Genome-Wide Identification of Candidate Genes Associated with β-glucan Traits in a Hulled and Hulless Barley (Hordeum vulgare L.) Population

Barley grain is a valuable source of beta-glucan, which is an important component of dietary fiber with significant human health benefits. Although the genetic basis of beta-glucan biosynthesis has been widely studied, a genome-wide association study (GWAS) is still required for a scan of the candidate genes related to the complex quantitative trait based on the high-quality barley reference genome. In this study, a GWAS was conducted using a population composed of 87 barley landraces (39 hulled and 48 hulless, beta-glucan from 2.07% to 6.56%) with 191,098 nucleotide polymorphisms (SNPs) markers to cover the chromosomes with the highest density. The population was divided into four sub-populations (POP1 similar to POP4), and the beta-glucan content in POP2 was significantly higher than that in other groups, in which most of the hulless barley landraces are from Qinghai-Tibet Plateau in China. Among seven SNP markers identified by GWAS, two (SNP2 and SNP3) of them showed positive correlation to beta-glucan trait and the remaining five (SNP1, SNP4, SNP5, SNP6 and SNP7) showed the negative relationship. Two candidate genes linked to SNP7, HORVU7Hr1G000320 and HORVU7Hr1G000040, belong to the nucleotide triphosphate hydrolase superfamily which is probable to affect the activities of beta-glucan synthase. Another candidate gene associated with SNP1, HORVU1Hr1G000010, is possibly involved in sugar response. In conclusion, our results provide new insights into the genetic basis of beta-glucan accumulation in barley grains, and the discovery of new SNP markers distributed in each chromosome and the associated candidate genes will be valuable for the breeding of functional barley varieties with high beta-glucan.