TriticeaeExpDB

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Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJDB4103	Hordeum vulgare subsp. vulgare strain:Harun Nijo (domesticated barley)	Improvement of barley genome annotations by deciphering the Haruna Nijo genome	Illumina MiSeq	A total of 305 Gbp of sequence data were generated by Illimina Hiseq paired end reads and 454 Titanium long paired and reads (8K and 20K). RNA-Seq data from four libraries of seedling shoot, seedling root, immature spike and immature seed were collected	Seedling shoot, seedling root, immature spike and immature seed
PRJDB4169	Transcriptome sequencing of diverse bio-geographical accessions of barley	Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley	Ion Torrent Proton	Total RNAs were extracted using RNEasy plant mini kit (QIAGEN GmbH, Hilden, Germany) from leaves and roots of 6 barley (H. vulgare) accessions and a wild barley (H. spontanium),according to the manufacture's instruction. The barley plants used for RNA extraction were grown by hydro- culture in a growth chamber. The growth chamber were maintained at 16-h light: 8- h dark at 22?C. Poly(A)+ RNAs were purified using MicroPoly(A)Purist Kit (Life Technologies, USA) according to the manufacture's instruction. Libraries for stranded-RNA sequencing using an Ion torrent sequencer were constructed using Ion Total RNA-Seq Kit v2 (Life Technologies, USA) according to the manufacture's instruction with the Ion Xpress Barcode Adapters (Life Technologies, USA) corresponding to each accession. Templates for 200 base-read libraries sequenced by the Ion Proton semiconductor sequencer (Life Technologies, USA) were prepared using Ion P1 Template OT2 200 Kit v3 (Life Technologies, USA), Ion P1 Sequencing 200 Kit v3 (Life Technologies, USA) and Ion P1 Chip Kit v3 (Life Technologies, USA), according to the manufacturer's instructions. The sequencing run was carried out using an Ion Proton sequencer (Life Technologies, USA) with an Ion P1 chip	Leaves and roots
PRJDB7393	RNA-seq analysis in callus of barley	-	Illumina HiSeq 3000	We have been identified three loci responsible for transformation amenability in barley, and we are investigating the genes for this phenotype which may be associated with callus induction, callus growth, Agrobacterium-barley interaction, green shoot regeneration and rooting. In this project, RNA-seq analysis was performed to isolate the genes involved in callus induction/growth and green shoot regeneration from callus in barley. The RNA was extracted from the calli of Golden Promise and Haruna Nijo which were transformation amenable and recalcitrant barley cultivars, respectively, as well as from the transgenic calli expressing baby boom (BBM) or Wuschel 2 (WUS2) genes regulated under the maize ubiquitin promoter	Callus
PRJDB7665	RNA-Seq of Japanese barley cultivars	Two dominant genes in barley (Hordeum vulgare L.) complementarily encode perfect resistance to Japanese soil-borne wheat mosaic virus	Illumina MiSeq	Genome sequences enable us to genotype genome wide polymorphisms among closely related genotypes. In barley, a highly-assembled genome sequences of six-row barley cv. Morex was available in 2017. Using this resource, we can map various markers physically on the genome. To construct new markers, whole genome resequencing is one of the best procedures. However, because of the large genome size and the high proportions of repetitive elements on the genome sequences, whole genome resequencing of multiple barley genotypes is not a practical solution. While SNP arrays were developed based on the limited donor genotypes, their application to the genotyping of barley germplasm other than these donor genotypes was less effective. Even though genotype by sequencing is the more effective method to detect random polymorphisms, frequent deficient alleles occurred in the alignment of sequenced genotypes. Here, we developed a de novo genotyping procedure using RNA-Seq in the germplasm used in Japanese barley breeding programs. By using RNAs from seedling shoot, seedling root and immature spike samples, we mapped NGS data on the transcribed regions corresponding to ~590 Mb of the total genome sequences (~ 4.8 Gbp). From 150 samples from 108 cultivars, we could detect more than 10,998 genome wide sequence polymorphisms whose minor allele frequencies were more than 0.1 both (?) in two-row and six-row barley. To evaluate the efficiency of polymorphism detection of this method, we conducted an amplicon sequencing using IonS5 platform on the 387 polymorphic sites. While more than 85% of SNPs evaluated were validated by the amplicon sequencing, half of indel/multiple alleles showed different or more diverged polymorphisms. These results demonstrated that our RNA-Seq based polymorphism detection could generate genome-wide markers even in the closely-related barley genotypes, such as genotypes from germplasm in Japanese breeding programs	Seedling shoot, seedling root and immature spike
PRJNA482688	RNA-Seq of barley seed tissues during germination using Laser Capture Microdissection	-	NextSeq 500	In present study, we used Laser Capture Microdissection (LCM) to isolate defined tissues including plumule, radicle, and scutellum in a contamination-free and precise manner during first 48 hours of barley seed germination and subjected to RNA-seq. The goal was to determine gene regulatory network in each of the main tissue types of the embryo in a tissue and time-specific manner during barley seed germination	Embryonic scutellum,embryonic radicle,embryonic plumule
PRJNA514114	RNA-seq of bulked segregants to identify resistant gene of barley yellow mosaice virus disease	Bulked segregant RNA-sequencing (BSR-seq) identified a novel rare allele of eIF4E effective against multiple isolates of BaYMV/BaMMV	Illumina NovaSeq 6000	The soil-borne yellow mosaic virus disease is a major threat to winter barley (Hordeum vulgare) production in Europe and East Asia. However, the exploration of resistant germplasm or casual genes used for barley breeding was rather limited in relative to the rapid diversification of viral strains. Here we identified an Iranian barley landrace ‘HOR3298’, which represented complete resistance to the bymovirus disease of barley. In contrast to the resistance donor rym4 and rym5, which act as predominant source in Europe and East Asia breeding over decades and which has been overcome by several virulent isolates, this landrace showed broad-spectrum resistance to multiple isolates of BaYMV/BaMMV in the disease prevalent fields of Germany and China. By employment of bulked segregant RNA sequencing (BSR-seq), test for allelism and haplotype analysis, a single recessive resistance gene in ‘HOR3298’ was genetically mapped coincident with the host factor eukaryotic translation initiation factor 4E (eIF4E, causal gene of rym4 and rym5). The eIF4EHOR3298 allele encoded for a novel haplotype that contained an exclusive nucleotide mutation (G565A) in the coding sequence. An easily handled marker was developed based on the exclusively rare variation, providing precise selection of this allele. Thus, this work provided a novel reliable resistance source and a feasible marker assisted selection assay that can be used in breeding for the yellow mosaic virus disease resistance in cultivated barley	Leaf(resistant/susceptible to BaYMV)
PRJNA563590	Hordeum vulgare cultivar:Conlon	-	Illumina HiSeq 4000	RNA-seq raw reads for barley cv. Conlon.	Leaf
PRJNA639036	Hulless barley (domesticated barley)	Stem lodging resistance in hulless barley: Transcriptome and metabolome analysis of lignin biosynthesis pathways in contrasting genotypes	Illumina NovaSeq 6000	Raw data of RNA-seq of hulless barley	Leaf
PRJNA680168	Hordeum vulgare cultivar:Navigator	Genes That Mediate Starch Metabolism in Developing and Germinated Barley Grain	Illumina HiSeq 1500	RNA-seq analysis of the developing barley grain	Developing Grain
