A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa
- Jian Wu†1,
- Keyun Wei†1,
- Feng Cheng1,
- Shikai Li2,
- Qian Wang2,
- Jianjun Zhao3,
- Guusje Bonnema3 and
- Xiaowu Wang1Email author
© Wu et al.; licensee BioMed Central Ltd. 2012
Received: 10 February 2012
Accepted: 14 August 2012
Published: 28 August 2012
Flowering time is an important trait in Brassica rapa crops. FLOWERING LOCUS C (FLC) is a MADS-box transcription factor that acts as a potent repressor of flowering. Expression of FLC is silenced when plants are exposed to low temperature, which activates flowering. There are four copies of FLC in B. rapa. Analyses of different segregating populations have suggested that BraA.FLC.a (BrFLC1) and BraA.FLC.b (BrFLC2) play major roles in controlling flowering time in B. rapa.
We analyzed the BrFLC2 sequence in nine B. rapa accessions, and identified a 57-bp insertion/deletion (InDel) across exon 4 and intron 4 resulting in a non-functional allele. In total, three types of transcripts were identified for this mutated BrFLC2 allele. The InDel was used to develop a PCR-based marker, which was used to screen a collection of 159 B. rapa accessions. The deletion genotype was present only in oil-type B. rapa, including ssp. oleifera and ssp. tricolaris, and not in other subspecies. The deletion genotype was significantly correlated with variation in flowering time. In contrast, the reported splicing site variation in BrFLC1, which also leads to a non-functional locus, was detected but not correlated with variation in flowering time in oil-type B. rapa, although it was correlated with variation in flowering time in vegetable-type B. rapa.
Our results suggest that the naturally occurring deletion mutation across exon 4 and intron 4 in BrFLC2 gene contributes greatly to variation in flowering time in oil-type B. rapa. The observed different relationship between BrFLC1 or BrFLC2 and flowering time variation indicates that the control of flowering time has evolved separately between oil-type and vegetable-type B. rapa groups.
Brassica rapa is a genus comprising a variety of vegetables such as Chinese cabbage (ssp. pekinensis), pak choi (ssp. chinensis), and turnip (ssp. rapa) as well as oil crops including turnip rape (ssp. oleifera) and sarson (ssp. tricolaris). Flowering time is an important trait in Brassica vegetables because early flowering often leads to low yield and low quality. It is also important for oilseed rape varieties as they are divided into “winter” and “spring” types according to their different flowering times and responsiveness to vernalization. Winter types must be exposed to cold to transition from the vegetative growth stage to the reproductive stage, while this is not necessary for the spring types, which are generally grown in shorter-season areas.
In Arabidopsis, studies of natural variation demonstrated that the vernalization requirement is largely conferred by two dominant genes, FRI and FLC [1–3]. FRI acts upstream of FLC to positively regulate FLC expression . FLC encodes a MADS-box transcription factor that functions as a repressor of flowering by inhibiting downstream floral integrator genes [5–9]. Vernalization represses the expression of FLC and induces flowering. The promoter and first exon of FLC are sufficient to initiate the repression of FLC during vernalization, while the maintenance of repression requires additional regions of the gene body .
There are four copies of FLC in B. rapa[11–13]. They are located on chromosomes A10 (BraA.FLC.a, named BrFLC1), A02 (BraA.FLC.b, named BrFLC2), and A03 (BraA.FLC.c, named BrFLC3 and BraA.FLC.d, named BrFLC5) owing to polyploidy evolution [13, 14]. Colinearity analysis indicated that BrFLC1, BrFLC2, and BrFLC3 are located in three R blocks (Xiaowu Wang et al. unpublished data), which is consistent with the three FLC copies that would be expected after a triplication event [12–15]. BrFLC5 is located between blocks I and J . Multiple gene copies are thought to be responsible for dose-regulated expression, and the mechanism appears to affect variations in flowering time in Brassica crops . These replicated genes may have additive effects. Depending on the specific cross studied, different alleles of the various FLC paralogs may exert different effects on flowering time. In a backcross population derived from two recombinant inbred lines, created from a cross between Per and R500, a quantitative trait locus(QTL) co-located with BrFLC1 explained more of the flowering time variation than BrFLC2. It was also reported that a naturally occurring splicing variation in BrFLC1 was associated with variation in flowering time in B. rapa, and this locus contributed most of its effect to late flowering . However, Zhao et al. studied a doubled haploid (DH) population derived from a cross between pak choi and yellow sarson, and reported BrFLC2 as a candidate gene for a major QTL for flowering time and the vernalization response in B. rapa. The decreased transcript level of BrFLC2 upon cold treatment provided further evidence for this hypothesis.
