Dataset Information

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.).

ABSTRACT: Barley seeds need to be able to germinate and establish seedlings in saline soils in Mediterranean-type climates. Despite being a major cereal crop, barley has few reported quantitative trait loci (QTL) and candidate genes underlying salt tolerance at the germination stage. Breeding programs targeting salinity tolerance at germination require an understanding of genetic loci and alleles in the current germplasm. In this study, we investigated seed-germination-related traits under control and salt stress conditions in 350 diverse barley accessions. A genome-wide association study, using ~24,000 genetic markers, was undertaken to detect marker-trait associations (MTA) and the underlying candidate genes for salinity tolerance during germination. We detected 19 loci containing 52 significant salt-tolerance-associated markers across all chromosomes, and 4 genes belonging to 4 family functions underlying the predicted MTAs. Our results provide new genetic resources and information to improve salt tolerance at germination in future barley varieties via genomic and marker-assisted selection and to open up avenues for further functional characterization of the identified candidate genes.

SUBMITTER: Mwando E

PROVIDER: S-EPMC7047234 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (<i>Hordeum vulgare</i> L.).

Mwando Edward E Han Yong Y Angessa Tefera Tolera TT Zhou Gaofeng G Hill Camilla Beate CB Zhang Xiao-Qi XQ Li Chengdao C

Frontiers in plant science 20200221

Barley seeds need to be able to germinate and establish seedlings in saline soils in Mediterranean-type climates. Despite being a major cereal crop, barley has few reported quantitative trait loci (QTL) and candidate genes underlying salt tolerance at the germination stage. Breeding programs targeting salinity tolerance at germination require an understanding of genetic loci and alleles in the current germplasm. In this study, we investigated seed-germination-related traits under control and sal ...[more]

PMID: 32153619

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Project description:BackgroundFrost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure.ResultsGWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress.ConclusionsHaplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.

Dataset Information

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.).

Publications

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (<i>Hordeum vulgare</i> L.).

Similar Datasets

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