Unraveling the Genetics of Seed Dormancy in Barley Using Genome-Wide Association and Biparental Mapping

Abstract

Seed dormancy is the delay or inability of viable seeds to germinate under favorable conditions. The differential expression of dormancy levels in barley (Hordeum vulgare L.) seeds impacts malt quality. While dormant genotypes are required to avoid the incidence of preharvest-sprouting, genotypes with low dormancy are needed for uniform germination of seeds during malting. The objective of this study was to determine the genetic basis underlying seed dormancy in spring barley using genome-wide association mapping (AM) and linkage mapping. A panel of 3,072 elite U.S. spring barley breeding lines from eight breeding programs participating in the USDA-NIFA Barley Coordinated Agricultural Project and 193 F1-derived doubled-haploid lines from the cross `Stander'/ `Robust' were used to map QTL controlling seed dormancy. The AM panel and the doubled-haploid population were genotyped with SNP markers using the Illumina Golden Gate assay. Four mixed linear models that controlled population structure and kinship were used for the AM analyses, while composite interval mapping was used for the analysis of the biparental population. Our results confirmed the existence of marker-trait associations delineating two QTL regions in the long arm of chromosome 5H (5HL) using the AM panel, and a large effect QTL in the same region using the biparental population. The locations and effects of these marker-trait associations are congruent with previously mapped QTL for seed dormancy and demonstrate the two mapping methods effectively targeted the same genetic regions on the barley genome and provide insights about the genetics of seed dormancy.