Novel Allelic Variation of Hd1 Involves in Photoperiod Sensitivity of Rice

Abstract Heading date is one of determinants of rice germplasms adapting to photoperiods. Genes regulating flowering time are extensively studied. Hd1 was identified as a determinant of the flowering time of rice. Understanding the haplotypes of rice Hd1 gene is critical for molecular breeding. Here, a major effect on chromosome 6 regulating flowering time in rice was identified by QTL-seq approach. Sequence and mRNA expression analyses indicated allelic variations of Hd1 on chromosome 6 were the major reason for phenotypic divergences between wild-type (Nipponbare) and mutant (HSS) lines. The Hd1 allele in HSS has a single-base substitution and a 36bp insertion compared to Nipponbare, which introduced an amino acid motif (RRHQR) to the C-terminus of zinc finger domain in Hd1. This weak functional Hd1 allele makes HSS less sensitive to photoperiod causing earlier flowering in long-day and later flowering in short-day compared to the wild type. Sequence and diurnal expression analyses confirmed the reduced the expression of Hd1 affected other flowering time regulators including Hd3a and DTH8 in both long-day and short-day. Expression pattern analyses demonstrated that DTH8 has a roughly positive correlation with Hd1. Our results indicated that Hd1 can positively regulate the expression of DTH8 and the abundance of DTH8-Hd1 complex in response to day length, and the DTH8-Hd1 complex subsequently controls flowering time in rice by regulating Hd3a.