naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time

• Published in: Journal of experimental botany Vol. 60; no. 4; pp. 1299 - 1308
• Main Authors: Yuan, Yu-Xiang, Wu, Jian, Sun, Ri-Fei, Zhang, Xiao-Wei, Xu, Dong-Hui, Bonnema, Guusje, Wang, Xiao-Wu
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.03.2009; Oxford Publishing Limited (England)
• Subjects: Alleles; Arabidopsis; arabidopsis-thaliana; Biological and medical sciences; Brassica; Brassica rapa; Brassica rapa - genetics; BrFLC1; Cabbages; chinese-cabbage; Cold Temperature; Exons; expression; Flowering; flowering time; Flowers - genetics; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation, Plant; Genes, Plant; Genetic Markers; Genetic variation; Genotype; Genotypes; Introns; l. ssp pekinensis; locus-c flc; Models, Biological; Mutation - genetics; pathways; Phenotype; Plant Proteins - genetics; Plants; Polymorphism, Single Nucleotide - genetics; repressor; Reproducibility of Results; RESEARCH PAPER; Research Papers; Reverse Transcriptase Polymerase Chain Reaction; RNA Splice Sites - genetics; RNA Splicing - genetics; Splicing; splicing pattern; splicing site mutation; Time Factors; trait loci; Vernalization; splicing pattern; flowering time; splicing site mutation; Brassica rapa; BrFLC1; Splicing; Vegetable crop; Gene; Cruciferae; Dicotyledones; Angiospermae; Botany; Flowering; Spermatophyta; Mutation
• ISSN: 0022-0957; 1460-2431
• DOI: 10.1093/jxb/erp010

FLOWERING LOCUS C (FLC), encoding a MADS-domain transcription factor in Arabidopsis, is a repressor of flowering involved in the vernalization pathway. This provides a good reference for Brassica species. Genomes of Brassica species contain several FLC homologues and several of these colocalize with flowering-time QTL. Here the analysis of sequence variation of BrFLC1 in Brassica rapa and its association with the flowering-time phenotype is reported. The analysis revealed that a G→A polymorphism at the 5' splice site in intron 6 of BrFLC1 is associated with flowering phenotype. Three BrFLC1 alleles with alternative splicing patterns, including two with different parts of intron 6 retained and one with the entire exon 6 excluded from the transcript, were identified in addition to alleles with normal splicing. It was inferred that aberrant splicing of the pre-mRNA leads to loss-of-function of BrFLC1. A CAPS marker was developed for this locus to distinguish Pi6+1(G) and Pi6+1(A). The polymorphism detected with this marker was significantly associated with flowering time in a collection of 121 B. rapa accessions and in a segregating Chinese cabbage doubled-haploid population. These findings suggest that a naturally occurring splicing mutation in the BrFLC1 gene contributes greatly to flowering-time variation in B. rapa.