Since there are apparent contradictions in the proposed roles of BrFLC1 and BrFLC2, we analyzed sequence variation of BrFLC1 and BrFLC2 in a large collection of B. rapa accessions, and the relationship between sequence variations and flowering time. Our results indicate that among the various B. rapa crop types, there are different genetic controls of flowering time.
Flowering time variation
Flowering time variation among the germplasm collection of B. rapa
No. of Acc.
Var. range (d)
Var. range (d)
ssp. chinensis var. purpurea
Nucleotide polymorphisms at the BrFLC2gene
Nine B. rapa accessions used to sequence BrFLC2 in this study
annual, very early
Relationship between flowering time and nucleotide polymorphisms in BrFLC2
Flowering time variation among germplasm collection of B. rapa
No. of lines
DTF Open field
No. of lines
DTF Open Field
108 ± 25b
105 ± 45 b
85 ± 12a
84 ± 25 a
132 ± 20a
137 ± 22 a
92 ± 25a
83 ± 33 a
112 ± 12b
115 ± 35 b
83 ± 12a
83 ± 18 a
119 ± 26
118 ± 30
90 ± 15a
93 ± 23 a
72 ± 4b
62 ± 18 b
78 ± 8b
70 ± 12 b
We further analyzed the 159 accessions using the previously reported BrFLC1MvaI CAPS marker, which can distinguish A/G alleles located at the splicing site of exon 4 and intron 4 of BrFLC1. The A allele results in alternative splicing, which is correlated with early flowering in B. rapa. BrFLC1 allelic variation was observed in both vegetable-types and oil-types, showing A, G, and heterozygous alleles (Table 3). The flowering time in vegetable-type B. rapa was significantly correlated with the A/G genotype; accessions with the A genotype had an average flowering time of 108 DTF in the open field experiment and 105 DTF in the greenhouse experiment. Accessions with G genotype flowered at 132 DTF in the open field experiment and 137 DTF in the greenhouse experiment. However, there was no significant relationship between the BrFLC1 A/G genotype and variations in flowering time among oil-type B. rapa accessions. The mean DTF of the 38 oil-type accessions with the A allele was 85 in the open field experiment and 84 in the greenhouse experiment. In contrast, the average flowering time of 11 accessions with the G allele was 92 DTF in the open field experiment and 83 DTF in the greenhouse experiment. Similar to BrFLC2, early flowering controlled by BrFLC1 was dominant over late flowering (Table 3).
Flowering time in BC 2 DH progenies with different BrFLC2 alleles
83 ± 1.64cde
78 ± 3.13ef
80 ± 2.41def
70 ± 2.00 g
76 ± 1.52 fg
85 ± 1.00bcd
89 ± 0.00abc
91 ± 2.17ab
92 ± 2.19a
83 ± 1.37cde
Alternative splicing of BrFLC2
An InDel polymorphism across exon 4 and intron 4 of BrFLC2 was discovered in a subset of oil-type B. rapa accessions, including ssp. oleifera and ssp. tricolaris. In this study, we investigated its relationship with flowering time both in a collection of B. rapa natural accessions and in a BC2DH population.
Plants need to sense their environment and initiate flowering at the appropriate time to ensure successful fertilization and production of abundant seeds. There is considerable variation in the flowering time among, but also within, natural populations, as we observed in the present study of a B. rapa germplasm collection. In A. thaliana, the FRI gene was shown to be a major determinant of flowering time variation in the natural population through its effects on the expression of FLC[21, 22]. An InDel variation in the COL1 gene was reported to be correlated with variation in flowering time in B. nigra. In A. thaliana, FLC encodes a MADS-box transcription factor that acts as a dose-dependent flowering repressor [9, 22]. Four copies of the FLC gene in B. rapa increase the potential variation in flowering time . In our previous study, we identified a splicing site polymorphism Pi6 + 1(G/A) in BrFLC1 that was significantly associated with the naturally occurring variation in flowering time in B. rapa. In that study, we examined 96 lines, six of which were oil-types. In contrast, half of the lines examined in the present study were oil-types. Because there were so few oil-types in our previous study, we did not identify that oil-type and vegetable-type B. rapa showed different relationships between alleles of BrFLC1 and flowering time variation. In the present study, we could not detect any effect of allelic variation in BrFLC1 Pi6 + 1(G/A) on the variation in flowering time for oil-type B. rapa, including ssp. oleifera and ssp. tricolaris. However, we detected an InDel polymorphism across exon 4 and intron 4 of BrFLC2 among the accessions of ssp. oleifera and ssp. tricolaris. This sequence polymorphism was not detected in any of the other vegetable-type B. rapa subspecies. Furthermore, this allelic variation was strongly associated with variations in flowering time in oil-type B. rapa. Zhao et al.  suggested that BrFLC2 was a major determinant of flowering time variation in B. rapa. However, there were no firm conclusions from several studies on BrFLC1[12, 18] and BrFLC2. Since BrFLC1 and BrFLC2 have specific roles in controlling flowering time in different B. rapa groups, we deduced that there was an independent evolution of the control of flowering time, at least the control of the vernalization pathway, between oil-type B. rapa including ssp. oleifera and ssp. tricolaris and the other vegetable-type and turnip B. rapa subspecies. The oil-type B. rapa formed an evolutionary branch that was independent of other B. rapa species in an analysis of molecular phylogeny based on whole genome re-sequencing data generated from 108 accessions (Dr. Xiaowu Wang, unpublished data). This indicates that the evolutionary history of oil-type B. rapa is isolated from that of the vegetable-type subspecies. The fact that the deletion mutation of BrFLC2 was absent from vegetable-type B. rapa indicates that this mutation may have arisen after the division of oil-type from vegetable-type B. rapa, while the splicing site mutation of BrFLC1 may have arisen before this division and been maintained during their respective evolutions.
