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 |
2013-1-1
|
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 |
2.74
|
Times Cited |
46
|
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 |