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

Yuan YX, Wu J, Sun RF, Zhang XW, Xu DH, Bonnema G, Wang XW - J. Exp. Bot. (2009)

Bottom Line: The analysis revealed that a G-->A polymorphism at the 5' splice site in intron 6 of BrFLC1 is associated with flowering phenotype.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

ABSTRACT
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.

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Related in: MedlinePlus

Distribution of flowering time and CAPS marker genotype in a collection of B. rapa germplasm (n=121). (A) Plants were grown in the open field; (B) plants were grown in the growth chamber. Black and white columns represent accessions with G and A alleles, respectively, at the Pi6+1 site of BrFLC1. Arrows indicate mean values of lines with an A or G allele. NF indicates lines that did not flower during the experiment.
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fig6: Distribution of flowering time and CAPS marker genotype in a collection of B. rapa germplasm (n=121). (A) Plants were grown in the open field; (B) plants were grown in the growth chamber. Black and white columns represent accessions with G and A alleles, respectively, at the Pi6+1 site of BrFLC1. Arrows indicate mean values of lines with an A or G allele. NF indicates lines that did not flower during the experiment.

Mentions: The remaining 91 accessions with recorded flowering-time phenotypes were genotyped with CAPS FLC1-MvaI to establish the correlation between the splicing site genotype and flowering-time phenotype. In total, 68 accessions had the Pi6+1(A) allele and 53 accessions had the Pi6+1(G) allele. There was a tendency for a relatively late flowering time in Pi6+1(G) accessions and a relatively early flowering time in Pi6+1(A) accessions, in both the open field (Fig. 6A) and the growth chamber (Fig. 6B). The association between the CAPS marker genotype and flowering-time phenotype across 121 B. rapa accessions was calculated. The results revealed that marker genotype was significantly correlated with flowering-time phenotype both in the open-field (r=0.681; (P <0.001) and growth-chamber trials (r=0.654; (P <0.001), respectively. When tested by ANOVA, mean DTF for accessions with the Pi6+1(G) allele is significantly later than those with the Pi6+1(A) allele ((P <0.001), with a delay of 13.8 d in the open-field trial and 15.4 d in the growth-chamber trial (Table 3). To exclude the possibility that the flowering-time difference is due to the genetic background of the materials, the flowering-time phenotype was also tested between different cultivar groups by ANOVA.


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

Yuan YX, Wu J, Sun RF, Zhang XW, Xu DH, Bonnema G, Wang XW - J. Exp. Bot. (2009)

Distribution of flowering time and CAPS marker genotype in a collection of B. rapa germplasm (n=121). (A) Plants were grown in the open field; (B) plants were grown in the growth chamber. Black and white columns represent accessions with G and A alleles, respectively, at the Pi6+1 site of BrFLC1. Arrows indicate mean values of lines with an A or G allele. NF indicates lines that did not flower during the experiment.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2657548&req=5

fig6: Distribution of flowering time and CAPS marker genotype in a collection of B. rapa germplasm (n=121). (A) Plants were grown in the open field; (B) plants were grown in the growth chamber. Black and white columns represent accessions with G and A alleles, respectively, at the Pi6+1 site of BrFLC1. Arrows indicate mean values of lines with an A or G allele. NF indicates lines that did not flower during the experiment.
Mentions: The remaining 91 accessions with recorded flowering-time phenotypes were genotyped with CAPS FLC1-MvaI to establish the correlation between the splicing site genotype and flowering-time phenotype. In total, 68 accessions had the Pi6+1(A) allele and 53 accessions had the Pi6+1(G) allele. There was a tendency for a relatively late flowering time in Pi6+1(G) accessions and a relatively early flowering time in Pi6+1(A) accessions, in both the open field (Fig. 6A) and the growth chamber (Fig. 6B). The association between the CAPS marker genotype and flowering-time phenotype across 121 B. rapa accessions was calculated. The results revealed that marker genotype was significantly correlated with flowering-time phenotype both in the open-field (r=0.681; (P <0.001) and growth-chamber trials (r=0.654; (P <0.001), respectively. When tested by ANOVA, mean DTF for accessions with the Pi6+1(G) allele is significantly later than those with the Pi6+1(A) allele ((P <0.001), with a delay of 13.8 d in the open-field trial and 15.4 d in the growth-chamber trial (Table 3). To exclude the possibility that the flowering-time difference is due to the genetic background of the materials, the flowering-time phenotype was also tested between different cultivar groups by ANOVA.

Bottom Line: The analysis revealed that a G-->A polymorphism at the 5' splice site in intron 6 of BrFLC1 is associated with flowering phenotype.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus