Fine Mapping and Characterization of Quantitative Trait Loci Hd4 and Hd5 Controlling Heading Date in Rice.

Abstract

Fine mapping of Hd4 and Hd5, quantitative trait loci (QTLs) for heading date in rice, was performed by using advanced backcross progeny derived from a cross between a japonica rice variety, Nipponbare, and an indica variety, Kasalath. Hd4 was mapped between restriction fragment length polymorphism (RFLP) markers R46 and C39 in the proximal region of chromosome 7, and Hd5 was mapped between C166 and R902 on the short arm of chromosome 8; both QTLs mapped as single Mendelian factors. We used marker-assisted selection to develop two nearly isogenic lines (NIL), designated NIL(Hd4) and NIL(Hd5), in which small chromosomal segments of Kasalath including Hd4 and Hd5, respectively, each were substituted into the genetic background of Nipponbare. Compared with that of Nipponbare, days-to-heading of NIL(Hd4) and NIL(Hd5) increased under long-day and natural-field conditions, but no differences were observed between those of the two NILs and Nipponbare under short-day conditions. Epistatic interaction was detected between Hd5 and Hd1, a key photoperiod sensitivity QTL, on the basis of an analysis of the F2 population derived from a cross between the NIL(Hd5) and NIL(Hd1). This result suggests that Hd5 is involved in photoperiod sensitivity and may act downstream or upstream of Hd1 in the same photoperiodic pathway. In comparison, the genetic effect of Hd5 was additive to that of Hd2, another key photoperiod-sensitivity QTL, indicating that Hd2 acts in a different photoperiodic pathway other than that of Hd1 and Hd5. The genetic effect of Hd4 was additive to those of Hd1 and Hd2; thus, epistatic interaction between these loci was not detected.