Ontology highlight
ABSTRACT:
PROVIDER: PRJEB58296 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| all_chromosome.filter.snp.vcf.csi | Other | |||
| all_chromosome.filter.snp.vcf.gz | Vcf |
Items per page: 5 1 - 2 of 2 |
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Project description:SNP and indel matrices of whole-genome shotgun data of the Wild Barley Diversity Collection
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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
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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
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