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

Cultivated rice is a crop of worldwide significance, but substantial losses in grain yield and quality occur each year due to diseases such as sheath blight, caused by the fungus Rhizoctonia solani. No commercial inbred varieties in the U.S. are resistant to infection by R. solani. We previously identified candidate SNP markers associated with resistance to sheath blight by whole genome sequencing (Silva et al. 2012). We aim to validate the selected SNP markers by development of elite U.S. breeding lines resistant to sheath blight by marker selection coupled with backcrossing, anther culture, and field assessment methods. Candidate SNPs were screened in extreme resistant and susceptible phenotypic groups from the RiceCAP SB2 mapping population. Twenty-one SNPs were identified whose frequencies were statistically greater in the resistant vs. the susceptible group.  A marker-assisted backcrossing strategy was used by crossing four resistant lines containing selected SNPs to four susceptible U.S. commercial varieties. A total of 335 doubled-haploid (DH) lines were developed from 28 BC3F1 populations containing different combinations of selected SNPs. Field evaluation of selected DH lines was carried out in 2014. Nine DH lines containing selected SNPs on chromosomes 6, 9 and 12 showed high levels of resistance after inoculation with R. solani. None of the selected SNPs was present in susceptible DH lines or four commercial varieties. Results from this research suggest that development of disease resistant rice can be successfully accomplished using whole genome sequencing combined with standard breeding methodology.