Ontology highlight
ABSTRACT:
PROVIDER: PRJEB58296 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Wild Barley Diversity Collection Exome Capture
| PRJNA472251 | ENA
Project description:Genotyping-by-sequencing data of the Wild Barley Diversity Collection
| PRJEB51697 | ENA
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.
2013-05-09 | GSE44293 | GEO
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. 1-2 replications of 8 barley cultivars and 6 wild barley accessions were hybridized to an array designed from 115,003 whole genome shotgun (WGS) contigs of the ‘reference’ genome of cv. Morex
2013-05-09 | E-GEOD-44293 | biostudies-arrayexpress
Project description:Cultivated barley (Hordeum vulgare ssp. vulgare) was domesticated from wild barley (Hordeum vulgare ssp. spontaneum) about 10,000 years ago in the Fertile Crescent. Domestication and intensive breeding have greatly narrowed the genetic diversity of the crop and rendered it vulnerable to various biotic (pathogens and pests) and abiotic (heat, drought, salinity cold, etc.) stresses. Wild barley is a rich source of genetic diversity for many traits and is fully compatible with the cultivated form. To make future gains in barley breeding and also mitigate current stresses, the genetic diversity of wild barley must be exploited. This Wild Barley Diversity Collection (WBDC) consists of accessions collected primarily from the Fertile Crescent, a region where diversity of the subspecies is the highest and large populations are common; however, representative samples were also included from Central Asia, South Central Asia, North Africa, and the Caucasus region. Whole genome sequencing (WGS) at 10x coverage depth was performed on 300 non-redundant accessions of the Wild Barley Diversity Collection (WBDC).
2023-12-01 | PRJEB58296 | EVA
Project description:We provide raw gene sequences of 174 flowering time regulatory genes and gene othologs across a large barley population (895 barley lines) selected from a collection of landrace, cultivated barley, and research varieties of diverse origin. This set represents the whole variety of cultivated barley lifeforms, namely two- and six-row genotypes with winter, spring, and facultative growth habits. We applied a target capture method based on in-solution hybridization using the myBaits® technology (Arbor Biosciences, Ann Arbour, MI, USA) which is based on in-solution biotinylated RNA probes. Baits were designed for flowering time regulatory genes and gene othologs, and used for production of 80mer capture oligonucleotides for hybridization. Genomic DNA was extracted from leaves of a single two-week old barley plant per variety using the cetyl-trimethyl-ammonium bromide (CTAB) method. Physical shearing of genomic DNA was performed with an average size of 275 bp. Library preparation was conducted with KAPA Hyper Prep Kit (KAPA Biosystems, Wilmington, MA). Hybridization of customised RNA baits with capture pools was performed at 65°C for 24 hours. Each pooled sequence capture library was sequenced on an Illumina HiSeq3000 instrument using three lanes to generate paired-end reads per sample. Genome sequencing was conducted at AgriBio, (Centre for AgriBioscience, Bundoora, VIC, Australia).
2019-02-15 | E-MTAB-7362 | biostudies-arrayexpress
Project description:Disease resistance is mediated by specific recognition of pathogen avriulence effectors (AVR) by nucleotide-binding leucine-rich repeat (NLR) receptors. The barley (Hordeum vulgare) mildew locus A (mla) resistance gene homolog 1 (RGH1) encoded NLRs (MLAs) confer isolate-specific resistance to the widespread mildew fungus Blumeria graminis forma specialis hordei (Bgh). In barley, MLA has been subject to extensive functional diversification, resulting in allelic resistance specificities, each recognizing a cognate Bgh AVRa. The by genetic association isolated AVRa1 and AVRa13 effectors belong to the candidate secreted effector protein (CSEP) gene family (Lu et al., 2016). To unravel the complex mechanisms underlying MLA functional diversification in barley and wheat, isolation of numerous Bgh AVRa genes and recognition of their gene products by MLA is necessary. Our here deployed higher resolution genetic association approach identified the Bgh avirulence gene candidate loci AVRa7, AVRa9, AVRa22 and AVRa10 by associating of transcript polymorphisms and AVRa phenotypes from a collection of 27 Bgh isolates. We collected 10 Bgh isolates from a local Bgh population in Cologne in addition to our previous collection of 17 Bgh isolates (Lu et al., 2016).
2019-02-19 | GSE110266 | GEO