PRJNA849931	Chloroplast activity provides invitro regeneration capability in contrasting cultivars	-	Illumina HiSeq 4000	Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. Little is known why only some cultivars in crop plants are tissue culture friendly? In this study, contrasting barley cultivars Golden Promise (GP) and DWRB91 (D91) were utilized for digging the molecular basis of regeneration efficiency. Multiomics studies involving transcriptomics, proteomics, metabolomics, and biochemical analysis were performed using GP and D91 callus to unravel the regulatory mechanisms. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS revealed 3062 protein groups and 16989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis also revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91. Overall design: Comparative gene expression profiling analysis of RNA-seq data for barley callus (Hordeum vulagre cvs. Golden promise (GP) and DWR91 (D91))	Callus
PRJNA872142	Transcriptome profiling of barley and tomato shoot and root meristems unravels physiological variations underlying photoperiodic sensitivity	-	Illumina HiSeq X	The average sowing date of crops in temperate climate zones has been shifted forwards by several days, resulting in a changed photoperiod regime at the emergence stage. In the present study, we performed a global transcriptome profiling of plant development genes in the seedling stage of root and shoot apical meristems of a photoperiod-sensitive species (barley) and a photoperiod insensitive species (tomato) in short-day conditions (8h). Variant expression indicated differences in physiological development under this short day-length regime between species and tissues. The barley tissue transcriptome revealed reduced differentiation compared to tomato. In addition, decreased photosynthetic activity was observed in barley transcriptome and leaf chlorophyll content under 8h conditions, indicating a slower physiological development of shoot meristems than in tomatoes. The photomorphogenesis controlling cryptochrome gene cry1, with an effect on physiological differentiation, showed an underexpression in barley compared to tomato shoot meristems. This might lead to a cascade of suspended sink-source activities, which ultimately delay organ development and differentiation in barley shoot meristems under short photoperiods	Root and shoot apical meristeme
PRJEB14349	RNA-Seq of 16 developmental stages of barley (Morex cultivar).	A chromosome conformation capture ordered sequence of the barley genome	Illumina HiSeq 2000	Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.	Embryos, Grain, Root, Lodicule, Palea, Epidermis
PRJEB21740	RNA-seq of enriched barley stomatal complexes versus total leaves.	A Tandem Amino Acid Residue Motif in Guard Cell SLAC1 Anion Channel of Grasses Allows for the Control of Stomatal Aperture by Nitrate	Illumina HiSeq 3000	We intend to identify transporters and their regulators involved in barley stomatal movement as well as components of the ABA signaling pathway. We isolated epidermal peels where only stomatal guard cells and their subsidiary cells survived, while other epidermal cell were mechanically disrupted and sequenced the resulting RNAs. Thus we analyzed transcripts differentially expressed between the barley stomatal complex and total leaves. These data served as the first overview of genes expressed in the stomatal complex and for cloning of relevant transporters.	Stomatal complex total leaf
PRJEB50400	RNA-seq of part of the root system of barley genotypes grown in an agricultural soil under controlled conditions.	-	Illumina NovaSeq 6000	This is a comparative experiments of three barley genotypes harbouring allelic differences at a locus designated QRMC-3HS putatively implicated in the assembly of the microbial communities thriving at the root-soil interface, the so called rhizosphere microbiota. The RNA-seq experiment aimed at identify genes differentially regulated among the genotypes at the locus of interest. As the selected genotypes host contrasting microbiotas, we hypothesised that differentially expressed genes at the locus represent primary candidates for the trait of interest (i.e., microbiota recruitment)	Root structure
PRJEB51523	Barley apical spikelet abortion transcriptome.	-	Illumina NovaSeq 6000	In barley (Hordeum vulgare), the indeterminate inflorescence meristem produces spikelet primordia along its axis and aborts a few terminally produced ones. In order to study the transcriptional changes involved in apical abortion of barley inflorescence, tissue-specific RNA-seq was performed at three early developmental stages by dividing the spikes into three parts, viz., apical, central, and basal. In two-rowed barley cv. Bowman, spikes were sampled at W5.0, W6.5, and W7.5 stages, whereas W5.5, W6.5 and W8.25 stages were collected from six-rowed barley cv. Morex. Three biological replicates were generated from each tissue type resulting in 54 RNA-seq samples	Apical Central Basal
PRJNA261456	Hordeum vulgare Transcriptome or Gene expression.	Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley	Illumina HiSeq 2000	We hypothesized that the genome segments of cultivated barley should show certain similarity with its ancestral wild barley. Instead of whole genome sequences, we employed RNA-Seq to investigated the genomic origin of modern cultivated barley using some representative wild barley genotypes from the Near East and Tibet, and representative world-wide selections of cultivated barley	Seeding
PRJNA275710	Next generation sequencing reveals gene transcription activities and alternative splicing events in germinating barley embryos.	Involvement of Alternative Splicing in Barley Seed Germination	Illumina HiSeq 2000	Seed germination triggers a transition of growth and metabolic activities from quiescent to active statuses. Germinating seeds is a good system to study many biological and biochemical processes including hormone metabolic activities and cell wall biosynthesis. Next generation sequence technology is used to study these processes. We have examined gene transcription activities and alternative splicing events in germinating embryos Overall design: We dissected barley embryos from four barley varieties at 2 time points 24 h and 48 h.	Germinating seeds
PRJNA378334	Leaf transcriptome sequencing of several barley accessions.	The barley immune receptor Mla recognizes multiple pathogens and contributes to host range dynamics	Illumina HiSeq 2500	RNAseq was performed on several barley accessions that vary for their reaction to wheat stripe rust (Puccinia striiformis f. sp. tritici) to identify markers and understand the gene content at the Rps7 (Resistant to Puccinia striiformis f. sp. tritici 7) locus. The majority of accessions were sequenced at 100 bp paired end, except CI 16147 which had 150 bp paired end reads. RNAseq read quality was assessed and trimmed using Trimmomatic (version 0.32) with the parameters ILLUMINACLIP:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:100. Transcriptome assembly was performed using Tophat (version 2013-11-10) with default parameters.	First leaf
PRJNA378723	Leaf transcriptome sequencing and assembly of several barley accessions.	An ancient integration in a plant NLR is maintained as a trans-species polymorphism	Illumina HiSeq 2500	RNAseq was performed on several barley accessions to understand their diversity, with an emphasis on the class of plant immune receptors that contain nucleotide-binding, leucine-rich repeats (NB-LRR). The accessions were sequenced at either 100 bp or 150 bp paired end, except CI 16147 which had 150 bp paired end reads. RNAseq read quality was assessed and trimmed using Trimmomatic (version 0.32) with the parameters ILLUMINACLIP:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:100. Transcriptome assembly was performed using Tophat (version 2013-11-10) with default parameters.	First leaf
