Identification of Quantitative Trait Loci for Grain Traits in Japonica Rice

Quantitative trait loci (QTLs) of grain traits were detected to provide theoretical basis for fine mapping and molecular marker-assisted breeding of grain traits in japonica rice. Using an F2 population including 200 individuals derived from a cross combination between two japonica rice DL115 with large grain and XL005 with small grain, the grain length, grain width, grain thickness, ratio of grain length to width and 1 000-grain weight were evaluated in Beijing; and the quantitative trait loci for above five grain traits were identified by composite interval mapping using SSR markers. The results showed that the five grain traits exhibited a normal continuous distribution in F2 population, indicating they were quantitative traits controlled by multiple genes. A total of 16 QTLs conferring the five grain traits were detected on chromosomes 2, 3, 5 and 12, respectively. Eight QTLs, namely qGL3a, qGW2, qGW5, qGT2, qRLW2, qRLW3, qGWT2 and qGWT3, were major QTLs and explained 15.42, 40.89, 13.54, 33.43, 13.82, 13.61, 12.51 and 10.1% of the observed phenotypic variance, respectively. Among them, qGW2, qGT2, qRLW2 and qGWT2 were mapped in same interval RM12776-RM324 on chromosome 2. The marker interval RM12776-RM324 on chromosome 2 was common marker intervals of four major QTLs, and the two SSR markers RM12776 and RM324 would be used in molecular marker-assisted breeding in japonica rice. The modes of gene action were mainly additive and partial dominance. Four QTLs' alleles were derived from small grain parent XL005, and other 12 QTLs' alleles were derived from large grain parent DL115. The alleles from larger parent were showed significant effects to grain length, grain width, grain thickness and 1 000-grain weight.