Association mapping resolving the major loci Scmv2 conferring resistance to sugarcane mosaic virus in maize

Sugarcane mosaic virus (SCMV) is one of the most damaging virus diseases in maize. Two major loci, Scmv1 and Scmv2, have been identified in many studies across a broad spectrum of germplasm by linkage mapping. In this study, we undertook a genome-wide association study (GWAS) in a maize association panel comprising 504 diverse inbred lines with over 556,000 SNP markers in three environments. Extensive phenotypic variation of resistance to SCMV was observed in the association panel. GWAS identified five genes significantly associated with resistance to SCMV. A cluster of four genes was detected near or within the Scmv2 region on chromosome 3 (bin 3.05). GRMZM2G116204, which encoded auxin binding protein and resided within the fine-mapped Scmv2 region, was predicted as the most likely candidate gene for Scmv2. In conclusion, we found that GWAS along with linkage analyses are effective approaches to the mapping of resistance to SCMV and to the subsequent identification of causal genes.