PRJNA558196	Hordeum vulgare anther and meiocyte transcriptome.	Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I	Illumina NextSeq	We performed Illumina sequencing of cytologically staged isolated barley anthers at four differend timepoints and purified meiocytes and two different timepoints. We also included three IsoSeq PacBio libraries from a mixture of the above stages.	Anthers, Meiocyte
PRJNA744021	Transcriptome raw data of 29 barley samples	Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China	HiSeq X Ten	Barley RNA-SEQ for evolution.	Leaf
PRJNA752285	Transcriptomic analysis of differentially expressed genes during the floret opening in barley.	Highly Conserved Evolution of Aquaporin PIPs and TIPs Confers Their Crucial Contribution to Flowering Process in Plants	Illumina HiSeq 2500	RNA-seq analysis in eight tissues and six stages during the floret opening in barley.	Lodicule, pistils, anthers, glumes, rachises, leaves, stems, roots
PRJNA755156	BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.	BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification	Illumina NovaSeq 6000	BaRTv2 represents a new and improved Reference Transcript Dataset built upon a broad framework of highly informative Pacbio Iso-seq full length transcripts incorporating accurate SJ, TSS and TES information. It is based upon the European 2-row spring barley cv. Barke which itself is highly relevant to contemporary barley agriculture and current research. The combination of the novel Iso-seq analysis and filtering pipeline, the new automated quality control pipeline for short read assembled transcripts and detailed transcript characterisation and annotation make BaRTv2 a high-quality community-wide reference dataset.	Palea, Embroyo, Root, Lodicule, Leaf, Shoot Apex, Coleoptile, Rachis

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB25386	RNA-seq of barley lines after dehydration, spider mite or combined stress.	Dehydration Stress Contributes to the Enhancement of Plant Defense Response and Mite Performance on Barley	Illumina HiSeq 2000	Drought and herbivores are main threats to crop production. Barley plants were subjected to dehydration, spider mite attack or to a combination of both stresses. RNA-seq analyses were done to know how individual and double abiotic-biotic stresses promote changes in the transcriptome	Dehydration, spider mite
PRJEB52944	RNA-seq on touch responses in cereals	The dynamics of touch-responsive gene expression in cereals	Illumina NovaSeq 6000	RNA-seq time course covering the first 2 hours after gentle brushing of the second leaf in oat, wheat and barley	Touch treatment
PRJNA544271	Hordeum vulgare subsp. vulgare (domesticated barley)	-	Illumina HiSeq 2500	A population of 9 accessions, each with 16 individuals, with varying germination rates were 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.	Stored after seed regeneration
PRJNA578897	Transcriptome and proteome analysis of molecular mechanism in response to salt stress during seed germination in hulless barley	Integrative Transcriptomic and Proteomic Analyses of Molecular Mechanism Responding to Salt Stress during Seed Germination in Hulless Barley	HiSeq X Ten	Seeds germination is seriously sensitive to salt stress. The mechanism in response to salt stress during seed germination is still little known. In this study, two genotypes of hulless barley lk621 and lk53 were selected to investigate the molecular mechanism of seeds salinity response during germination stage through RNA-seq and iTRAQ technologies	Salt
PRJNA661163	RNA-seq for ABA treatment in roots of barely	Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment	HiSeq X Ten	To investigate the differences of gene expressions between the control and ABA treatment in roots of barley, two sets of root samples were taken after 1h, 3h, 6h and 24h of treatments respectively, and their mRNAs were sequenced by next generation sequencing on an Illumina Hiseq platform. The data will be used for further analysis.	ABA
PRJNA715112	Hordeum vulgare, Bipolaris sorokiniana, Serendipita vermifera	The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley	Illumina HiSeq 3000	We addressed the question how the the beneficial root endophyte Serendipita vermifera (Sv) and the pathogen Bipolaris sorokiniana (Bs) affect each other in presence of bacterial synthetic communities and determined barley host responses using phenotypic and transcriptional analyses	Serendipita vermifera, Bipolaris sorokiniana
PRJNA731362	Hordeum vulgare subsp. vulgare (domesticated barley)	The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei	Illumina NovaSeq 6000	We performed RNA-seq analysis of cv. Bowman and BW746 to measure the response of barley to P. hordei in the presence and absence of Rph3 two days after inoculation with Rph3-avirulent P. hordei pathotype 5453 P+ or the application of oil (mock)	Puccinia hordei 5453P+ inoculated
PRJNA875119	Surfactant-induced transcriptomic changes in barley leaves	Transcriptomic changes in barley leaves induced by alcohol ethoxylates indicate potential pathways of surfactant detoxification	Illumina HiSeq 4000	Detoxification of surfactants in crop plants. Specific changes in gene expression allowed to postulating three potential metabolic pathways of detoxification in barley leaves. Results clearly show that alcohole ethoxylates lead to pronounced changes in the expression of key genes potentially contributing to the detoxification of surfactants	Surfactants(BrijL/C12E4)
PRJNA889532	Genome-wide association scan and transcriptome analysis reveal candidate genes of waterlogging in cultivated barley	Genome-wide association study and transcriptome sequencing to identify candidate genes for waterlogging tolerance during germination in barley (Hordeum vulgare L.)	Illumina NovaSeq 6000	To explore the mechanism controlling waterlogging tolerance in barley, physiological, anatomical and transcriptional analysis were performed in two contrasting barley varieties viz. Franklin (susceptible) and TX9425 (tolerant).	Waterlogging
PRJNA892763	GP-20200604-1981_damai_RNA-Sequence_Gairdner	Integrated GWAS and transcriptomic analysis reveal the candidate salt-responding genes regulating Na+/K+ balance in barley (Hordeum vulgare L.)	HiSeq X Ten	RNA-Sequence of barley after salt treatment for 0,3,12, and 48 hour	Salt
PRJNA898434	Hordeum vulgare Transcriptome or Gene expression	Heat and drought induced transcriptomic changes in barley varieties with contrasting stress response phenotypes	Illumina HiSeq 4000	Plant growth and productivity are significantly impacted by drought and heat stress. Plants exhibit reduced growth as a result of drought or heat stress, which reduces yields. These two stresses occurring simultaneously worsen their effects. Breeding crops that are able to withstand changing climates depends on unraveling the molecular changes brought on by multiple abiotic stresses. In this study, barley genotypes exposed to heat, drought, and combined heat and drought stress for five days during heading stage were compared with genotypes that were more sensitive to stress (Otis).	Heat and drought
PRJNA902282	Hordeum vulgare Raw sequence reads	Response of salt stress resistance in highland barley (Hordeum vulgare L. var. nudum) through phenylpropane metabolic pathway	Illumina NovaSeq 6000	RNA-seq of Hordeum vulgare	NaCl
PRJNA908121	Hordeum vulgare subsp. vulgare (domesticated barley)	-	Illumina HiSeq 2500	Physiology and transcriptomic analyses were used to investigate the responses of two highland barley cultivars, ES (a variety sensitive to dark-induced leaf yellowing) and LS (a variety tolerant to dark-induced leaf yellowing), to dark-induced leaf senescence.	Dark induced
PRJNA910139	Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response	Transcriptional analysis in multiple barley varieties identifies signatures of waterlogging response	BGISEQ-500	Waterlogging leads to major crop losses globally, particularly for waterlogging sensitive crops such as barley. Waterlogging reduces oxygen availability and results in additional stresses, leading to the activation of hypoxia and stress response pathways that promote plant survival. Although certain barley varieties have been shown to be more tolerant to waterlogging than others and some tolerance-related QTLs have been identified, the molecular mechanisms underlying this trait are mostly unknown. Transcriptomics approaches can provide very valuable information for our understanding of waterlogging tolerance. Here, we surveyed 21 barley varieties for the differential transcriptional activation of conserved hypoxia-response genes under waterlogging, and selected five varieties with different levels of induction of core hypoxia-response genes. We further characterized their phenotypic response to waterlogging in terms of shoot and root traits. RNA-sequencing to evaluate the genome-wide transcriptional responses to waterlogging of these selected varieties led to the identification of a set of 98 waterlogging-response genes common to the different datasets. Many of these genes are orthologs of the so-called ‘core hypoxia response genes’, thus highlighting the conservation of plant responses to waterlogging. Hierarchical clustering analysis also identified groups of genes with intrinsic differential expression between varieties prior to waterlogging stress. These genes could constitute interesting candidates to study ‘predisposition’ to waterlogging tolerance or sensitivity in barley. Overall design: Differential gene expression analysis from RNA-seq from 10-day old roots from 5 barley varieties (Golden Promise, Infinity, Passport, Pilastro, Regina) under waterlogged and control conditions, with 3 replicates per sample	Waterlogging
PRJNA934830	Genome-wide association mapping and transcriptomic analysis reveal key drought-responding genes in barley seedlings	Genome-wide association mapping and transcriptomic analysis reveal key drought-responding genes in barley seedlings	Illumina NovaSeq 6000	RNA-seq was carried out on the leaves of BCS8 and BCS24 after 7 days of drought treatment in order to better understand the molecular pathways underlying drought tolerance and to find the relevant candidate genes. Overall design: Comparative gene expression profiling analysis of RNA-seq data for barley BCS8 and BCS24 under drought treatment	Drought
PRJNA938131	Transcriptome analysis of three barley varieties in response to barley yellow mosaic disease	Molecular insights into the responses of barley to yellow mosaic disease through transcriptome analysis	Illumina NovaSeq 6000	We used a transcriptome sequencing approach to analyze different expression levels of three barley varieties under both infected and uninfected conditions Overall design: Comparative gene expression profiling analysis of RNA-seq data for BaYMV and/or BaMMV-infected and disease-resistant barley leaves	BaYMV and BaMMV-infected
PRJNA946963	Hordeum vulgare cultivar:Anni	Transcriptome profiling of barley in response to mineral and organic fertilizers	Illumina NovaSeq 6000	This bioproject contains 20 samples (5 different treatments with 4 biological replicates) of RNA-seq data from barley leaves	Nitrogen fertilizer/Cattle manure
PRJEB8748	Expression profiling of developing barley main shoot apices and leaves during the vegetative phase and early inflorescence development in response to the photoperiod and natural allelic variation at Ppd-H1	Global Transcriptome Profiling of Developing Leaf and Shoot Apices Reveals Distinct Genetic and Environmental Control of Floral Transition and Inflorescence Development in Barley	Illumina HiSeq 2000	The timing of reproductive development determines spike architecture and thus yield in temperate grasses such as barley (Hordeum vulgare L.). Reproductive development in barley is controlled by the photoperiod response gene Ppd-H1 which accelerates flowering time under long-day (LD) conditions. A natural mutation in Ppd-H1 prevalent in spring barley causes a reduced photoperiod response, and thus, late flowering under LD. However, it is not very well understood how LD and Ppd-H1 control pre-anthesis development, and thus spike architecture and yield in barley. We performed a detailed morphological analysis of the pre-anthesis development in the spring barley cultivar Scarlett and its wild barley derived introgression line S42-IL107, carrying the photoperiod responsive Ppd-H1 allele. Characterization of shoot apex development in these genotypes indicated that floral transition and initiation of floral primordia occurred under LD (16h light/ 8h dark) and short day (SD, 8h light/ 16h dark) conditions, while inflorescence and seed development strictly required LDs. Additionally, a fast photoperiod response in the presence of the dominant Ppd-H1 allele promoted floret fertility under LDs. To characterize the effects of the photoperiod and allelic variation at Ppd-H1 on gene expression during pre-anthesis development we performed RNA sequencing of leaves and developing main shoot apices during the vegetative phase and early stages of inflorescence development in Scarlett and S42-IL107 grown under SD and LD conditions. Main shoot apices of both genotypes were sampled at defined developmental stages, i.e. Waddington stage W0.5, W1.0, W2.0 and W3.5, respectively. Leaf samples were harvested from plants before (W1.0) and after floral transition (W2.0). We identified genes that were specifically regulated at floral transition independent of day-length and Ppd-H1 and thus may serve as markers for the staging of floral transition. Furthermore, we identified transcripts differentially expressed between photoperiods and between genotypes in leaves and in shoot apices. This set of transcripts might act as candidates downstream of Ppd-H1 and are correlated with the promotion of shoot apex development and higher floret fertility under LD and in the presence of the photoperiod responsive Ppd-H1 allele	Photoperiod
PRJEB12540	RNAseq transcriptome assembly and expression profiling of a drought-control experiment with barley cultivar Scarlett and Spanish landrace SBCC073.	Large Differences in Gene Expression Responses to Drought and Heat Stress between Elite Barley Cultivar Scarlett and a Spanish Landrace	Illumina HiSeq 2000	Plants from barley cultivar Scarlett and barley Spanish landrace SBCC073 were grown until maturity in both greenhouse and growth chamber. Then, plants were irrigated every two days to maintain 70 and 20% RWC in the growth chamber and 50% RWC in the greenhouse. Samples from leaves and developing flowers were obtained after one month of treatment. RNA was obtained from 2 or 3 biological replicates of both genotypes, tissues and treatments. RNA from a total 28 samples was sequenced in a single Illumina Hiseq 2000 flowcell	Drought,heat
PRJEB13621	A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar	De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure	Illumina HiSeq 2000	Paired-end RNA-Seq libraries were constructed for three root sections of the roots of barley cv. Clipper, and landrace Sahara, grown under control and salt-treated (100 mM NaCl) conditions on agar plates in quadruplicate. Experiments were conducted in a temperature-controlled growth cabinet at 17 °C in the dark. After three days of germination, seminal roots were dissected according to the following steps: A 1.5 mm long section marked ‘Zone 1’ (meristematic zone) was taken from the root tip. A second section (‘Zone 2’) was dissected from the elongation zone up to a third section, ‘Zone 3’ (maturation zone), which was excised at the point of visible root hair elongation up to 3⁄4 of the entire root. Four biological replicates were generated for each sample in four separate experiments totaling 48 samples. All RNA-seq libraries were constructed and paired-end sequenced (100 bp) on an Illumina HiSeq 2000 system at the Australian Genome Research Facility (Melbourne, Australia).	Salt
