Fine mapping of DTH3b, a minor heading date QTL potentially functioning upstream of Hd3a and RFT1 under long-day conditions in rice

Abstract

Flowering time or heading date in rice is an important agronomic trait that determines cultivation area and cropping season of a given variety. The genes/loci that have minor effect on the heading date are believed to play a critical role in adaptation of rice to different geographical regions and are preferred by breeders. Previously, we detected a stable minor-effect quantitative trait locus, qDTH-3b (for Days to heading 3b; hereafter referred to as DTH3b), using a small population consisting of recombinant inbred lines derived from a cross between the japonica cv. Asominori (Aso) and the indica cv. IR24. However, its precise location remains to be defined. In this study, we fine-mapped DTH3b by using advanced backcrossing lines and explored its role in regulating the heading date. First, we constructed a BC4F2 population by backcrossing a chromosome segment substitution line (CSSL23) with Aso as a recurrent parent. Then, we developed a near-isogenic line (NIL) from this population by marker-assisted selection. This NIL has the genetic background of Aso but carries a 12-cM DTH3b-containing chromosome segment from IR24. Compared with Aso, the NIL showed 6.9-day delay in flowering time and 63.8 % lower seed maturation rate under long-day (LD) conditions, whereas there was no significant difference between the NIL and Aso under short-day conditions. Using a total of 1500 Asominori/NIL F2:3 or F3:4 late-heading families grown under LD conditions, we finally dissected DTH3b to a single Mendelian factor and delimited it to a 46-kb genomic region which contains seven open reading frames. Further, our quantitative real-time PCR analysis indicated that transcription level of Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T 1), the two florigen genes, was significantly lower in the NIL than in Aso, suggesting that DTH3b functions upstream of Hd3a and RFT1 under LD conditions. We propose that DTH3b Aso positively regulates flowering time and contributes to adaptation of rice to the north. Cloning and then manipulation of DTH3b can be a useful approach to optimize flowering time in rice breeding.