RiceCAP: Progress in Identifying QTL for Sheath Blight Resistance and Milling Yield.

The RiceCAP project was initiated to utilize genomics to address two recalcitrant breeding traits that are economically important to the US rice industry. Sheath blight disease resistance (SB) and rice milling yield (MY) are both complexly inherited traits, sensitive to environmental fluctuations, and require labor intensive methods for phenotyping. Development of germplasm and breeding methods that will facilitate the creation of new rice cultivars improved for these two traits will benefit rice farmers and millers. Seven mapping populations were developed to identify QTL associated with SB and MY that varied from interspecific crosses, to wide indica/japonica crosses, to elite/elite breeding lines. The populations varied in how they were developed: through pedigree advance of RILs, backcross populations, or double haploid progeny. Some 900 SSRs were scored on the parentals to identify a set of polymorphic markers and, depending on the population, 123 to 325 progeny were phenotyped in replicated multi-environment trials. New methods were developed for evaluating SB and quantifying grain dimensions and grain fissuring, components of MY. Because MY is influenced not only by genetics and growing environment, but also post-harvest handling methods, greater progress was made in identifying QTL for SB, a trait more easily phenotyped. Although a number of QTL were identified for SB, a region on the short arm of chromosome 9 that explained 24% of the variance in resistance was validated in several populations. No such major QTL was identified for MY. Outcomes of this research include development of genotyped mapping populations that can be phenotyped for other traits, hundreds of SSRs that are polymorphic in elite US breeding material, RILs in adapted backgrounds that possess novel SB and MY QTL, QTL that can be used in marker assisted selection, robust phenotyping methods, and access to newly introduced  wild species of rice.