Allelic diversity of flowering-time regulatory gene Hd3a in rice

Abstract

ABSTRACTFlowering time (FT) of rice (Oryza sativa L.) marks its transition from vegetative to reproductive stage. The FT is controlled by many internal and external factors, where Hd3a is the main florigen regulating FT under short-day conditions. This study was designed to identify the different types of Hd3a promoter and genic haplotypes using 2,638 rice accessions and to detect genetic polymorphisms that are diagnostic to FT. Haplotype analysis was conducted for the promoter and genic region of Hd3a. The FT data were analyzed to reveal associations with genic and promoter polymorphisms. The analysis revealed 12 novel promoter haplotypes and four previously identified genic haplotypes based on 36 polymorphic sites. A high haplotype diversity was reported in both promoter (0.78) and genic (0.67) regions. The 12-bp InDel in the promoter, which was previously defined as diagnostic for FT, could not be generalized to predict FT in the current rice panel. The cis-regulatory elements (CRE) belonging to 32 transcription factor families (TFF) were identified in the promoter, of which four TFF families were related to regulation of reproduction, and two of these families had changed in some accessions because of single nucleotide polymorphisms (SNPs). Of the 36 polymorphic sites used to identify haplotypes, none could be generalized as diagnostic to serve as potential site(s) for marker development. Two SNPs on the Hd3a promoter that caused changes in TFFs could possibly be target sites to study Hd3a expression.