Analysis of minor quantitative trait loci for eating and cooking quality traits in rice using a recombinant inbred line population derived from two indica cultivars with similar amylose content

Improvement of eating and cooking quality (ECQ) traits is a major breeding target in indica rice due to market demand. In this study, amylose content, gel consistency, gelatinization temperature and 15 parameters from the viscosity profile were analyzed for quantitative trait loci (QTLs) with main effect, epistatic effects and their environmental interactions with ECQ, using 237 recombinant inbred lines (RILs) derived from a cross between indica cultivars Huahui 3 and Zhongguoxiangdao. Sixty-six QTLs were found across 2 years, of which 17 loci were detected in both years. No QTL was detected at the Wx locus, possibly because of allelism between the parents. A QTL cluster in the interval ALK6–RM549 on chromosome 6 had the largest effect on alkali spreading value, pasting time, time needed from initial viscosity increase to peak viscosity, pasting temperature, temperature needed from initial viscosity increase to peak viscosity, and pasting viscosity, and a minor effect on six traits (parameters): gel consistency, amylose content, peak viscosity, cool paste viscosity, breakdown viscosity and setback viscosity. Moreover, the Alk gene was responsible for two traits studied for the first time, namely peak temperature and pasting viscosity, controlled by QTLs qBAtime6 and qVA6, respectively. QTL clusters on other chromosomes showed similar characteristics to the Alk locus, although the variations explained were relatively minor. The OsBEIIb gene locus is linked to the interval RM301–RM424, which defined an important QTL cluster on chromosome 2. Moreover, a study using the same RIL population showed that a QTL for protein content and Rapid Visco Analyzer parameters was tightly linked to the same gene and directly affected ECQ. These findings not only demonstrate the complexity of ECQ, but also have important implications for map-based cloning of the underlying genetic factors and for breeding for rice quality.