PRJEB18276	Transcriptional responses to cold in five Pooideae species	Evolution of Cold Acclimation and Its Role in Niche Transition in the Temperate Grass Subfamily Pooideae	Illumina HiSeq 2000	To investigate the evolution of cold response in Pooideae, five species spanning early to later diverging lineages were sampled before and after subjecting them to a drop in temperature (17°C to 6°C), shorter days (12 to 8 hours of light) and less intensive light. Short-term response was sampled in the afternoon 8 hours after drop in temperature but 24 hours after the respective control sample to control for diurnal rhythm. Long-term response was sampled after 4 and 9 weeks in the morning directly after lights were turned on with a respective control sample also taken in the morning on the day before the temperature drop.	Cold
PRJEB21096	RNA-Seq data analysis of Hordeum vulgare cv. Morex transcriptome to study photomorphogenesis.	-	Illumina HiSeq 2000	Hordeum vulgare is one of the first domesticated grains in the world and it has been reported that variations in the light environment have a substantial effect on barley plant development and biological processes. High-throughput RNA-Seq study was performed to investigate the complex transcriptome network required for photomorphogenesis in barley. Seedlings were grown in dark and light conditions and three biological replicates were sampled from each condition. Six libraries from poly-A rich mRNA fraction were subjected to 51bp single-end RNA-seq sequencing.	Light, dark
PRJEB34648	RNA-seq of leaf tissue of barley cultivar Bowman and three derived introgression lines.	-	Illumina HiSeq 2500	In order to understand effects of defective circadian clock on the global barley transcriptome, we analyzed the diel and circadian leaf transcriptomes in the barley cultivar Bowman and derived introgression lines carrying mutations in EARLY FLOWERING 3 (ELF3), LUX1, and EARLY MATURITY 7 (EAM7).	Circadian clock
PRJEB40905	Comparative hormonal and expression analyses of two barley genotypes with contrasting drought tolerance.	The Effect of Drought on Transcriptome and Hormonal Profiles in Barley Genotypes With Contrasting Drought Tolerance	Illumina NovaSeq 6000	Barley is negatively impacted by drought stress. In this study, comparative hormonal and expression profiling were conducted between drought tolerant and drought sensitive barley genotypes. The results revealed less changes in the expression profile of the tolerant genotype compared to the sensitive genotype. The expression level of some drought tolerance genes was higher in the drought tolerant genotype compared to the sensitive genotype. Moreover, few drought tolerance genes were uniquely and highly induced in the drought tolerant genotype. These results shed light into new mechanisms of drought tolerance in barley. This will deepen our understanding of the complex drought response in barley, and will help in the improvement of drought tolerant barley genotypes.	Drought
PRJNA324116	RNA-seq (strand-specific library) of barley shoots and roots from control and heat conditions.	Heat Stress Affects Pi-related Genes Expression and Inorganic Phosphate Deposition/Accumulation in Barley	Illumina HiSeq 2000	Samples were collected after 1 h of the heat treatment. Samples were collected for control and heat stressed plants. Overall design: RNA-seq was performed for shoot (in triplicate for each condition) and root (in duplicate for each condition).	Heat
PRJNA382490	Transcriptome of barley under three different heavy metal stress conditions.	Transcriptome of barley under three different heavy metal stress reaction	Illumina HiSeq 2000	The aim of the study is to identify gene regulated by three heavy metal: copper, zinc and cadmium.	Copper, zinc and cadmium
PRJNA400519	Hordeum vulgare Raw sequence reads.	Reference gene selection for quantitative RT-PCR normalisation in barley under low-nitrogen stress, based on RNAseq data	Illumina HiSeq 2000	RNA sequencing of Hordeum vulgare L. under low nitrogen stress.	Nitrogen
PRJNA430281	RNA-seq transcriptome profiling of barley under Pi starvation and recovery conditions	Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.)	HiSeq X Ten	RNA-seq transcriptome profiling of barley under Pi starvation and recovery conditions	Phosphorus
PRJNA439267	Barley seminal root zone specific gene expression in response to water deficit.	Osmotic stress enhances suberization of apoplastic barriers in barley seminal roots: analysis of chemical, transcriptomic and physiological responses	Illumina HiSeq 4000	Barley seminal roots were divided into three zones according their developmental stage. Transcript changes by RNA-seq in response to water deficit were measured.	Water deficit
PRJNA489775	Transcriptome profiles of salt treated roots of H.brevisubulatum and H.vulgare Transcriptome	-	Illumina HiSeq 2500	Total RNA was isolated from root tissue of H. brevisubulatum and H. vulgare with RNAprep Pure Plant Kit (Tiangen Biotech Co., Ltd.)，transcriptome libraries were constructed using Ribo-Zero-rRNA Removal Kits (Plant/Bacteria) (Illumina, San Diego, CA, USA) and NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs), sequence was generate on Illumina Hiseq 2500 sequencer instrument	Salt
PRJNA566107	Low nitrogen tolerance related study in barley.	Novel low-nitrogen stress-responsive long non-coding RNAs (lncRNA) in barley landrace B968 (Liuzhutouzidamai) at seedling stage	HiSeq X Ten	Reducing the dependence of crop production on chemical fertilizer with its associated costs, carbon footprint and other environmental problems is a challenge for agriculture. New solutions are required to solve this problem, and crop breeding for high nitrogen use efficiency or tolerance of low nitrogen availability has been thought to be a promising approach. However, the molecular mechanisms of high nitrogen use efficiency or low-nitrogen tolerance in crop plants are still to be elucidated, including the role of long non-coding RNAs.	Nitrogen
PRJNA602700	Genome-Wide analysis of gene expression responses to waterlogging stress in roots of barley (Hordeum vulgare L.)	Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley (Hordeum vulgare L).	Illumina HiSeq 4000	Waterlogging is a major abiotic stress causing oxygen depletion and carbon dioxide accumulation in the rhizosphere. Barley is more susceptible to waterlogging stress than other cereals. To gain a better understanding of the effect of waterlogging stress in barley, we carried out a genome-wide gene expression analysis in roots of Yerong and Deder2 barley genotypes under waterlogging and control (well-watered) conditions by RNA-Sequencing, using Illumina HiSeq 4000 platform. Overall design: Two-week-old Yerong and Deder2 seedlings were exposed to waterlogging treatment. Root tissue samples were collected at the time-points 0 and 72 h of treatment for Yerong from both treated and control plants, and at the points 0, 72, and 120 h of treatment for Deder2 from both treated and control plants. Total RNA was prepared and used for the RNA-seq analysis. Four independent biological replicates were used for each plant sample.	Waterlogging
PRJNA679445	Sequencing of wild and cultivated barley leaves under osmotic stress sensed by roots	Cuticular transpiration is not affected by enhanced wax and cutin amounts in response to osmotic stress in barley	Illumina HiSeq 4000	Leaf 2 of wild barley (ICB181243 originating from Pakistan) and cultivar Scarlett subjectect to control or -0.8 MPa osmotic stress were sequenced (RNA-seq).	Osmotic stress
