Marker-Trait Association Mapping of Sorghum Mosaic Virus Resistance in Sugarcane

Mosaic is a potentially devastating disease of sugarcane that had severe economic impact on Louisiana’s sugarcane industry in the 1920’s and has caused periodic problems ever since. The disease is vectored by migrating aphids that transmit Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) in a non-persistent manner. Mosaic in Louisiana is currently caused by strains of SrMV. Mosaic has been controlled primarily by developing resistant cultivars. Recently, mosaic was detected in some near-commercial clones in the cultivar selection program. This prompted extensive screening of breeding program parent populations that detected infiltration of susceptibility and revealed the need for more effective methods to breed and select resistant cultivars. Therefore, marker-trait association was performed using a genome-wide association study (GWAS) on a diversity panel of 213 clones from the Louisiana sugarcane breeding program to identify candidate genes responsible for SrMV resistance that might serve as resistance markers. The panel previously phenotyped for resistance via mechanical inoculation, was genotyped using genotyping by sequencing-derived SNP markers. A mixed linear model was employed using population structure (Q) and kinship (K) in a Q-K analysis to inflate type I error at a genome-wide level. Marker-trait association identified 33 significant nonredundant SNPs of which some are known to be associated with virus resistance while others were involved in direct defense mechanisms or induced systemic resistance against various pathogens. This study exhibited the potential use of GWAS to identify putative genes for resistance, which upon validation, can be used to develop markers for marker-assisted breeding of resistant cultivars in the future