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)

► Rice appearance grain traits QTL detected in two BILs populations in 2 years. ► Two or three main effects QTLs were detected for every traits. ► Main QTLs of milled and cooked traits were located on chromosomes 3, 5 and 6, respectively. ► Some identified QTL clusters suggested pleiotropic effects could control these traits. ► The phenotypic variation explained by AAE and AA QTLs effects were smaller than main QTLs.