Validation of SNP Markers Selected by Whole Genome Sequencing for Rice Disease Resistance

Sheath blight, caused by the fungus R. solani, is a disease of worldwide significance in rice. We previously identified 333 candidate nsSNPs on 11 chromosomes associated with sheath blight resistance using whole genome sequencing (Silva et al. 2012). The goal of our current research was to validate candidate nsSNPs associated with sheath blight resistance using the RiceCAP SB2 mapping population and a panel of elite varieties with known reaction to R. solani. Ten extreme resistant and susceptible sheath blight lines each of SB2 were used to evaluate 134 candidate nsSNPs that were ranked by ANOVA based on phenotypic and genotypic profiles. A total of 21 nsSNPs were selected that mapped within or near three published QTLs. The selected nsSNPs were assigned to 15 categories based on gene family/ontology. Presence or absence of selected nsSNPs corresponded to known resistant or susceptible phenotypes of 12 additional inbred varieties. Our results suggest that variant selection by whole genome sequencing followed by screening among extreme phenotypic lines of a well characterized mapping population is a useful approach as part of the overall goal to identify markers associated with disease resistance or other traits of interest.