QTL Analysis of Rice Grain Size Using Segregating Populations Derived from the Large Grain Line

Grain size affects the yield and quality of rice. The large grain line (LGL), showing a large grain size and japonica -like genome, was selected in the breeding field. The 94 F 2 plants derived from a cross between LGL and Hanareum (a high-yielding tongil-type variety) were used for the quantitative trait loci (QTL) analysis of grain length (GL), grain width (GW), and grain thickness (GT). A linkage map of the F 2 population, covering 1312 cM for all 12 chromosomes, was constructed using 123 Fluidigm SNP markers. A total of nine QTLs for the three traits were detected on chromosomes two, three, four, six, and seven. Two QTLs for GL on chromosomes two and six explained 17.3% and 16.2% of the phenotypic variation, respectively. Two QTLs were identified for GW on chromosomes two and three, and explained 24.3% and 23.5% of the phenotypic variation, respectively. The five QTLs for GT detected on chromosomes two, three, five, six and seven, explained 13.2%, 14.5%, 16.6%, 10.9%, and 10.2% of the phenotypic variation, respectively. A novel QTL for GT, qGT2 , was validated on the same region of chromosome two in the selected F 3 population. The QTLs identified in this study, and LGL, could be applied to the development of large-grain rice varieties.