Candidate Gene Sequence Analyses toward Identifying Rsv3-Type Resistance to Soybean Mosaic Virus

Rsv3 is one of three genetic loci conferring strain-specific resistance to Soybean mosaic virus (SMV). The Rsv3 locus has been mapped to a 154-kb region on chromosome 14, containing a cluster of five nucleotide-binding leucine-rich repeat (NB-LRR) resistance genes. High sequence similarity between the Rsv3 candidate genes challenges fine mapping of the locus. Among the five, Glyma14g38533 showed the highest transcript abundance in 1 to 3 h of SMV-G7 inoculation. Comparative sequence analyses were conducted with the five Rsv3 candidate NB-LRR genes from susceptible (rsv-type) soybean [Glycine max (L.) Merr.] cultivar Williams 82, resistant (Rsv3-type) cultivar Hwangkeum, and resistant lines L29 and RRR. Sequence comparisons revealed that Glyma14g38533 had far more polymorphisms than the other candidate genes. Interestingly, Glyma14g38533 gene from Rsv3-type lines exhibited 150 single-nucleotide polymorphism (SNP and six insertion-deletion (InDel) markers relative to rsv-type line, Furthermore, the polymorphisms identified in three Rsv3-type lines were highly conserved. Several polymorphisms were validated in 18 Rsv3-type resistant and six rsv-type susceptible lines and were found associated with their disease response. The majority of the polymorphisms were located in LRR domain encoding region, which is involved in pathogen recognition via protein-protein interactions. These findings associating Glyma14g38533 with Rsv3-type resistance to SMV suggest it is the most likely candidate gene for Rsv3.