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

Abstract

In rice (Oryza sativa L.), there is a diversity in flowering time that is strictly genetically regulated. Some indica 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 RFT1 are the main cause of late flowering in an indica cultivar, Nona Bokra. Mapping and complementation studies revealed that sequence polymorphisms in the RFT1 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 RFT1. We also identified an amino acid substitution (E105K) that leads to a functional defect in Nona Bokra RFT1. Sequencing of the RFT1 region in rice accessions from a global collection showed that the E105K mutation is found only in indica, and indicated a strong association between the RFT1 haplotype and extremely late flowering in a functional Hd1 background. Furthermore, SNPs in the regulatory region of RFT1 and the E105K substitution in 1,397 accessions show strong linkage disequilibrium with a flowering time–associated SNP. Although the defective E105K allele of RFT1 (but not of another florigen gene, Hd3a) 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 RFT1 occurred relatively recently. These findings indicate that natural mutations in RFT1 provide flowering time divergence under long-day conditions.

Antagonistic Transcription Factor Complexes Modulate the Floral Transition in Rice

“…This observation suggests the existence of a mechanism that downregulates their expression upon commitment to flowering and that could possibly depend on Ehd1, encoding a common upstream promoter of Hd3a and RFT1 expression (Goretti et al, 2017;Ogiso-Tanaka et al, 2013;Gómez-Ariza et al, 2015). Under our growing conditions, expression of the florigens reached a peak ;12 to 15 d after shifting plants from LD to SD (Galbiati et al, 2016).…”

“…Since seasonal expression of the rice florigens is transient and is strongly reduced upon completion of the floral transition, a plausible biological role for this autoregulatory loop could be to switch off transcription of the florigens upon floral commitment. Alternatively (or in parallel), it could fine-tune the production of Hd3a and RFT1 during photoperiodic induction (Gómez-Ariza et al, 2015;Ogiso-Tanaka et al, 2013). More data will be required to distinguish between these possibilities and validate them, but it is clear that reproductive commitment requires a tight balance between flowering promoting and repressive complexes, whose equilibrium could be controlled by modulating the expression levels of distinct bZIPs by developmental or environmental factors (Tang et al, 2016;Wu et al, 2014;Zhang et al, 2016) or by controlling their activity through phosphorylation (Kagaya et al, 2002;Choi et al, 2005;Furihata et al, 2006).…”

Genetic interactions between diverged alleles of Early heading date 1 (Ehd1) and Heading date 3a (Hd3a)/ RICE FLOWERING LOCUS T1 (RFT1) control differential heading and contribute to regional adaptation in rice (Oryza sativa)

“…Notably, mRNA levels of Hd3a also increased in the transgenic plants (Fig. e), similar to a previous observation (Ogiso‐Tanaka et al ., ). This suggests the existence of feedback regulation of Hd3a through an unknown mechanism.…”

“…() demonstrated that Hd3a has a stronger effect in the cultivar (cv) Kasalath than in cv Nipponbare, but this difference may be attributable to variation in expression or protein function. An RFT1 allele with a single nucleotide polymorphism (SNP) causing an E105K change in the Nona Bokra cultivar probably causes late flowering (Ogiso‐Tanaka et al ., ), but whether this allele is completely nonfunctional remains unclear.…”

Photoperiod sensitivity of very early maturing Sri Lankan rice for flowering time and plant architecture

“…It exhibits a wide range of variation in degree of sensitivity to photoperiod, which controls its growth and flowering (Izawa 2008;Ogiso-Tanaka 2013;Uwatoko et al 2008;Yano et al 2001;Xu et al 2014). Sri Lankan rice varieties also exhibit a wide https://doi.org/10.1515/opag-2017-0061 received October 30, 2016;accepted September 22, 2017 Abstract: Unavailability of information on photoperiod sensitivity of traditional rice is a disadvantage in breeding rice for adaptation to changing climatic conditions and for optimum plant architecture.…”