Detection of QTLs with main, epistatic and QTL × environment interaction effects for rice grain appearance quality traits using two populations of backcross inbred lines (BILs)

Abstract Quantitative trait loci (QTLs) of rice ( Oryza sativa L.) grain appearance traits with additive, epistatic and QTL × environment (QE) interaction effects were studied using a mixed-model-based composite interval mapping (MCIM) method and two populations of back cross inbred lines (BILs) with a common maternal parent. In each of the populations, two or three main effects of QTLs were detected for grain length, width, length to width ratio, length of cooked rice, elongation ratio, elongation index and water absorption traits. The main effects of QTLs explained 12.4–43.9% and 20.4–50.4% of the variation of measured traits in the two populations, respectively. Some identified QTL clusters suggested that co-located QTL or maybe genes with pleiotropic effects could control these traits. When the QTLs detected for cooked versus milled rice were compared, it was found that the main QTLs with large effects for appearance in milled rice were on chromosomes 3 and 5, but those for appearance of cooked rice traits were on chromosome 6 close to the Wx gene. The phenotypic variations which were explained by the effects of the additive × additive × environment interaction (AAE) and additive × additive epistasis (AA) QTLs were less significant than those of the main QTLs. We conclude that although the major genes are frequent determinants of the rice grain appearance traits, the interactions between genes of minor effects may culminate in sizable effects on rice grain appearance traits. The information obtained in this study could be useful for manipulating the QTLs of these traits by molecular marker-assisted selection.