Project description:Barley (Hordeum vulgare L.) is amongst the oldest domesticated crop plants and remains one of the world's most important crop species. It is diploid with a haploid genome of 5.1 gigabases (Gb), twice the size of those of human and maize, and closely related to the most widely grown crop, hexaploid wheat. To meet global demand for food, feed and fibre, it is commonly agreed that reference genome sequences of our crop plants are urgently required to enable genome-assisted crop improvement. As part of the The International Barley Genome Sequencing Consortium (IBSC) we present here raw data obtained from Illumina (GAII) sequencing of RNA samples from nine different barley cultivars for the purpose of Single Nucleotide Polymorphism (SNP) discovery.
Project description:To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a chromatin immunoprecipitation of H3K27me3 followed by high-throughput sequencing (ChIP-seq) in barley endosperm at 16 days after pollination.
Project description: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.
Project description:To provide comprehensive spatiotemporal information about biological processes in developing grains of cultivated barley (Hordeum vulgare subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from 4 to 32 days after pollination.
Project description:Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012). B. graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to address the temporal regulation of membrane trafficking associated gene expression in barley-powdery mildew interactions. We created an isogenic panel of immune signaling mutants to address three main questions: (i) which Blumeria secreted proteins are differentially regulated in response to different compromised genotypes, (ii) which barley membrane trafficking genes are altered in response to pathogen attack, and (iii) how are these genes interacting across genotypes and infection stages.
Project description:Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to identify small RNAs (sRNAs) from both barley and Bgh that regulate gene expression both within species and cross-kingdom.
Project description:There is growing evidence for the prevalence of DNA copy number variation (CNV) and its role in phenotypic variation in recent years. Comparative genomic hybridization (CGH) was used to explore the extent of this type of structural variation in the barley genome. In a panel of 14 genotypes including domesticated cultivars and wild barleys, we found that 14.9% of all the sequences on the array are affected by CNV. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. A substantial portion (37%) of the CNV events are present in both wild and domesticated barley. CNVs are enriched in telomeric regions for all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. CNV affected 9.5% of the coding sequences represented on the array. The genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases, suggesting the potential for CNV to influence variation for responses to biotic and abiotic stress. The analysis of CNV breakpoints indicated that DNA repair mechanisms of double-strand breaks (DSBs) via single-stranded annealing (SSA) and synthesis-dependent strand annealing (SDSA) play an important role in the origin of many structural changes in barley. Here we present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance.
Project description:Tibetan hulless barley (Hordeum vulgare L.) growing in the Qinghai-Tibet Plateau is the major staple food crop for the Tibetans. However, because of soil salinity, the agricultural production of hulless barley is challenged by salinity stress. Here, we perform data-independent acquisition (DIA)-based quantitative proteomics of two barley cultivars with differential salinity tolerance under salt stress
Project description:Purpose: The powdery mildew fungus, Blumeria graminis, is an obligate biotrophic pathogen of cereals and has significant impact on food security (Dean et al., 2012. Molecular Plant Pathology 13 (4): 414-430. DOI: 10.1111/j.1364-3703.2011.00783.x). Blumeria graminis f. sp. hordei (Bgh) is the causal agent of powdery mildew on barley (Hordeum vulgare L.). We sought to discover novel transcripts expressed following barley infection with blumeria.