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

Loss of a Premature Stop Codon in the Rice Wall-Associated Kinase 91 (<i>WAK91</i>) Gene Is a Candidate for Improving Leaf Sheath Blight Disease Resistance

Leaf sheath blight disease (SB) of rice caused by the soil-borne fungus Rhizoctonia solani results in 10–30% global yield loss annually and can reach 50% under severe outbreaks. Many disease resistance genes and receptor-like kinases (RLKs) are recruited early on by the host plant to respond to pathogens. Wall-associated receptor kinases (WAKs), a subfamily of receptor-like kinases, have been shown to play a role in fungal defense. The rice gene WAK91 (OsWAK91), co-located in the major SB resistance QTL region on chromosome 9, was identified by us as a candidate in defense against rice sheath blight. An SNP mutation T/C in the WAK91 gene was identified in the susceptible rice variety Cocodrie (CCDR) and the resistant line MCR010277 (MCR). The consequence of the resistant allele C is a stop codon loss, resulting in an open reading frame with extra 62 amino acid carrying a longer protein kinase domain and additional phosphorylation sites. Our genotype and phenotype analysis of the parents CCDR and MCR and the top 20 individuals of the double haploid SB population strongly correlate with the SNP. The susceptible allele T is present in the japonica subspecies and most tropical and temperate japonica lines. Multiple US commercial rice varieties with a japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high-yielding commercial varieties to reduce yield losses incurred by the sheath blight disease