Detection of quantitative trait loci for white-back and basal-white kernels under high temperature stress in japonica rice varieties

Several quantitative trait loci (QTLs) associated with the apparent quality of brown rice were identified. QTL analysis was carried out using F-2 and F-3 populations derived from a cross between two japonica varieties, Hana-echizen (high quality of brown rice) and Niigatawase (low quality with numerous white-back and basal-white kernels). F2 individuals were grown in paddy fields in 2003, and F3 lines were grown in paddy fields and in a greenhouse to expose them to high temperature stress during the ripening period in 2004. Apparent quality of brown rice was evaluated based on the percentage of white-back and basal-white kernels. Two putative QTLs associated with white-back kernels in the F2 population grown under low temperature conditions in paddy fields in 2003 were identified on chromosomes 3 and 6. The closest SSR markers were RM4512 and RM3034, respectively. One putative QTL associated with basal-white kernels in the F2 population was identified on chromosome 6. The closest marker was RM3034. Two putative QTLs associated with white-back kernels in the F3 population grown under high temperature conditions in paddy fields in 2004 were identified on chromosomes 4 and 6. The closest SSR markers were RM3288 and RM3034, respectively. One putative QTL associated with white-back plus basal-white kernels in the F3 population grown under high temperature stress in the greenhouse was identified on chromosome 6. The closest marker was RM3034. The QTLs identified near RM3034 on the short arm of chromosome 6 contributed most to the apparent quality of brown rice. The QTLs identified near RM4512 and RM3288 which also affected the apparent quality of brown rice, were detected in either the F2 or F3 Population. The QTLs identified in the present study should be useful for marker-assisted selection to breed varieties with a high apparent quality of brown rice, especially varieties with tolerance to kernel damage due to high temperature stress during the ripening period.