QTL‐Seq Associated With Grain Elongation in Rice (Oryza sativa L.) Using Bulked Segregant Analysis (BSA) Approach

ABSTRACT Quantitative trait locus (QTL) identification is the prerequisite for an effective molecular plant breeding programme for introgression of genes of interest via marker‐assisted selection (MAS) technology. The bulk segregant analysis (BSA) is a high‐throughput QTL mapping approach to rapidly identify genomic loci regulating the trait of interest. QTL‐Seq identifies candidate genomic regions more efficiently and entails an improved understanding of the molecular mechanisms underlying the traits. Among the various grain quality characteristics, grain elongation (GE) is one of the most important and targeted traits of basmati rice. GE is the most desirable feature of basmati rice that is influenced by starch properties. The inheritance of GE in rice has not been evidently illuminated because of its composite and variable pattern. In this study, we reported the QTLs responsible for GE using a QTL‐seq (bulked segregant analysis + whole genome resequencing) approach based on the F2 population of the rice crop. Genome‐wide SNP profiling of extreme phenotypic bulks from the F 2 population of Basmati 370 and Pusa Basmati 1121 identified the genomic regions on Chromosomes 1, 2, 3 and 6. These genomic regions were further validated using CAPS/dCAPS markers in the F 3 population of rice. Identified markers can be used in future rice improvement programmes to enhance the export potential of basmati rice with improved GE with distinct starch properties.