Abstract：To reveal the differentiation of phenotypic values and QTLs for grain quality traits in rice, we evaluated a doubled haploid (DH) population from a cross between two japonica cultivars for milling quality traits including brown rice (BR), milled rice (MR) and head milled rice (HR) and grain appearance traits including grain length (GL), grain breadth (GB), grain length- breadth ratio (LWR), and chalkiness (C) cultivated under upland and lowland environments. The analysis of variance (ANOVA) between upland and lowland environments for all the traits showed that HR, GL, GB and C were more easily influenced by environment than BR, MR and LWR. The values of BR, MR and HR of the lowland parent Yuefu were higher than that of the upland parent IRAT109 under lowland environment. But under upland environment, the BR and MR for the parents were both declined by 5.8% and 5.5% for IRAT109，and 11.7% and 11.5% for Yuefu respectively. The values of GL, GB and C were all reduced under upland condition than that under lowland condition for all the two parents while the value of LWR had the opposite tendency. Compared to lowland environment, some quality traits changed such as an increased HR, decreased C, and thinner grain shape when cultivated under upland environment. Using a complete genetic linkage map with 165 molecular markers covering 1535 cM, QTLs for these traits were mapped under upland and lowland environments. A total of eleven additive QTLs and ten pairs of epistatic QTLs associated with BR, MR, HR, GL, GB, LWR, and C were detected. It was found that epistasis was an important genetic component underlying BR, MR, HR and C. The result also showed that MR, GL, GB and LWR were less affected by upland environment. However, HR was affected greatly by upland environment. Four intervals on chromosomes 1, 3, 6 and 7 were found to contain multiple QTLs(co-localization). Eight common QTLs for these traits across different studies were also revealed. These co-localized QTLs and common QTLs will facilitate marker- assisted selection for grain quality traits in rice breeding.
