Detection of epistatic interactions of three QTLs for heading date in rice using single segment substitution lines

A library consisting of 1123 single segment substitution lines (SSSLs) in the same genetic back-ground of an elite rice variety Huajingxian74 (HJX74) was evaluated for heading date. From this library, two SSSLs, W23-03-8-9-1 and W15-03-1-31, with substitution segments on chromosome 3 and 2, respectively, were found to have significantly different heading date from the recipient HJX74. For genetic dissection and epistatic interaction of quantitative trait loci (QTLs) for heading date in two SSSLs, three secondary SSSLs with smaller substitution segments and genic pyramiding lines (GPLs) were developed from an F2 segregating population of a cross between the two donor SSSLs, W23-03-8-9-1 and W15-03-1-31, using marker-assisted selection (MAS). The QTL analysis revealed that QTL for heading date detected in SSSL W23-03-08-9-1 was genetically dissected into two QTLs, qHD3-1 and qHD3-2, by overlapping mapping. At the same time, one QTL, qHD2-1 in the donor SSSL W15-03-1-31 was also identified. Analysis of GPLs for heading date showed epistatic interactions between qHD3-1 and qHD3-2, between qHD3-1 and qHD2-1, and between qHD3-2 and qHD2-1. These QTLs and epistatic interactions were confirmed in three cropping seasons under different natural daylength conditions, and their physiological functions for heading date were performed.