Genetic diversity and genome-wide association analysis of the hulled/naked trait in a barley collection from Shanghai Agricultural Gene Bank.

Barley is one of the most important cereal crops in the world, so the research and use of barley germplasm are very important for global food security. Although a large number of barley germplasm have been collected globally, their specific genetic compositions are not well understood, and in many cases their origins are disputed. In this study, barley germplasm from Shanghai Agricultural Gene Bank were genotyped by genotyping-by-sequencing (GBS) technology and their genetic relationships were investigated. In addition, genome-wide association study (GWAS) was carried out for the hulled/naked grain trait. The results showed that these barley germplasm could be roughly divided into three categories according to phylogenetic analysis, which was generally consistent with the classification of the traits of row type and hulled/naked grain, among which the combination of the two-rowed and naked traits was relatively rare. Population structure analysis showed that the whole barley population could be divided into four sub-populations (SPs), the main difference from previous classifications being that that the two-rowed and hulled genotypes were sub-divided into two SPs. The GWAS analysis of the hulled/naked trait showed that many associated loci were unrelated to the nud locus, indicating that there might be new loci controlling the trait. A KASP marker was developed for one exon type SNP on chromosome 7. Genotyping based on the KASP assay was consistent with that based on SNPs, indicating that the gene of this locus might be associated with the hulled/naked trait. The above work not only lays a good foundation for the future utilization of this barley germplasm population, but also provides new loci and candidate genes for the hulled/naked trait.