Identification of SNP Markers Associated with Grain Quality Traits in a Barley Collection (Hordeum vulgare L.) Harvested in Kazakhstan

Abstract

Barley (Hordeum vulgare L.) is a cereal crop traditionally used in animal feed, malting, and food production. In this study, a collection of barley was analyzed according to key grain quality traits, including protein content (GPC), starch content (GSC), extractivity (EX), and grain test weight per liter (TWL). A genome-wide association study (GWAS) was conducted to identify the quantitative trait loci (QTLs) associated with GPC, GSC, EX, and TWL using a collection of 658 barley accessions from the USA and Kazakhstan. The collection was grown at three breeding organizations in Kazakhstan in 2010 and 2011 and genotyped using the 9K SNP Illumina chip. As a result, 18 marker-trait associations (MTAs) for GPC, 19 MTAs for GSC, 12 MTAs for EX, and 27 MTAs for TWL were detected, resulting in 30 identified QTLs. It was shown that the genetic locations of 25 of these 30 QTLs were in similar positions to the QTLs and genes previously reported in the scientific literature, suggesting that the 5 remaining QTLs are novel putative genetic factors for the studied grain quality traits. Five of the most significant SNP markers (p < 2.6 × 10−5) for the studied quality traits identified in the GWAS were used for the development of reliable and informative competitive allele-specific PCR (KASP) genotyping assays. The effectiveness of two assays (ipbb_hv_6 and ipbb_hv_128) was confirmed via validation in a separate collection of barley breeding lines grown in large field plots in northern Kazakhstan. Therefore, these KASP assays can be efficiently used in a marker-assisted selection of grain quality traits in barley breeding.