QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice (Oryza sativa L.)

Grain appearance quality traits, measured as grain length (GL), grain width (GW), length to width ratio (LWR), grain thickness (GT) and the percentage of grain with chalkiness (PGWC), as well as 1 000-grain weight (TGW), are very important factors that contribute to rice grain quality and yield. To detect quantitative trait loci (QTLs) affecting these traits, we developed a set of recombinant inbred lines (RILs) derived from Gang46B (G46B) and K1075, a G46B introgression line with lower PGWC. Based on a linkage map containing 33 simple sequence repeat (SSR) markers, a total of 15 additive QTLs governing six measured traits were identified on 4 chromosomes across two environments. Of these, the five major QTLs which controlled GW, LWR, GT, PGWC, and TGW, each explaining up to 44.30, 55.29, 62.30, 30.94, and 28.78% of the variation, respectively, were found in the same interval of RM18004–RM18068 on chromosome 5. The G46B alleles contributed to the increase in GW, GT and PGWC at all loci, as well as the increase in TGW at its major QTL locus. Significant interactions between additive QTL and the environment were found at most loci, in which the largest, accounting for 15.06% of variation, was observed between qPGWC-5 and the environment. A total of 15 epistasis QTLs were detected for all the traits, and GL, GW and PGWC had significant epistasis QTLs based on environment interactions with minor effects. These results are valuable for future map-based cloning of the QTLs and the collaborative improvement of G46B in grain appearance quality and yield.