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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

Discovery of five splicing patterns. SpG represents the constitutive splicing pattern; SpA1–SpA3 indicate alternative splicing patterns; solid boxes, exons; the dotted box, a missing exon; dotted lines, introns that are missing completely or partly compared with the constitutive spliced transcripts; continuous lines, retention of intron parts; the numbers 25 and 55 indicate the number of nucleotides retained in intron 6; the shaded region, the transcribed region from exon 7 for different splicing patterns. Premature stop codons (12–14nt for SpA1 and SpA2) are indicated by an arrow. In SpA3, an alternative splice acceptor site in the last exon is used, leading to a deletion of exon 6 sequences.
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fig4: Discovery of five splicing patterns. SpG represents the constitutive splicing pattern; SpA1–SpA3 indicate alternative splicing patterns; solid boxes, exons; the dotted box, a missing exon; dotted lines, introns that are missing completely or partly compared with the constitutive spliced transcripts; continuous lines, retention of intron parts; the numbers 25 and 55 indicate the number of nucleotides retained in intron 6; the shaded region, the transcribed region from exon 7 for different splicing patterns. Premature stop codons (12–14nt for SpA1 and SpA2) are indicated by an arrow. In SpA3, an alternative splice acceptor site in the last exon is used, leading to a deletion of exon 6 sequences.

Mentions: DTF (days to flowering) is represented as means ±standard error. CC, Chinese cabbage. PC, pak choi. SpG and SpA represent the G or A genotype at the Pi6+1 site (for specific explanation, see Fig. 4). DTF is average flowering time from five individuals grown in the growth chamber.


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)

Discovery of five splicing patterns. SpG represents the constitutive splicing pattern; SpA1–SpA3 indicate alternative splicing patterns; solid boxes, exons; the dotted box, a missing exon; dotted lines, introns that are missing completely or partly compared with the constitutive spliced transcripts; continuous lines, retention of intron parts; the numbers 25 and 55 indicate the number of nucleotides retained in intron 6; the shaded region, the transcribed region from exon 7 for different splicing patterns. Premature stop codons (12–14nt for SpA1 and SpA2) are indicated by an arrow. In SpA3, an alternative splice acceptor site in the last exon is used, leading to a deletion of exon 6 sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Discovery of five splicing patterns. SpG represents the constitutive splicing pattern; SpA1–SpA3 indicate alternative splicing patterns; solid boxes, exons; the dotted box, a missing exon; dotted lines, introns that are missing completely or partly compared with the constitutive spliced transcripts; continuous lines, retention of intron parts; the numbers 25 and 55 indicate the number of nucleotides retained in intron 6; the shaded region, the transcribed region from exon 7 for different splicing patterns. Premature stop codons (12–14nt for SpA1 and SpA2) are indicated by an arrow. In SpA3, an alternative splice acceptor site in the last exon is used, leading to a deletion of exon 6 sequences.
Mentions: DTF (days to flowering) is represented as means ±standard error. CC, Chinese cabbage. PC, pak choi. SpG and SpA represent the G or A genotype at the Pi6+1 site (for specific explanation, see Fig. 4). DTF is average flowering time from five individuals grown in the growth chamber.

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