PRJNA704034	Transcriptome analysis of barley root meristem under Al and low pH stress.	Aluminum or Low pH – Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress	Illumina HiSeq 4000	Aluminum (Al) is the most common metal in the Earth’s crust and Al toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. The first symptom of Al toxicity is the reduction of root growth, resulting in decreased water and nutrients uptake, plant growth retardation, and finally, yield reduction. Barley (Hordeum vulgare L.), which is the fourth cereal crop in regards to cultivation area and production tonnage, belongs to crops most sensitive to toxic aluminum ions in low pH soils. We present the RNA-seq transcriptome analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 µM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. Interestingly, in the short-term experiment, more genes were differentially expressed between root meristems grown at pH=6.0 and pH=4.0, than between those grown at pH=4.0 with and without Al treatment. The upregulated genes that were overrepresented at conditions of low pH, compared to optimal pH, were associated with response to oxidative stress, cell wall organization, and iron ion binding. Among genes downregulated by low pH were mainly those related to chromatin organization. These results show that low pH itself is a severe stress for barley plants. Among genes upregulated by short Al treatment, overrepresented were those related to response to stress condition and calcium ion binding. After 7 days of hydroponics, the number of DEGs between hydroponics at pH=4.0 and 6.0 were still high but lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 day Al treatment caused massive changes in the transcriptome profile compared to the condition of low pH alone. Over 4 000 genes were upregulated and almost 2 000 genes were downregulated by long-term Al stress. These DEGs were related to e.g. stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants.Additionally, we phenotyped in detail the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH=6.0, pH=4.0, and pH=4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress facor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be underlined that in the acidic arable lands, plants are exposed simultaneously to both of these stresses (low pH and Al), as Al becomes soluble at pH below 5.5. The presented transcriptome analysis may help to find potential targets for breeding barley plants more tolerant to such conditions. Overall design: We examined the influence of low pH and aluminum on transcriptome of barley root meristems in two independent hydroponic experiments (short- and long-term). Root meristems from at least 8 plants from one hydroponic container were considered as one repetition (with an average of 5 root meristems per plant). Each experimental combination (optimal pH=6, low pH=4 and Al treated) was analyzed in three replicates in both experiments.	Al and low pH
PRJNA728113	Transcriptome alterations of an in vitro-selected, moderately-resistant, two-row malting barley in response to 3ADON, 15ADON and NIV chemotypes of Fusarium graminearium.	Transcriptome Alterations of an in vitro-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of Fusarium graminearum	Illumina HiSeq 4000	Fusarium head blight caused by Fusarium graminearum is a devastating disease of malting barley. Mycotoxins associated with contaminated grain can be transferred from malt to beer and pose a health risk to consumers. In western Canada, F. graminearum has undergone an adaptive shift from 15ADON constituency to dominance by virulent 3ADON-producers, likewise NIV-producers have established in regions of southern United States. Lack of adapted resistance sources with adequate malting quality has promoted the use of alternative breeding methodologies such as in vitro selection. We studied the low-deoxynivalenol characteristic of in vitro selected, two-row malting barley variety ‘Norman’ by RNAseq in contrast to its parental line ‘CDC Kendall’, when infected by 15ADON-, 3ADON- and NIV-producing isolates of F. graminearum. The current study documents higher mycotoxin accumulation by 3ADON isolates, thereby representing increased threat to barley production. At 72-96 hours post infection, significant alterations in transcription patterns were observed in both varieties with pronounced upregulation of the phenylpropanoid pathway and detoxification gene categories (UGT, GST, CyP450 and ABC) particularly in 3ADON treatment. Defense response was multi-tiered, where differential expression in ‘Norman’ associated with antimicrobial peptides (thionin 2.1, defensing, non-specific lipid-transfer protein) and stress-related proteins such as late embryogenesis abundant proteins, heat-shock, desiccation-related and a peroxidase (HvPrx5). Several gene targets identified in ‘Norman’ would be useful in application of breeding varieties with reduced deoxynivalenol content. Overall design: Adult plants of Norman and CDC Kendall were sprayed with macroconidia (5 x 10^4 spores ml-1) of Fusarium graminearum (3ADON, 15ADON and NIV chemotypes + mock control). Seed tissue samples were collected at the time-points 72 h and 96h post-inoculation for Norman and CDC Kendall from all Fusarium treated and control plants. Total RNA was prepared and used for the RNA-seq analysis. Three independent biological replicates were sampled.	Fusarium head blight
PRJNA744693	RNA-seq analysis of barley leaves responding to waterlogging stress.	Cultivar-, stress duration- and leaf age-specific hub genes and co-expression networks responding to waterlogging in barley	Illumina HiSeq 2500	cultivar-, waterlogging stage- and leaf age- specific hub genes and regulatory networks in baley leaves were revealed under waterlogging stress.	Waterlogging
PRJNA767196	The RNA-seq datasets of monocot and eudicot plants under cold stress (4 degrees centigrade) at 0, 2, 24, and 168 hours (h).	Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms	Illumina NovaSeq 6000	We performed RNA-seq experiments with the leaf tissues from five monocots (Setaria italica, Zea mays, Hordeum vulgare, Oryza sativa, and Phyllostachys edulis) and six eudicots (Betula pendula, Carya illinoinensis, Glycine max, Cucumis sativus, Populus trichocarpa, and Arabidopsis thaliana) subjected to cold treatment (4 degrees centigrade) for 0, 2, 24, and 168 hours (h). Before cold stress treatment, all the plant seedlings were cultured in an artificial climate chamber with 25 degrees centigrade at a photoperiod of 16/8 h light/dark cycle. For A. thaliana, three-week old seedlings were used for cold stress treatments. For other species, young seedlings growing up to ~30 cm in height were utilized. Total RNA of the leaves collected from each species was isolated, purified, and assessed by NanoDrop ND-1000 and Bioanalyzer 2100. Poly(A)-RNA was enriched for cDNA library construction and sequencing by Illumina NovaSeq 6000 (2 x 150 bp paired-end reads).	Cold
PRJNA781996	Transcriptome and physiology of salt tolerance in barley.	-	Illumina HiSeq 2500	Barley is used as a model cereal to decipher salt tolerance mechanisms, due to its simpler genome than wheat and better salt tolerance compared to rice and wheat. An enhanced understanding of molecular mechanisms underlying salt tolerance is essential for the genetic improvement of crops. The keen comparative RNA-Seq study to elucidate the molecular mechanisms underlying the adaptive strategies used by wild barley genotype to combat salt stress when compared with the salt-sensitive barley cultivar in this article will have something to offer a wide range of readers interested in. Physiological and functional outcomes were assessed as a function of salt stress and several mechanisms were advanced to explain the observed effects in contrasting barley genotypes.	Salt
