QTL Mapping and Q×E Interactions of Grain Cooking and Nutrient Qualities in Rice Under Upland and Lowland Environments

Abstract Grain cooking and nutrient qualities are the most important components of rice ( Oryza sativa L.) quality. A doubled haploid (DH) population from a cross between two japonica cultivars was used to examine the phenotypic values and potential QTLs for the quality traits. The cooking and nutrient quality traits, including the amylose content (AC), the gel consistency (GC), the gelatinization temperature (GT), and the protein content (PC), in rice grown under upland and lowland environments were evaluated. Significant differences for AC, GC, GT, and PC between upland and lowland environments were detected. The phenotypic values of all four traits were higher under upland environment than lowland environment. The value of PC under upland environment was significantly higher (by 37.9%) than that under lowland environment. This suggests that upland cultivation had large effect on both cooking and nutrient qualities. A total of seven QTLs and twelve pairs of QTLs were detected to have significant additive and epistatic effects for the four traits. Significant Q × E interaction effects of two QTLs and two pairs of QTLs were also discovered. The general contribution of additive QTLs ranged from 1.91% to 19.77%. The Q × E interactions of QTLs QGt 3 and QAc 6 accounted for 8.99% and 47.86% of the phenotypic variation, respectively, whereas those of the 2 pairs of epistatic QTLs, QAc 6- QAc 11b and QAc 8- QAc 9, accounted for 32.54% and 11.82%, respectively. Five QTLs QGt 6b, QGt 8, QGt 11, QGc 1, and QPc 2, which had relatively high general contribution and no Q × E interactions, were selected to facilitate the upland rice grain quality breeding.