Epistasis Effects of Chalkiness and Application Using Marker-Assisted Recurrent Selection in Indica Rice

Chalkiness is a complex quantitative trait regulated by both genetic and environmental factors. Reducing chalkiness has long been a research focus in rice genetics and breeding. A total of 108 markers on/closely linked to starch biosynthesizing genes, grain shape and chalkiness QTLs were used to detect interactions affecting chalkiness. A total of 30 and 39 marker pairs with significant bigenic epistasis were identified for percentage of grain with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), respectively, of which 16 were commonly found in both traits. Using markers associated with chalkiness and marker pairs with significant epistatic effects as candidate predictors increased the coefficient of determination (R2) of the best multiple regression models for predicting both traits. GBSSI, SSIIa and the interaction between GBSSI and GBSSII were consistently identified in optimal models, indicating their critical roles in regulating rice chalkiness. R2 for DEC and PGWC ranged from 36.5% to 42.7% and from 52.9% to 73.8% in two environments, respectively. PGWC decreased significantly from 38.9% to 15.10% after three cycles using marker-assisted recurrent selection (MARS). This study suggests that epistasis contributes substantially to the regulation of chalkiness, and demonstrates that MARS can effectively improve chalkiness without imposing obvious negative impacts on eating quality.