Application of Genotyping-by-Sequencing for Analysis of Breeding Signatures in Russian Spring Barley Collection

The high adaptability of barley (Hordeum vulgare L.) facilitated its cultivation across almost the whole Russian territory and various extreme environments. However, the genetic diversity and population structure of historical Russian barley collections remain poorly characterized at the genomic level. This study provides the first comprehensive genomic description of the barley panel maintained in the GeneAgro seed bank. Using genotyping by sequencing (GBS), we obtained high-quality genotyping data of 158 Russian and 21 foreign accessions. We evaluated genome-wide diversity and population structure, revealing a clear genetic stratification into two-rowed and six-rowed barley. Russian accessions complemented the diversity of the more than 19,000 domesticated barley accessions from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), expanding the representation of germplasm developed specifically for Russian environments and economic demands. To identify genomic regions that may have been shaped by breeding, we scanned the native GeneAgro barley accessions for selective footprints. We detected multiple such regions across the genome. Some were shared by two-rowed and six-rowed barley, while others were specific to one row type, which may reflect differences in their breeding histories. These regions contain candidate genes previously associated with spike architecture, plant morphology, flowering time, fertility, grain color, photosynthesis, seed dormancy and resistance to fungal pathogens. These candidates provide hypotheses for future allele-level and phenotypic studies.