Exploratory genomic sequence analysis reveals structural differences at key loci for growth habit, seed dormancy, and rust resistance in barley

Barley (Hordeum vulgare L.) is a major cereal grain with uses in the feed, food, and malting industries. Growth habit, seed dormancy, and disease resistance are important considerations when selecting germplasm for production or release. With the ever-increasing availability of sequencing technologies, a deeper understanding of the genes underlying these key traits is within reach. In the present case study, the VRN-H1 (HvBM5A), SD2 (HvMKK3), and the novel stem and stripe rust resistance quantitative trait locus (QTL) described by Hernandez et al. (Hernandez et al. Phytopathology 110:1082–1092, 2020b) were investigated. These loci in three advanced barley inbred genotypes were the focus of the present study using next-generation sequencing. The intent behind the study was the identification and exploration of possible causal sequence variation in the genotypes within the context of the whole gene or QTL region. The sequence data was used to identify an intron one deletion in the HvBM5A sequence of the spring genotype that was conserved in the winter and facultative genotypes. Interestingly, a tandem duplication of the HvMKK3 sequence was identified in one of the genotypes, Thunder, that merits further investigation. Finally, 13 high confidence genes were identified within the Morex V3 reference genome in proximity to the rust QTL identified previously. Sequence variation between all tested genotypes was identified for 11 of the genes. This study explored structural and sequence variation of key genes in barley development and outlined directions for future research. The remaining, unexplored genome sequence will be a resource for identifying allelic variation and will contribute to the growing barley pangenome.