Minor QTLs and the temperature during the grain filling stage contributed to the considerable variation in rice eating and cooking quality.

Eating and cooking quality (ECQ) in rice is significantly associated with the temperature during the grain filling stage. Besides major genes, minor QTLs also benefit the improvement of ECQ. To identify minor QTLs for ECQ and evaluate environment effects and QTL by environment interactions (QEIs), a RIL population fixed for Waxy and ALK was grown in three environments: the early season (E1) and the late season (E2) in Nanning, and the middle season in Wuhan (E3). The average daily and nighttime temperatures during the grain filling stage were 28.8 °C and 27.3 °C in E1, 23.4 °C and 22.3 °C in E2, and 28.0 °C and 25.5 °C in E3. Eight ECQ traits were measured in three environments. The comparison of ECQs between E1 and E3, which shared similar high daily temperatures but varied average nighttime temperatures, suggested that high nighttime temperatures may exert a more significant impact on ECQ. Genetic effects, environmental effects, and their interactions each account for substantial phenotype variance of eight traits except for cool paste viscosity (CPV). A total of 40 minor QTLs for ECQ were identified across the three individual environments, but only two QTLs were commonly detected in two environments, indicating a large proportion of minor QTLs are environment-dependent. The G by E model identified 21 QTLs, with eight QTLs involved in QEIs. Most QEIs exhibited the largest positive effects in E2, indicating a favorable environment for ECQ. Furthermore, the most significant QTL for amylose content, qAC9, was validated with a BC