Genome-wide association study identifies novel associations with barley yellow dwarf virus and soil-borne wheat mosaic virus resistance in winter wheat association mapping panel

Viral pathogens adversely affect wheat (Triticum aestivum L.) development and are responsible for significant wheat yield losses. Barley yellow dwarf virus (BYDV) is one of the most serious worldwide virus threats to cereal crops. Soil-borne wheat mosaic virus (SBWMV) has been present in the Great Plains and responsible for wheat damage for over a century. Identification of additional sources of genetic resistance is paramount to combat the potential damage from these viruses. We constructed a panel of 269 winter wheat cultivars and breeding lines to assess the resistance to naturally occurring BYDV and SBWMV in a Kansas nursery. These lines were sequenced using exome and promoter capture identifying over 640,000 variants for association analysis with visual disease severity ratings. We found 10 and seven significant regions affecting resistance to BYDV and SBWMV, respectively. These regions include the Bdv2 and Sbwm1 loci, as well as novel loci affecting virus resistance. Most of the novel associations are rare, with effect sizes ranging from 5% to 22%. We performed a survey of the viral population present in the disease nursery, which confirmed the presence of both BYDV and SBWMV and revealed differences in virus population from year to year. Additionally, it suggested that co-infections of multiple viruses are common, demonstrating the need for breeding lines harboring resistance to multiple viruses. Deployment of these novel genetic resistance regions in combination with existing resistance loci should allow for increased resistance and potentially more sustainable viral control and reduce the risks associated with wheat yield loss due to these viruses.