Epistatic interactions of three loci regulate flowering time under short and long daylengths in a backcross population of rice.

The short-day plant rice varies greatly in photoperiod sensitivity (PS) for flowering. The hybrid F(1) from a cross between the day-neutral pure line EM93-1 and the weedy rice accession SS18-2 had stronger PS than SS18-2. Some BC(1) (EM93-1/F(1)) segregates were even more sensitive to photoperiod than the F(1), as indicated by later flowering or no flowering after 250 days under a 14-h long daylength. A genome-wide scan identified the quantitative trait loci Se (7.1), Se (7.2) and Se (8) for PS from the BC(1) population, with all alleles that inhibit flowering derived from SS18-2. These three loci regulate the time of flowering under long daylength through their main effects, and di- and trigenic epistases. Under a 10-h short daylength, the regulation is through Se (7.1) and Se (8) main effects and digenic epistases involving all three loci. The short daylength not only nullified the main effect of Se (7.2), but also changed its epistatic effects from inhibiting flowering under long daylength to promoting flowering. The epistases indicate that genes underlying the three PS loci work in the same pathway for the control of flowering. Many non-flowered BC(1)s were the trigenic heterozygote; this suggests that the three PS loci are also involved in genetic control of critical daylength.