Natural Variation of the <i>RICE FLOWERING LOCUS T 1</i> Contributes to Flowering Time Divergence in Rice

<div><p>In rice (<i>Oryza sativa</i> L.), there is a diversity in flowering time that is strictly genetically regulated. Some <i>indica</i> cultivars show extremely late flowering under long-day conditions, but little is known about the gene(s) involved. Here, we demonstrate that functional defects in the florigen gene <i>RFT1</i> are the main cause of late flowering in an <i>indica</i> cultivar, Nona Bokra. Mapping and complementation studies revealed that sequence polymorphisms in the <i>RFT1</i> regulatory and coding regions are likely to cause late flowering under long-day conditions. We detected polymorphisms in the promoter region that lead to reduced expression levels of <i>RFT1</i>. We also identified an amino acid substitution (E105K) that leads to a functional defect in Nona Bokra RFT1. Sequencing of the <i>RFT1</i> region in rice accessions from a global collection showed that the E105K mutation is found only in <i>indica</i>, and indicated a strong association between the <i>RFT1</i> haplotype and extremely late flowering in a functional <i>Hd1</i> background. Furthermore, SNPs in the regulatory region of <i>RFT1</i> and the E105K substitution in 1,397 accessions show strong linkage disequilibrium with a flowering time–associated SNP. Although the defective E105K allele of <i>RFT1</i> (but not of another florigen gene, <i>Hd3a</i>) is found in many cultivars, relative rate tests revealed no evidence for differential rate of evolution of these genes. The ratios of nonsynonymous to synonymous substitutions suggest that the E105K mutation resulting in the defect in <i>RFT1</i> occurred relatively recently. These findings indicate that natural mutations in <i>RFT1</i> provide flowering time divergence under long-day conditions.</p>