Dataset Information

SNP matrices of the wild barley diversity collection WBDC

ABSTRACT: 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).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Hordeum Vulgare

SUBMITTER: IPK Gatersleben - Leibniz Institute of Plant Genetics and Crop Plant Research

PROVIDER: PRJEB58296 | EVA | 2023-12-01

REPOSITORIES: EVA

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Dataset's files

Source:

			Action	DRS
	all_chromosome.filter.snp.accessioned.vcf.gz	Vcf
	all_chromosome.filter.snp.accessioned.vcf.gz.csi	Vcf
	all_chromosome.filter.snp.vcf.csi	Other
	all_chromosome.filter.snp.vcf.gz	Vcf

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Project description:Grape powdery mildew (PM), caused by the biotrophic ascomycete Erysiphe necator, is a devastating fungal disease that affects most Vitis vinifera cultivars. We have previously identified a panel of V. vinifera accessions from Central Asia with partial resistance to PM that possess a Ren1-like local haplotype. In this study we show that in addition to the typical Ren1-associated late post-penetration resistance, these accessions display a range of different levels of disease development suggesting that alternative alleles or additional genes contribute to determining the outcome of the interaction with the pathogen. To identify potential Ren1-dependent transcriptional responses and functions associated with the different levels of resistance, we sequenced and analyzed the transcriptomes of these Central Asian accessions at two time-points of PM infection. Transcriptomes were compared to identify constitutive differences and PM-inducible responses that may underlie their disease resistant phenotype. Responses to E. necator in all resistant accessions were characterized by an early up-regulation of 13 genes, most encoding putative defense functions, and a late down-regulation of 32 genes, enriched in transcriptional regulators and protein kinases. Potential Ren1-dependent responses included a hotspot of co-regulated genes on chromosome 18. We also identified 81 genes whose expression levels and dynamics correlated with the phenotypic differences between the most resistant accessions ?Karadzhandahal?, DVIT3351.27, and O34-16 and the other genotypes. This study provides a first exploration of the functions associated with varying levels of partial resistance to PM in V. vinifera accessions that can be exploited as sources of genetic resistance in grape breeding programs. Eight varieties (7 resistant to powdery mildew, 2 of which are V. vinifera spp. sylvestris, 5 of which are V. vinifera spp. sativa) are infected with powdery mildew (E. necator) at two timepoints (1 dpi and 5 dpi) with three replicates for each timepoint for each condition (uninfected vs. infected), for a total of 96 samples

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SNP matrices of the wild barley diversity collection WBDC

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