat	Illumina NovaSeq 6000	RNA-seq of wheat young spikes	Mutant_Spike(WFZP)
PRJNA648242	Towards the identification of the ph2 gene in hexaploid wheat	Ph2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination	Illumina NovaSeq 6000	In spite of being hexaploid, recombination in wheat only occurs between homologous chromosomes whereas recombination between homoeologous chromosomes is suppressed. The two main loci controlling homoeologous recombination are located on chromosome-arms 5BL and 3DS, named Ph1 and Ph2 respectively. While Ph1 has been characterized, the causative gene sequence for Ph2 is yet to be determined. The present study aims at the identification of Ph2 gene candidates by RNASeq and exome capture of DNA from the ph2a deletion and the ph2b EMS-derived mutants	Mutant_ph2a
PRJNA649398	RNA-seq analysis of Fusarium graminearum mutant osp24 infected wheat heads	An orphan protein of Fusarium graminearum modulates host immunity by mediating proteasomal degradation of TaSnRK1α	Illumina HiSeq 2000	To identify genes suppressed or induced by Osp24 during plant infection, we conducted RNA-seq analysis with infected wheat heads that were collected at 3 dpi.	Mutant_Fusarium graminearum(TaSnRK1α)
PRJNA656089	wheat endosperm transcriptome sequencing	The endosperm-specific transcription factor TaNAC019 regulates glutenin and starch accumulation and its elite allele improves wheat grain quality	Illumina NovaSeq 6000	Plant sample from Triticum aestivum	Mutant_the endosperm-specific nuclear protein TaNAC019
PRJNA657146	Spike development inhibition in the ftin mutant is associated with multiple phenotypes and regulated by multiple biological pathways	Spike development inhibition in the ftin mutant is associated with multiple phenotypes and regulated by multiple biological pathways	HiSeq X Ten	In order to study the relationship between spike development inhibition and response to cold stress, we systematically investigated the genes and pathways underlying the differences using ITRAQ proteomics and RNA-sequencing technologies	Mutant_Cold-sensitive mutation(ftin)
PRJNA670838	Triticum aestivum cultivar:Guomai 301 (bread wheat)	Key auxin response factor (ARF) genes constraining wheat tillering of mutant dmc	HiSeq X Ten	The transcriptome data of Guomai 301 and a wheat mutant derived from Guomai 301.	Mutant_Tillering(Mutant dmc)
PRJNA682455	Transcriptome analysis of wild type and qd mutant of wheat	Transcriptome Analysis Reveals a Potential Role of Benzoxazinoid in Regulating Stem Elongation in the Wheat Mutant qd	Illumina HiSeq 4000	To identify the cirtical factors that can regulate wheat stem elongation.	Mutant_The quick development mutant (qd)
PRJNA683728	wheat spike transcriptome	FRIZZY PANICLE defines a regulatory hub for simultaneously controlling spikelet formation and awn elongation in bread wheat	Illumina NovaSeq 6000	The wheat RNA-seq data of Fielder and TaFZP mutants from four stage in developing young spike.	Mutant_Spike(wfzp mutant)
PRJNA704463	Guomai301 Transcriptome	Enhanced SA and Ca2+ signaling results in PCD-mediated spontaneous leaf necrosis in wheat mutant wsl	HiSeq X Ten	Guomai301 and mutant wsl	Mutant_Leaf(wsl)
PRJNA705378	RNA-seq data in immature seeds of taiaa21 mutant	TaIAA21 represses TaARF25-mediated expression of TaERFs required for grain size and weight development in wheat	Illumina HiSeq 2000	To study the effect of TaIAA21 mutation, RNA-seq was performed on RNAs isolated from 0, 4, 8 DAF immature grains of L1786 and Cadenza	Mutant_Wheat grain size and weight development
PRJNA705399	BSA RNA-seq	Fine mapping of the tiller inhibition gene TIN4 contributing to ideal plant architecture in common wheat	Illumina HiSeq 2500	BSR-SEQ for wheat	NIL_The tiller
PRJNA705852	Transcriptome data of a multi-pistil trait in wheat	Gene co-expression modules behind the three-pistil formation in wheat	Illumina HiSeq 2500	Transcriptomic changes in young spikes reveal candidate genes and a potent molecular mechanism behind the formation of a multi-pistil trait in wheat	Mutant_Three-pistil mutant