PRJNA428086	Differential expression profiling of microspores during the early stages of isolated microspore culture in barley using the embryogenic-responsive cultivar Gobernadora.	Differential Expression Profiling of Microspores During the Early Stages of Isolated Microspore Culture Using the Responsive Barley Cultivar Gobernadora	Illumina HiSeq 2000	mRNA library from Illumina TrueSeq; Barley (Hordeum vulgare ssp. vulgare; cv. Gobernadora) starting material in barley androgenesis: uninucleate and haploid microspores (Day 0), microspore after stress pre-treatment (Day 2) and microspore after three days in embryogenesis culture (Day 5).	Thermal and osmotic stress

Mutant and Experimental Genetic Population

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB6343	RNA-seq data of phenotypic pools of lax.a.	-	Illumina HiSeq 2000	The barley mutant laxatum.a (lax.a) displays a set of pleiotropic phenotypic characteristics compared to the wild type: (i) increased spike length due to extended rachis internodes, (ii) awns with a very wide base, (iii) thin and exposed grains, (iv) as well as a homeotic conversion of the lodicules into two additional anthers. High resolution mapping in ~2000 F2 plants delimited the gene locus to a 0,2 cM target interval in a region which is characterized by reduced recombination. Thus, a large physical distance that comprises up to 200 genes required further mapping effort. On the basis of advanced genomic resources (IBSC, 2012) our aim was to test an adapted version of cloning-by-sequencing method in barley. By combining whole-genome-shotgun sequencing (WGS) data of the parental genotypes, RNA-seq data of phenotypic pools as well as exome capture (Mascher et al. 2013) re-sequencing of genetically closely linked lax.a recombinant plants a single candidate gene could be identified for lax.a. These results proof the feasibility of adapting high-throughput sequencing methodology for gene isolation in barley.	Laxatum.a
PRJEB22124	RNA-seq of barley lines overexpressing or silencing HvPap-1 gene	The Subcellular Localization and Protein-protein Interactions of Barley Mixed-Linkage (1→3),(1→4)-β-D-Glucan Synthase CSLF6 and CSLH1	Illumina HiSeq 2000	HvPap-1 is a C1A cysteine protease from barley that has been associated to endogenous processes and responds to abiotic and biotic stresses. Overexpressing and silencing lines were constructed to test the response of plants with variations in the levels of HvPap-1 to different stresses. RNA-seq analyses were done to know how changes in HvPap-1 expression levels affect the expression of other genes and the effect of these changes in the response of the plant	HvPap-1
PRJEB28286	RNA-Seq of developing shoot apical meristems of barley cultivar Golden Promise (null segregant and Ubi::HvFT3 overexpressor) grown under long- and short-day photoperiods	-	Illumina HiSeq 2500	FLOWERING LOCUS T-like genes have duplicated and functionally diverged between dicot and monocots species. The purpose of this study was to characterize the function of HvFT3 in barley (Hordeum vulgare). For this purpose, we generated transgenic lines overexpressing HvFT3 and characterized its effects on global gene expression changes in the main shoot apices at two developmental stages (spikelet initiation, lemma primordium). Analysing the function of different HvFT homologs in barley gives important insights into the genetic control of spike development and hence of yield in barley	Photoperiods
PRJEB51366	Barley spikelet abortion transcriptome	A molecular framework for grain number determination in barley	Illumina NovaSeq 6000	Bowman and BW-NIL-tst2.b were grown in a phytochamber condition (light/dark: 12h/12h; day/night temperature: 12℃/8℃) in a 24-well plate. Spike samples at awn primordium (W4.5), white anther (W5.5) and green anther (GrA) stages were collected under a light microscope. Each spike was divided into three sections: apical (spikelet1-10) + central (spikelet15-20) + basal (spikelet25-30). Anthers from top three spikelets at W8 and W9 of Bowman and BW-NIL-tst2.b were collected. All sample collections were conducted between 11:00am – 14:00pm within a day	Spike,Anther
PRJNA431836	Hordeum vulgare cultivar:Golden Promise	WRKY Transcription Factors Associated With NPR1-Mediated Acquired Resistance in Barley Are Potential Resources to Improve Wheat Resistance to Puccinia triticina	Illumina HiSeq 4000	Draft a profile of genes associated with NPR1-mediated acquired resistance triggered by Pseudomonas syringae pv. tomato DC3000 in barley	Pst Infection
PRJNA579960	Transcriptome of endosperm transfer cells (ETCs) in barley seeds	Barley HISTIDINE KINASE 1 (HvHK1) coordinates transfer cell specification in the young endosperm	Illumina HiSeq 2500	Transcriptome profiling of endosperm transfer cells (ETCs) during and after cellularization in wild type (WT) and HvHK1-RNAi grains of barley. RNA-seq of ETC regions from two RNAi-lines with most severe repression of HvHK1 (lines: 4_9 + 16_6) and corresponding WT cells was performed to identify HvHK1-mediated pathways. Cells were isolated by laser capture microdissection (LCM) at 4/5 and 7 DAF to extract commonly differentially expressed genes (DEGs) in the two RNAi-lines.	HvHK1
PRJNA746688	Hordeum vulgare RNA-seq data	Excess nitrogen responsive HvMADS27 transcription factor controls barley root architecture by regulating abscisic acid level	NextSeq 500	Transcriptome analysis of barley roots growing in nitrogen excess and control condition	Nitrogen
PRJNA877794	Hordeum vulgare cultivar:Tamalpais	Role of reactive oxygen species in lesion mimic formation and conferred basal resistance to Fusarium graminearum in barley lesion mimic mutant 5386	Illumina NovaSeq 6000	RNA-seq of barley cultivar Tamalpais and the lesion mimic mutant (LMM) 5386. The differentially expressed genes between WT and LMM were identified.	Barley lesion mimic mutant (LMM) 5386
PRJNA878682	Barley FASCIATED EAR genes determine inflorescence meristem size and yield traits	Barley FASCIATED EAR genes determine inflorescence meristem size and yield traits	Illumina HiSeq 4000	Three FASCIATED EAR genes genetically determine the IM size, spike morphology and yield traits. We performed gene expression profiling analysis using data obtained from RNA-seq of 2 genotypes (FEA mutant and wild type) at two developmental points. Overall design: Comparative gene expression profiling analysis of RNA-seq data FEA mutant and wild type with W2.0 and W3.0 inflorescence	Inflorescence meristem size and yield traits(FEA mutant)
PRJNA886698	Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2	Nutrient regulation of lipochitooligosaccharide recognition in plants via NSP1 and NSP2	Illumina NovaSeq 6000	Many plants associate with arbuscular mycorrhizal fungi for nutrient acquisition, while legumes also associate with nitrogen-fixing rhizobial bacteria. Both associations rely on symbiosis signaling and here we show that cereals can perceive lipochitooligosaccharides (LCOs) for activation of symbiosis signaling, surprisingly including Nod factors produced by nitrogen-fixing bacteria. However, legumes show stringent perception of specifically decorated LCOs, that is absent in cereals. LCO perception in plants is activated by nutrient starvation, through transcriptional regulation of Nodulation Signaling Pathway (NSP)1 and NSP2. These transcription factors induce expression of an LCO receptor and act through the control of strigolactone biosynthesis and the karrikin-like receptor DWARF14-LIKE. We conclude that LCO production and perception is coordinately regulated by nutrient starvation to promote engagement with mycorrhizal fungi. Our work has implications for the use of both mycorrhizal and rhizobial associations for sustainable productivity in cereals. Overall design: RNA-seq of M. truncatula genes after various nutrient treatments (+P+N, +P-N, -P+N, -P-N) in wildtype (A17) and mutant (Mtnsp1-1, Mtnsp2-2) lines, with transgenic lines (MtNSP1ox, MtNSP2ox, miRR-MtNSP2ox) under +N+P treatment; RNA-seq of H. vulgare genes after various nutrient treatments (+P+N, +P-N, -P+N, -P-N) in wildtype (Golden Promise) and mutant (Hvnsp1-1, Hvnsp2-1) lines, with transgenic lines (MtNSP1ox, MtNSP2ox) under +N+P treatment	Mtnsp1-1, Mtnsp2-2
