Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice

A new quantitative trait locus (QTL), Hd9, controlling rice heading date was detected in a BC4F2 backcross population derived from a cross between a japonica rice variety, Nipponbare, as the recurrent parent, and an indica variety, Kasalath, as the donor parent. Hd9 was precisely mapped on the short arm of chromosome 3 as a single Mendelian factor; progeny testing of BC4F3 lines derived from BC4F2 plants revealed that it co-segregated with the RFLP marker S12021. In addition, a nearly isogenic line (NIL) of the target QTL, NIL(110), in which a small chromosomal segment of Kasalath including Hd9 was substituted into the genetic background of Nipponbare, was selected from the progeny based on marker-assisted selection. Days to heading of NIL(Hd9) increased under long-day and natural field conditions at Tsukuba, but remained almost the same under short-day conditions as that of the isogenic control, Nipponbare. Analysis of F-2 populations derived from crosses between NIL(H(19) and either NIL(Hd1) or NIL(Hd2) revealed that the phenotypic gene effect of H(19 was additive to that of lid] and Hd2. This result suggests that no epistatic interaction was involved. Based on these results, we discussed the biological function of Hd9.