PRJNA718479	Modified expression of TaCYP78A5 enhances grain weight and yield by accumulating AUXIN and prolonging the growth and development of organ in wheat (Triticum aestivum L.)	Modified expression of TaCYP78A5 enhances grain weight with yield potential by accumulating auxin in wheat (Triticum aestivum L.)	Illumina HiSeq 2500	Bread wheat (Triticum aestivum L.) is one of the most important food crops. In this study, we performed Transcriptome analysis of 1mm ovary for wild type wheat JW1 and pINO lines that overexpression of the TaCYP78A5 under pINO promoter. To investigate the mechanisms underlying TaCYP78A5 affects the grain size and possible mobile molecular downstream	Mutant_Grain(TaCYP78A5)
PRJNA741399	wheat seedlings transcriptome and translatome RNA-seq raw data	Stress granule-associated TaMBF1c confers thermotolerance through regulating specific mRNA translation in wheat (Triticum aestivum)	Illumina NovaSeq 6000	RNA-seq and Ploysome-seq data of wheat seedlings	Mutant_Heat
PRJNA742655	Transcriptome analysis of two near-isogenic lines with different NUE under normal nitrogen conditions in wheat	Transcriptome Analysis Reveals Different Responsive Patterns to Nitrogen Deficiency in Two Wheat Near-Isogenic Lines Contrasting for Nitrogen Use Efficiency	Illumina HiSeq 2500	Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the nitrogen application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. The use of near-isogenic lines (NILs) in transcriptome analysis can reduce genetic background noise. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling in NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions. The results showed that 7,023 DEGs (4,738 up-regulated and 2,285 down-regulated) were identified in the 1Y vs 1W comparison. The responses of 1Y and 1W to normal nitrogen differed significantly in the transcriptional regulation mechanisms. Several genes belonging to the GS and GOGAT gene families were up-regulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members such as ERF, WRKY, NAC, and MYB were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE Overall design: A total of twelve samples, including two treatments (N1 and N0). Each treatment was detected at a time point with 3 replicates. Two forms of Nitrogen fertilizers treatments: normal nitrogen (1.6g pot–1), which is referred to as N1, and a control (no nitrogen application), which is referred to as N0	NIL_N fertilizer treatment
PRJNA774156	RNA SEQ of wheat	Identification of the Q Gene Playing a Role in Spike Morphology Variation in Wheat Mutants and Its Regulatory Network	Illumina NovaSeq 6000	RNA SEQ of wheat	Mutant_Spike morphology variation
PRJNA779997	Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [RNA-seq]	Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat	Illumina NovaSeq 6000	To systematically study the regulatory networks mediated by wheat SPLs, we performed DAP-seq for 40 wheat SPLs (SPLs), ATAC-seq and RNA-seq seq for four tissues (leaves, roots, axillary buds and shoot apices) of wheat (Triticum aestivum L.).	Mutant_Squamosa promoter-binding protein-like (SPL) transcription factors
PRJNA786783	wheat shoot base and tiller bud RNA-seq	Tiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat	Illumina HiSeq 4000	wheat shoot base and tiller bud RNA-seq	Mutant_The low-tillering tn1 mutant
PRJNA852953	Transcriptome analysis of wheat seedings stem to reveal genes responding to different hormones.	Reducing brassinosteroid signalling enhances grain yield in semi-dwarf wheat	Illumina NovaSeq 6000	Wheat seedings stem RNA-seq at the early jointing stage.	Mutant_Semi-dwarf wheat
PRJNA861076	Triticum aestivum Transcriptome sequencing of TaeIF4E-triple mutants and non-edited wheat	-	Illumina NovaSeq 6000	To investigate if triple-edited TaeIF4E-aabbdd plants represent transcriptional variations to non-edited TaeIF4E-AABBDD plants, RNA sequencing (RNA-seq) was performed at the two-week-old seedling leaves.	Mutant_TaeIF4E-triple mutants
