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Background  Sugarcane mosaic virus (SCMV) disease causes substantial losses of grain yield and forage biomass in susceptible maize cultivars. Maize resistance to SCMV is associated with two dominant genes,  Scmv1  and  Scmv2 , which are located on the short arm of chromosome 6 and near the centromere region of chromosome 3, respectively. We combined both linkage and association mapping to identify positional candidate genes for  Scmv1 .    Results   Scmv1  was fine-mapped in a segregating population derived from near-isogenic lines and further validated and fine-mapped using two recombinant inbred line populations. The combined results assigned the  Scmv1  locus to a 59.21-kb interval, and candidate genes within this region were predicted based on the publicly available B73 sequence. None of three predicted genes that are possibly involved in the disease resistance response are similar to receptor-like resistance genes. Candidate gene–based association mapping was conducted using a panel of 94 inbred lines with variable resistance to SCMV. A presence/absence variation (PAV) in the  Scmv1  region and two polymorphic sites around the  Zmtrx-h  gene were significantly associated with SCMV resistance.    Conclusion  Combined linkage and association mapping pinpoints  Zmtrx-h  as the most likely positional candidate gene for  Scmv1 . These results pave the way towards cloning of  Scmv1  and facilitate marker-assisted selection for potyvirus resistance in maize.

Combined linkage and association mapping reveals candidates for Scmv1, a major locus involved in resistance to sugarcane mosaic virus (SCMV) in maize