TriticeaeExpDB

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Tissue and Stage

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB4947	Illumina sequencing of RNA from 14 wild barley samples (Hordeum spontaneum)	The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression	Illumina Genome Analyzer II	In this study 14 wild barley samples (Hordeum spontaneum) from the World Barley Diversity Collection (WBDC) were selected to represent as much as possible of the full diversity for the wild species. Seeds were grown at room temperature in the dark. After 4 days post-germination, embryonic tissue (coleoptile, mesocotyl and seminal roots) was dissected and flash-frozen. Total RNA was extracted and cDNA prepared. Sequencing was carried out on an Illumina GAII instrument using standard TruSeq RNA (Illumina) library generation, with single-end 75bp reads obtained from a single lane for each sample. The following samples were used: WBDC032, WBDC115, WBDC170, WBDC182, WBDC255, WBDC319, WBDC344, WBDC016, WBDC035, WBDC142, WBDC173, WBDC227, WBDC307, WBDC336. See also: BJ Steffenson, P Olivera, JK Roy A Yue, B Jin, KP Smith and GJ Muehlbauer (2007) A walk on the wild side: mining wild wheat and barley collections for rust resistance genes. Australian Journal of Agricultural Research, 2007, 58, 532–544	Embryonic tissue (coleoptile, mesocotyl and seminal roots)
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.	Leaf
PRJNA507455	Hordeum spontaneum Genome Sequencing Using RNA Seq	Intensified Selection, Elevated Mutations, and Reduced Adaptation Potential in Wild Barley in Response to 28 Years of Global Warming	Illumina HiSeq 2500	Ten populations of wild barley (Hordeum spontaneum) were collected 28 years apart. Single nucleotide polymorphisms (SNPs) were detected using RNA Seq sequences. Focus was placed on those SNPs that were deleterious and associated with the two sample times to examine the change in diversity over time	4th leaf
PRJNA665933	transcriptome analysis of leaves and roots in 10 wild barley from Tabigha Evolution Slope	Multi-Omics Analysis Reveals the Mechanism Underlying the Edaphic Adaptation in Wild Barley at Evolution Slope (Tabigha)	Illumina HiSeq 4000	transcriptome analysis of leaves and roots in 10 wild barley from Tabigha Evolution Slope	Leaf, root
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	Leaves

Stress and Treatment

Project ID	Title	Related Publication	Sequencing Type	Description	Notes
PRJEB8700	Drought tolerance RNA-Seq experiment in Hordeum spontaneum	RNA-Seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley Hordeum spontaneum	Illumina HiSeq 2000	The evolutionary basis of reproductive success in different environments is of a major interest in the study of plant adaptation. Since the reproductive stage is articularly sensitive to drought, genes affecting reproductive success during that stage are key players in the evolution of adaptive mechanisms. We used an ecological genomics approach to investigate the reproductive response of drought-tolerant and sensitive wild barley accessions originating from different habitats in the Levant. We sequenced mRNA extracted from spikelets at flowering stage in drought-treated and control plants. The barley genome was used for reference-guided assembly and differential expression analysis. Our approach enabled to detect biological processes affecting grain production under drought stress. We detected novel candidate genes and differentially expressed alleles associated with drought tolerance. Drought associated genes were shown to be more conserved than non-associated genes, and drought-tolerance genes were found to evolve more rapidly than other drought associated genes. We show that reproductive success under drought stress is not a habitat-specific trait but a shared physiological adaptation that appeared to evolve recently in the evolutionary history of wild barley. Exploring the genomic basis of reproductive success under stress in crop wild progenitors is expected to have considerable ecological and economical applications	Drought
PRJNA227211	Hordeum vulgare ssp. spontaneum RNA-seq	Molecular Networking of Regulated Transcription Factors under Salt Stress in Wild Barley (H. spontaneum)	Illumina HiSeq 2000	RNA-Seq of the wild barley (H. spontaneum) under salt stress	Salt
PRJNA432492	Hordeum vulgare subsp. spontaneum Transcriptome or Gene expression	Subfamily-Specific Specialization of RGH1/MLA Immune Receptors in Wild Barley	Illumina HiSeq 2500	To allow for a more exhaustive assessment of Mla (mildew resistance locus A ) sequence diversity, we here used transcriptome sequencing and assembly to identify Mla sequences from a set of 50 wild barley (Hordeum spontaneum) accessions representing nine populations distributed throughout the Fertile Crescent.	Blumeria graminis f. sp. hordei
PRJNA491382	Transcriptome analysis of barley epidermal cells under drought stresses	-	Illumina HiSeq 2500	Comparative transcriptomic study with two wild barley genotypes X5 & X54	Drought
PRJNA543388	Wild Barley (ICB181243) root zone specific RNA-Seq in response to water deficit	Seminal roots of wild and cultivated barley differentially respond to osmotic stress in gene expression, suberization, and hydraulic conductivity	Illumina HiSeq 4000	Wild barley (ICB181243 originating from Pakistan) seminal roots were divided into three zones according their developmental stage. Transcript changes by RNA-seq in response to water deficit were measured.	Water potential
PRJNA629999	Genomic Evolution of Drought Adaptive Stomata of Wild Cereals	Molecular evidence for adaptive evolution of drought tolerance in wild cereals	Illumina HiSeq 2500	Drought is a major environmental stress threatening biodiversity and human civilization. Grasses cover more than 40% of the world land area and provide habitats for many animal species and represent the main source of grain and forage. Securing staple food for humans and animal feed (e.g. Wheat and barley) by future crop improvement depends on wild progenitors of cereal crops. However, the ecological and evolutionary significance of their wild relatives was not comprehensively studied in an integrated physiological, transcriptomic and genomic framework. Here, we assessed the genetic basis of adaptation and quantified the selection pressures that act on natural variation in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium collected from contrasting African Slope and European Slope of the Evolution Canyon I, Israel. We report that hot-dry savannoid tropical African Slope contrasting with the abutting cool humid temperate European slope, has shaped the distinct stomatal and photosynthetic traits of H. spontaneum, T. dicoccoides and Brachypodium, which have strong genomic and transcriptomic basis for stomatal regulation, photosynthesis, and drought tolerance. Moreover, polyploidy may provide drought adaptive advantages to tetraploid B. hybridum at African Slope. We highlight the value of evaluating wild relatives in search of novel alleles and provides clues to resilience mechanisms underlying crop adaptations to abiotic stress. This study will provide useful information for the breeding of resilient wheat and barley in a changing global warming climate with higher temperature and more frequent drought events	Drought
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).	Water potential
PRJNA748178	Hordeum vulgare breed:wild barley Genome sequencing and assembly	Genome architecture and diverged selection shaping pattern of genomic differentiation in wild barley	Illumina NovaSeq 6000	High-quality genome sequencing and assembly of 2 wild barley from Evolutionary Canyon. And the transcriptome data of these 2 wild barley under drought stress.	Drought
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
PRJNA828098	Hordeum vulgare subsp. spontaneum breed:wild barley | cultivar:wild barley Transcriptome or Gene expression	HvbZIP21, a Novel Transcription Factor From Wild Barley Confers Drought Tolerance by Modulating ROS Scavenging	-	the RNA-seq data of cultivated and wild barley	Drought
PRJNA896249	Barley transcriptome in low nitrogen and nitrogen recovery	Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply	Illumina NovaSeq 6000	In this study, the nitrogen efficient variety (W26) and the nitrogen sensitive variety (W20) were treated with low nitrogen stress for 3 days, 18 days, and recover nitrogen 18 days later.	Nitrogen