Application of genetic and statistical tools for improvement of Louisiana rice

Breeding for grain quality traits and resistance to sheath blight (SB), a disease caused by Rhizoctonia solani Kuhn, are important objectives for the rice (Oryza sativa L.) industry. Grain quality traits and SB resistance play an important role in the economic prosperity of commercial rice markets. The objectives of our research were to: (1) Explore performance and stability for SB resistance among doubled-haploid (DH) lines of the SB2 mapping population using GGE biplots (2) Exploit whole genome sequences of 13 inbred lines to identify non-synonymous SNPs (nsSNPs) and candidate genes for SB resistance. Genotype-by-environment interaction for SB analysis was performed using heritability-adjusted GGE (HA-GGE) biplot. DH lines were evaluated for two years in Louisiana and Arkansas; a single “mega-environment” was identified consisting of the four year-location combinations. HA-GGE biplot analyses identified 11 high and stable DH lines; five susceptible DH lines were also identified with greater stability than the susceptible parent used to develop the SB2 population. Material identified in this study represents a potential source of SB resistance for cultivar development. Two filtering strategies were developed to identify nsSNPs between two groups of known resistant and susceptible lines. More than 200 genes with selected nsSNPs were assigned to 42 categories based on family/gene ontology. Individual alleles of 24 nsSNPs were evaluated by PCR whose presence/absence corresponded to known resistant/susceptible phenotypes of nine additional lines. “Resistant” alleles were detected in two accessions of O. nivara that suggests sources for resistance occur in additional Oryza sp. Results from this study provide a foundation for future marker-assisted breeding of rice for SB resistance