Development of Disease Resistant Rice Using Whole Genome Sequencing and Standard Breeding Methods

Cultivated rice is the most important staple crop in the world, but diseases cause substantial losses in grain yield and quality. Sheath blight disease caused by the fungus Rhizoctonia solani is the second most important disease in rice. Most U.S varieties are tropical japonica type, but known sources of resistance in this subspecies are rare. Silva et al. (2012) identified candidate SNP associated with resistance to sheath blight by whole genome sequencing. The objectives of this study were to develop SNP-based markers from the information reported by Silva et al. (2012), to validate the markers by selective genotyping in the RiceCAP SB2 mapping population, and to develop and evaluate breeding lines resistant to sheath blight by marker-assisted selection coupled with backcrossing, anther culture, and field assessment methods. A total of 136 SNP-based markers were developed and screened in extreme resistant and susceptible phenotypic groups from the RiceCAP SB2 mapping population. SNPs in reported genomic regions for sheath blight resistance were identified including eight markers located on chromosomes 6, 8, 9, and 12 that were used in a marker-assisted backcrossing strategy by crossing seven different resistant lines to four susceptible U.S. commercial varieties. A total of 45 doubled-haploid (DH) lines were developed from 28 BC2F1 individuals containing different combinations of selected SNPs. Field evaluation of selected DH lines was carried out in 2014 and 2015. Additional evaluations were performed using a mist chamber to reproduce optimal conditions for disease development. Fourteen DH lines containing different combinations of resistant alleles from chromosomes 2, 6, 8, 9 and 12 showed high levels of resistance after inoculation with R. solani. Results from this research suggest that development of disease resistant rice can be successfully accomplished using whole genome sequencing information combined with standard breeding approaches.