Quantitative Trait Locus Mapping by Whole Genome Re-Sequencing and Analysis of Candidate Genes for Heading Date in Rice

Abstract

Heading date (HD) is a critical traits of rice that significantly affects yield and quality. Although researchers identified major-effect genes that involving in HD, they often have dramatic effects on HD and other vital agronomic traits, making them not easy to be applied in molecular breeding practices. To address this constraint, we focused on identifying genes with minor effects on HD that allow fine-tuning flowering time without significant yield loss. Previously, a 150-recombinant inbred lines (RILs) population was constructed from the early-heading date variety V20B and the lateheading variety CPSLO17, and the line RIL-111 showed the intermediate phenotype of heading date between V20B and CPSLO17. In our work, we applied bulked segregant analysis (BSA) with whole genome re-sequencing (WGS) to map quantitative trait locus (QTL) for heading date. In the results, a minor effect QTL, designated as qDTHR, was identified within the 647.1 kb on chromosome 1 of the F2 population, constructed from RIL-111 and V20B, associating with 14 non-synonymous mutant genes in the interval. The results provide a basis for molecular breeding to improve rice varieties, and lay a foundation for further cloning and functional analysis.