PRJNA869883	RNA-seq data of TaARF12 wild and TaARF12-CRISPR-CAS9 mutant	Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat	Illumina HiSeq 2000	A time series RNA seq data of peduncle and rachis of TaARF12 wild and TaARF12-CRISPR-CAS9 mutant at W5.5, 7.0, 7. 5, 8. 0 8.5, 8.75, and 9.0.	Mutant_TaARF12
PRJNA874550	Triticum aestivum Transcriptome or Gene expression	Tal1NXtc01 in Xanthomonas translucens pv. cerealis Contributes to Virulence in Bacterial Leaf Streak of Wheat	HiSeq X Ten	In order to explore host genes responding to the wild type Xanthomonas translucens pv. cerealis strain NXtc01, tal1 deletion mutant, tal2 deletion mutant, tal free deletion mutant, T3SS hrcC deletion mutant, T2SS gspD deletion mutant, tal free and T2SS gspD deletion mutant and mock, we did RNA-Seq of two wheat cultivars Chinese spring and Yangmai-158.	Mutant_Xanthomonas, tal1, tal2
PRJNA877303	RNA-Seq of Yr10 independent mutants	Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM	Illumina NovaSeq 6000	RNA-Seq data of 7 independent Yr10 mutants	Mutant_wheat rust-resistance gene YrNAM
PRJNA890758	Triticum aestivum Raw sequence reads	Thermosensitive SUMOylation of TaHsfA1 defines a dynamic ON/OFF molecular switch for the heat stress response in wheat	Illumina NovaSeq 6000	normal RNA-seq of wheat	Mutant_Heat, TaHsfA1
PRJNA896512	Bulked segregant RNA-Seq of WYMV-resistant or WYMV-susceptible pools	N6-methyladenosine RNA modification promotes viral genomic RNA stability and infection	Illumina HiSeq 2000	Three resistant pools (IT<1) and three susceptible pools (IT>4) of the XX-RIL population were used for bulked segregant RNA-Seq. Each WYMV-resistant or WYMV-susceptible pools were composed of an equivalent mixture of leaves from 10 lines of the RIL population.	RIL_Wheat yellow mosaic virus
PRJNA897023	parent material stem transcriptome	TaACTIN7-D regulates plant height and grain shape in bread wheat	Illumina NovaSeq 6000	parent material stem transcriptome，RNA-seq data of the middle part of the second internode	Mutant_TaACTIN7-D, semi-dwarfing
PRJNA903472	RNA-Seq analysis was performed with total RNA isolated from mature axillary bud of Fielder and tfl1-5 mutant	Genome-edited TaTFL1-5 mutation decreases tiller and spikelet numbers in common wheat.	Illumina NovaSeq 6000	To establish the regulatory roles of TaTFL1-5 in wheat axillary bud development , we identified the regulated genes whose transcriptional activities are associated with relative abundance of TaTFL1-5 transcripts by transcriptomic analysis. Differentially expressed genes are mainly enriched in the metabolic pathway and the lifetime metabolic pathway, but also in many plant hormone signal transduction pathways such as auxin, gibberellin, brassinosteroids and cytokinin. Overall design: Three biological repeats of the wheat axillary bud from tfl1-5(Mutant-1, Mutant-2, Mutant-3) and Fielder (Fielder-1, Fielder-2, Fielder-3) were used for RNA sequencing.	Mutant_TaTFL1-5, spikelet and tiller
PRJNA930156	RNA-seq of wheat	A Glu209Lys substitution in DRG1/TaACT7, which disturbs F-actin organization, reduces plant height and grain length in bread wheat	Illumina HiSeq 4000	The RNA-seq data of bread wheat accessions YZ1 and drg1-D	Mutant_drg1-D, dwarf and round grain
PRJNA979921	RNA-Seq Transcriptome Profiling of Immature Grain Wheat: A Comparative Modeling of Baking Quality	RNA-Seq Transcriptome Profiling of Immature Grain Wheat: A Comparative Modeling of Baking Quality	Illumina HiSeq 2500	RNA-Seq analysis of various wheat genotypes has opened up new avenues for research on grain development and its composition, which ultimately determines the nutritional and functional quality of wheat. Identifying genes expressed during the grain filling stage can be useful for improving yield and grain quality. RNA-Seq has provided a platform for research on grain development and the determination of grain yield and grain composition that controls functional and nutritional properties. We compared RNA-Seq data from immature grains of the O-64.1.10 wheat genotype and its wild type cultivar, Omid, which have significantly different baking qualities	Mutant_The high baking quality mutant "O-64.1.10" genotype