QTL Analysis for Rice Quality-Related Traits and Fine Mapping of .

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BCF and BCF, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BCF population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, , was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, and , exhibited sequence variations between the parents. Furthermore, the variation of leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the gene, thus offering new genetic resources for rice quality improvement.