Exploratory genomic sequence analysis reveals structural differences at key loci for growth habit, seed dormancy, and rust resistance in barley
  • 03/04/2024

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

Lead author: Christopher Massman (formerly from the Crop and Soil Science Department at Oregon State University)

Barley is an important cereal grain with uses in the feed, food, and malting industries. Vernalization requirement, seed dormancy, and disease resistance are important considerations when selecting barley varieties for breeding 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, VRN-H1 (causal gene HvBM5A), SD2 (causal gene HvMkk3), and a 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. VRN-H1 and SD2 are key determinants of vernalization requirement and seed dormancy, respectively. These loci in three barley varieties were the focus of the present study using next-generation sequencing. One of the varieties was winter planted, one was spring planted, and one was facultative. Facultative varieties do not require vernalization but maintain the low temperature tolerance of traditionally winter planted barleys. This allows them to be planted in either the winter or spring seasons for added flexibility. 

The goal of this study was to identify differences in the genetic sequences of these loci across the three varieties that could be responsible for differences in plant growth and development. The majority of the genetic sequence for each of the tested varieties was identified and recorded. This sequence data was used to identify a deletion in one of the non-coding regions of the HvBM5A gene of the spring genotype that was present in the winter and facultative genotypes. Interestingly, the HvMkk3 gene was found to be duplicated in the variety, Thunder. 

Thunder is a popular barley in the malting industry and this finding merits further investigation. Finally, thirteen genes were identified using the Morex reference genome in proximity to the rust QTL identified previously. Sequence variation between all tested genotypes was identified for eleven of these genes. Additional study is required to precisely identify which of these genes is responsible for differences in rust resistance. This study explored variation at the sequence level of key genes in barley development. The remaining, unexplored, genome sequence will be a resource for identifying additional variation and will contribute to the growing barley pangenome.

This work was published in the 31 January 2024 edition of Genetic Resources and Crop Evolution.
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