Mapping of qChalk1 controlling grain chalkiness in japonica rice

BackgroundRice 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 resultsIn this study, two japonica rice cultivars with similar grain shapes but different grain chalkiness rates were crossed and the F-2 and BC1F2 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 BC1F2 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.ConclusionA QTL controlling grain chalkiness qChalk1 was detected in both F-2 and BC1F2 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.

Automated summary

This study aimed to map the QTLs controlling grain chalkiness in japonica rice by crossing two cultivars and performing QTL-seq analysis. A QTL controlling grain chalkiness, qChalk1, was detected in both F-2 and BC1F2 segregating populations, and it was located in a 1.1 Mb genomic region on chromosome 1.