RRC ID 31825
Author Ogiso-Tanaka E, Matsubara K, Yamamoto S, Nonoue Y, Wu J, Fujisawa H, Ishikubo H, Tanaka T, Ando T, Matsumoto T, Yano M.
Title Natural variation of the RICE FLOWERING LOCUS T 1 contributes to flowering time divergence in rice.
Journal PLoS ONE
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.
Volume 8(10)
Pages e75959
Published 2013
DOI 10.1371/journal.pone.0075959
PII PONE-D-13-20508
PMID 24098411
PMC PMC3788028
MeSH Amino Acid Sequence Amino Acid Substitution Chromosomes, Plant / genetics Flowers / growth & development* Gene Expression Regulation, Developmental Genomics Haplotypes Linkage Disequilibrium Molecular Sequence Data Mutation* Oryza / genetics* Oryza / growth & development* Plant Proteins / chemistry Plant Proteins / genetics* Polymorphism, Single Nucleotide Quantitative Trait Loci / genetics Time Factors
IF 2.766
Times Cited 21
WOS Category PLANT SCIENCES
Resource
Rice W0106 W0120 W0157 W0574 W0593 W0630 W1294 W1666 W1715 W1807 W1865 W1943 W1944 W1981 W2003 W2014 W2263 W2265 Oryzabase