New sources and identification of haplotypes for the soybean durable Rsv4 resistance gene for implementation of a breeding strategy and as a framework for map-based cloning.. Identification of haplotypes at the Rsv4 region associated with resistance to soybean mosaic virus in soybean

Rsv4, a Soybean mosaic virus (SMV) resistance gene, is interesting because it appears to confer durable resistance in soybean. With an objective to understand the molecular nature of this interesting gene, we defined the Rsv4-residing chromosomal region at a single recombination-event level in an F2 population consisting of 309 individuals. The information obtained was used to quickly determine that Haman and Ilpumgeomjeong are new sources of Rsv4 alleles based on virus reaction screening and genetic analyses. These two new sources along with three other Rsv4-containing accessions were used us to analyze sequence variations in the vicinity of the Rsv4 locus in a high-depth genome-resequenced population of 19 soybean accessions. Association analysis indicated that one major biological signal associated with the Rsv4 resistance exists within the ~120 kb interval defined by the genetic mapping. As somewhat expected for a durable resistance gene, the 120-kb interval do not contain genes homologous to members of known major resistance gene families. However, peak SNPs was not associated with coding sequences of the genes annotated on the current reference genome sequence. Linkage disequilibrium analysis refined the ~120 kb signal to a region spanning ~70 kb having at least two distinct Rsv4 haplotypes. Therefore, we have provided additional sources for the implementation of a breeding strategy for durable SMV resistance in soybean and a framework for eventual elucidation of this elusive durable resistance gene.