Quantitative Trait Loci Mapping for Appearance Quality in Short-Grain Rice

Rice (Oryza sativa L.) appearance quality, as defined by both grain shape and lack of chalkiness, are key breeding goals throughout the world's rice-producing areas. To understand the genetic effects on rice appearance quality, we grew a double-haploid (DH) population derived from the cross between two short-grain rice cultivars, japonica Chunjiang 06 (CJ06) and indica Taichung Native 1 (TN1), in both subtropical Hangzhou and tropical Hainan, China. Transgressive segregation was noted for all measured traits: grain length (GL), grain width (GW), length/width ratio (LW), percentage of kernels with chalk (CK), average chalk size (CS) per kernel, and chalkiness degree (CD, calculated as CK x CS). High positive correlations observed between the chalkiness measures (CK, CS, and CD) with GL and GW indicate that grain shape may have pleiotropic effects on grain chalkiness. Nineteen main-effect QTL and nine epistatic interaction pairs were detected for grain chalkiness and shape. Quantitative trait loci (QTL) were on all 12 chromosomes and explained 8.0 to 23.6% of the phenotypic variance observed under the two environments. One chalkiness QTL and one shape QTL had main effects in both locations. However, when epistasis was considered, seven of 10 identified main-effect regions also had epistatic effect on either grain chalkiness or shape. This demonstrated that epistasis plays an important role in determining grain chalkiness, shape, and the association between chalkiness and shape. The identified QTL and epistatic interactions provide further understanding of the genetic basis of grain appearance quality and assistance in improving grain appearance quality of rice through breeding.