Mapping of qChalk1 controlling grain chalkiness in japonica rice

Background Rice grain chalkiness is an undesirable characteristic that affects grain quality. The aim of this study was to map QTLs controlling grain chalkiness in japonica rice. Methods and results In this study, two japonica rice cultivars with similar grain shapes but different grain chalkiness rates were crossed and the F 2 and BC 1 F 2 populations were subjected to QTL-seq analysis to map the QTLs controlling the grain chalkiness rate. QTL-seq analysis revealed SNP index differences on chromosome 1 in both of the segregating populations. Using polymorphic markers between the two parents, QTL mapping was conducted on 213 individual plants in the BC 1 F 2 population. QTL mapping confined a QTL controlling grain chalkiness, qChalk1 , to a 1.1 Mb genomic region on chromosome 1. qChalk1 explained 19.7% of the phenotypic variation. Conclusion A QTL controlling grain chalkiness qChalk1 was detected in both F 2 and BC 1 F 2 segregating populations by QTL-Seq and QTL mapping methods. This result would be helpful for further cloning of the genes controlling grain chalkiness in japonica rice.