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.
Highlights
Soil salinity is a major global environmental factor limiting plant growth and productivity (Allakhverdiev et al, 2000; Ashraf et al, 2015)
Angessa et al (2017) reported transgressive phenotypic segregation for germination rate and biomass at the seedling stage using a doubled haploid (DH) barley population derived from a CM72 Gairdner cross, with both traits controlled by different quantitative trait loci (QTL) on chromosomes 2H and 3H, respectively
A total of 350 barley genotypes selected from a larger set of 594 accessions in a worldwide collection were evaluated for salinity response at the germination stage to map the locations of genes associated with tolerance (Supplementary Tables 1 and 2)
Summary
Soil salinity is a major global environmental factor limiting plant growth and productivity (Allakhverdiev et al, 2000; Ashraf et al, 2015). The germination process begins when a quiescent dry seed imbibes water, and terminates on the emergence of the radicle (Gupta et al, 2019); barley is a model plant for studying the germination stage in monocots (Gorzolka et al, 2016). Depending on their ability to germinate and survive under salinity stress, barley genotypes are either tolerant or sensitive depending on their genetic diversity (Shelden et al, 2013; Shelden et al, 2016; Gupta et al, 2019). A single QTL on chromosome 5H, detected at three salt concentrations, was responsible for 42% of the phenotypic variation (Cattivelli et al, 2002)
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