PRJNA315041	Hordeum vulgare subsp. vulgare cultivar:Morex Transcriptome or Gene expression	RNA-seq reveals few differences in resistant and susceptible responses of barley to infection by the spot blotch pathogen Bipolaris sorokiniana	Illumina HiSeq 2000	The purpose of this study was to characterize the transcriptomic response of Morex (which carries durable resistance to Cochliobolus sativus Isolate ND85F) to a susceptible Morex mutant.	Bipolaris sorokiniana
PRJNA396950	RNA sequencing of Hordeum vulgare near-isogenic lines.	Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley.	Illumina HiSeq 2500	RNA sequencing of ILs of vrs1, vrs3, vrs4 and int-c.5 in cv. Bowman Purpose: Expression analysis and variant calling Overall design: Enriched apical meristem tissue was isolated at Waddington stage (W) 3.5 and W5.0. The samples were harvested at the middle of the day, 6 to 8 h before the end of the light period.	VRS3
PRJDB4754	Hordeum vulgare Transcriptome or Gene expression.	Extreme Suppression of Lateral Floret Development by a Single Amino Acid Change in the VRS1 Transcription Factor	Illumina HiSeq 2500	Total RNA was extracted from immature spikes at the awn primordium stage of cultivated barley (Hordeum vulgare L.). Total RNA was measured by using Agilent 2100 Bioanalyzer (Agilent Technologies, Technologies, PaloAlto, CA, USA) and used for construction of sequencing library. Strand-specific RNA libraries were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) following the instructions in the TruSeq Stranded mRNA Sample Preparation Guide Rev.E (Illumina). Poly(A)-RNA was fragmented and single-strand and double-strand cDNA were synthesized. High-throughput sequencing was conducted using HiSeq 2500 (Illumina, San Diego, CA, USA).	Def2 mutant (NGB115174)
PRJNA558703	mRNA and lncRNA analysis of the barley shrunken endosperm mutant	Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq	Illumina HiSeq 2500	In recent years, research on barley (Hordeum vulgare L.) has focused on breeding, quality analysis, agronomic traits, but there are few studies on grain traits, especially shrunken endosperm trait. In this project, we selected Bowman and sex1 seeds from different flowering stages for transcriptome analysis (RNA-seq), combined with bioinformatics techniques to mine lncRNAs and mRNAs that associated with shrunken endosperm. Through the corresponding gene annotation to understand the metabolic pathways that cause shrunken endosperm, and proposed the molecular mechanism of sex1 regulation of shrunken endosperm	Shrunken endosperm
PRJNA890449	Bulked segregant transcriptome bulks and additional alleles for barley (Bowman) eceriferum mutants	Isolation and characterization of the gene HvFAR1 encoding acyl-CoA reductase from the cer-za.227 mutant of barley (Hordeum vulgare) and analysis of the cuticular barrier functions	NextSeq 1000	The two eceriferum loci cer-za and cer-ye were suggested to be involved in the biosynthesis of cuticular waxes (Patwari 2019), but the identities of the genes Cer-za and Cer-ye as well as their function remained unclear. This data is part of the effort to determine causal genes and unravel their function in the context of wax synthesis	Waxes
PRJNA922199	Fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley by exploiting near isogenic lines, transcriptome profiling and a large near isogenic line-derived population	Fine mapping of a Fusarium crown rot resistant locus on chromosome arm 6HL in barley by exploiting near isogenic lines, transcriptome profiling, and a large near isogenic line-derived population	Illumina HiSeq 2000	RNA sequences for three pairs of 6HL NILs conferring FCR resistance	F. pseudograminearum isolate
PRJNA924522	Hordeum vulgare subsp. vulgare (domesticated barley)	A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley	Illumina NovaSeq 6000	RNA-seq raw data for the publication: "A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley"	Leaf rust
PRJNA294716	Hordeum vulgare cultivar:M69, Lacey and Chevron Transcriptome or Gene expression.	Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance	Illumina HiSeq 2500	Fusarium graminearum infects barley spikes and causes Fusarium head blight (FHB), a major disease problem worldwide. Resistance to FHB is partial and controlled by quantitative trait loci (QTL) of which two are located on barley chromosomes 2H bin8 (2Hb8) and 6H bin7 (6Hb7). To understand the molecular mechanisms of FHB resistance, transcriptomes of near-isogenic lines (NILs) carrying Chevron-derived resistant alleles for the two QTL and recurrent parents (M69 and Lacey) were investigated with RNA sequencing after F. graminearum or mock inoculation. A total of 2,083 FHB-responsive transcripts were detected and provide a gene expression atlas for the barley-F. graminearum interaction. Comparative analysis of the 2Hb8 resistant (R) NIL and M69 revealed that the 2Hb8 R NIL exhibited an elevated defense response in the absence of fungal infection and responded quicker than M69 upon fungal infection. The 6Hb7 R NIL displayed a more rapid induction of a set of defense genes than Lacey during the early stage of fungal infection. Overlap of differentially accumulated genes were identified between the two R NILs, suggesting that certain defense mechanisms may represent basal resistance to F. graminearum and/or general biotic stress response and were co-regulated by the two QTL. Long noncoding RNAs (lncRNAs) have emerged as potential key regulators of transcription. A total of 12,366 lncRNAs were identified of which 604 were FHB responsive. The current transcriptomic analysis revealed the differential mechanisms conferred by two QTL in response to F. graminearum infection and identified genes and lncRNAs that were associated with FHB resistance.	6Hb7 S NIL, 6Hb7 R NIL
PRJNA668924	INTERMEDIUM-M encodes an HvAP2L-H5 ortholog and is required for inflorescence indeterminacy and spikelet determinacy in barley.	INTERMEDIUM-M encodes an HvAP2L-H5 ortholog and is required for inflorescence indeterminacy and spikelet determinacy in barley	Illumina HiSeq 2500, Illumina Genome Analyzer IIx	Inflorescence architecture dictates the number of flowers and hence seeds. The architectural differences between two related cereals barley and wheat are controlled by differences in determinacy of inflorescence and spikelet meristems. Here, we characterize two allelic series of mutations named intermedium-m (int-m) and double seed1 (dub1) that convert barley indeterminate inflorescences into wheat-like determinate inflorescences bearing a multi-floreted terminal spikelet and indeterminate spikelets with additional florets. We collected mRNA from developing spikes from the double ridge (DR), triple-mound-spikelet meristem (TM-SM), floret meristem (FM, a.k.a lemma primordium), stamen primordium (StP) and awn primordium (AP) stages. We then used the RNA-sequencing (RNA-seq) to sequence the mRNA samples for both variants calling for introgression mapping and differential gene expression analysis between the wildtype Bowman and two int-m Near-isogenic lines (NIL).	int-m.85 NIL, int-m.1a NIL
PRJEB25969	Transcriptome analysis on mature, non aged seeds of the spring barley landraces Cebada Capa and L94 and L94 NILs by RNA sequencing.	Genes for seed longevity in barley identified by genomic analysis on near isogenic lines	Illumina HiSeq 2000	Widespread natural variation in barley offers an opportunity to study seed longevity in an important temperate cereal crop. For example, the spring barley landraces Cebada Capa (Argentina) and L94 (Ethiopia) display long and short-term seed longevity, respectively. We have used this contrast to identify and characterize seed longevity genes in barley by RNA sequencing analysis of mature, non aged seeds of Near Isogenic Lines (NILs) with a L94 background but harboring introgressions from Cebada Capa in four putative QTLs on chromosomes 1H and 2H.	-