Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-nucleotide polymorphism matrices for 281 wild barleys (Hordeum vulgare) subsp. spontaneum from the Wild Barley Diversity Collection (WBDC)

ABSTRACT: SNP and indel matrices of whole-genome shotgun data of the Wild Barley Diversity Collection

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Hordeum

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

PROVIDER: PRJEB80165 | EVA | 2024-11-19

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	all.indel.re.accessioned.vcf.gz	Vcf
	all.indel.re.accessioned.vcf.gz.csi	Vcf
	all.indel.re.vcf.csi	Other
	all.indel.re.vcf.gz	Vcf
	all.set2.snp.re.accessioned.vcf.gz	Vcf

Items per page:

1 - 5 of 18

Similar Datasets

Hordeum vulgare subsp. spontaneum breed:wild barley | cultivar:wild barley

Project description:Hordeum vulgare subsp. spontaneum breed:wild barley | cultivar:wild barley Transcriptome or Gene expression

| PRJNA828098 | ENA

Wild barley RNASeq

Project description:Illumina sequencing of RNA from 14 wild barley samples (Hordeum spontaneum)

| PRJEB4947 | ENA

Proteome of Pseudomonas aeruginosa PAO1 wild-type and mutant containing a single nucleotide polymorphism in fusA1

Project description:The gene encoding elongation factor G, fusA1, is frequently mutated in clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis. Recent work has shown that fusA1 mutants often display elevated aminoglycoside resistance due to increased expression of the aminoglycoside efflux pump, MexXY. We isolated a spontaneous gentamicin-resistant fusA1 mutant (FusA1-P443L) in which mexXY expression was increased. We compared the proteome of this fusA1 mutant (EMC1) with the P. aeruginosa PAO1-derived progenitor strain (EMC0) and complemented mutant strain expressing the wild-type fusA1 gene in trans (EMC1*).

2020-09-16 | PXD017266 | Pride

Hordeum vulgare breed:wild barley

Project description:Hordeum vulgare breed:wild barley Genome sequencing and assembly

| PRJNA748178 | ENA

SNP matrices of the wild barley diversity collection WBDC

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

Barley

Project description:A wild barley accession WB-1 and a barley cultivar Golden Promise Raw sequence reads

| PRJNA485436 | ENA

Microarray of barley genes in wheat-barley chromosome addition lines

Project description:Transcript levels of barley genes were examined in the wheat-barley chromosome addition lines having one of six barley chromomes, 2H, 3H, 4H, 5H, 6H and 7H. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Seungho Cho. The equivalent experiment is BB8 at PLEXdb.]

2011-11-22 | GSE33415 | GEO

Construction and analysis of single nucleotide polymorphism-single nucleotide polymorphism interaction networks.

Project description:The study of gene regulatory network and protein-protein interaction network is believed to be fundamental to the understanding of molecular processes and functions in systems biology. In this study, the authors are interested in single nucleotide polymorphism (SNP) level and construct SNP-SNP interaction network to understand genetic characters and pathogenetic mechanisms of complex diseases. The authors employ existing methods to mine, model and evaluate a SNP sub-network from SNP-SNP interactions. In the study, the authors employ the two SNP datasets: Parkinson disease and coronary artery disease to demonstrate the procedure of construction and analysis of SNP-SNP interaction networks. Experimental results are reported to demonstrate the procedure of construction and analysis of such SNP-SNP interaction networks can recover some existing biological results and related disease genes.

| S-EPMC8687305 | biostudies-literature

Identification of microRNAs in response to low potassium stress in the shoots of Tibetan wild barley and cultivated barley [degradome]

Project description:Soil potassium deficiency has become a global problem in agricultural production, seriously restricting crops productions and agricultural sustainable development. Identification of the microRNAs and understanding their functions in response to low K stress will be helpful for developing crop varieties with low K tolerance. Our previous study identified a low K tolerant accession XZ153 from Tibetan wild barley. In this study, small RNA and degradome analysis were performed on two barley genotypes differing in low K tolerance (XZ153, tolerant; ZD9, sensitive) to identify the miRNAs and their targets responding to low K stress. A total of 1108 miRNAs were detected in shoots of XZ153, and ZD9 at 2 d and 7 d after low K stress, and their targets were identified through bioinformatics prediction and degradome analysis. We identified 65 differentially expressed miRNAs responding to low K stress. The results also showed that miR164c, miR169h and miR395a modules could mediate TCA cycle, glycolysis pathway and pentose phosphate pathway responding to low K stress. The osa-miR166g-3p and ghr-miR482b may act as the regulators in Ca2+ signaling pathway in response to low K stress. The methionine salvage cycle involved in ethylene biosynthesis process mediated by miR396c-3p and osa-miR171e-5p might be also involved in responding to low K stress. Some miRNAs, including miR160a, miR396c and miR169h modules, which participated in photosynthesis regulation under low K stress, differed between the two barley genotypes. In conclusion, these exclusively expressed miRNAs and their targets play the crucial roles in low K tolerance.

2020-12-06 | GSE162540 | GEO

Identification of microRNAs in response to low potassium stress in the shoots of Tibetan wild barley and cultivated barley [miRNA-seq]

2020-12-06 | GSE162539 | GEO