Relationships between naturally occurring alternative splicing variants and flowering time variation have been reported for the FLC gene in A. thaliana and Capsella bursa-pastoris, and for BrFLC1 in B. rapa. Alternative splicing variants were also reported for BrFLC5 in a biennial oilseed cultivar, although their relationship with flowering time was not addressed . In the present study, we detected three alternative splicing patterns for BrFLC2 in the yellow sarson accession L143, which has a homozygous deletion allele of BrFLC2. All three alternative splicing variations led to the insertion of premature stop codons in the transcripts. The alternative splicing pattern iii of BrFLC2 has been reported by Zhao et al.  using DH lines derived from a cross between the same yellow sarson accession and a pak choi accession, and was deduced to be a regulatory mechanism for the differential expression of BrFLC2 in response to vernalization. In the present study, the transcripts from splicing pattern iii were the minor fraction of transcripts from the deletion allele of BrFLC2. This could be due to the different cultivation conditions in the two studies, as the plants were not cold-treated in this study. A possible reason for the differential expression in response to cold treatment might be that alternative splicing transcripts were eliminated by the mRNA surveillance system. Eukaryotes have an mRNA surveillance system to eliminate the transcripts that are deliberately spliced to contain premature stop codons as a part of their intricate autoregulatory system .
B. rapa is a mesohexaploid that has undergone whole genome triplication after divergence from a common ancestor of A. thaliana. During the diploidization process afterwards, which involved considerable gene loss, some gene family showed preferential retention such as circadian clock genes , and also many of flowering time genes. It has been speculated that polyploidy and lost of the duplicated genes may have contributed to the evolution of variations in flowering time, a key component of morphological diversity . After the hexaploid process, the three sub-genomes of the ancestor were partitioned into LF, MF1, and MF2 . BrFLC1 is located in LF, BrFLC2 in MF2, and BrFLC3 in MF1 , while BrFLC5 is located in the homologous region generated from an α-duplication event that occurred before the diversification of Arabidopsis-Brassica. The fact that a non-functional BrFLC1 mutation introduces early flowering time variation in vegetable-type B. rapa, while the non-functional BrFLC2 introduces early flowering time variation in oil-type B. rapa, indicates that these two loci of FLC in B. rapa play different roles in different groups. It has been proposed that non-functionalization of duplicate genes could provide an important source of phenotypic variation . We have shown that the deletion in BrFLC2 also promoted flowering in a genetic background of Chinese cabbage line Z16. However, it remains unknown why different alleles of BrFLC1 show no difference in flowering time in oil-type B. rapa accessions. We need to sequence all of the BrFLC1 alleles in these accessions to determine whether they contain additional mutations. Genetic redundancy provides flexibility for plants growing in changeable environments. It is also possible that the other two homologs of FLC might function to compensate for the loss of function of BrFLC1 or BrFLC2. We sequenced BrFLC3 or BrFLC5 using primers designed from sequences in exon 4 and exon 7, respectively, and we did not identify any functional sequence variation for the nine accessions (unpublished data). However, we can not exclude the possibility that there are sequence variations located in other regions that might affect their functions. Further research on BrFLC3 in sub-genome MF1 and BrFLC5 as a relic of the α-duplication event and their influence on flowering is underway. We anticipate that they may have differentiated from, and are functionally different from, BrFLC1 and BrFLC2.
Our results suggest that the naturally occurring deletion mutation across exon 4 and intron 4 in BrFLC2 contributes greatly to the variation in flowering time in oil-type B. rapa. The different relationships between BrFLC1 or BrFLC2 and the variation in flowering time of vegetable-type and oil-type B. rapa indicate that control of flowering time undergone separate evolution between these two groups.
Plant materials and flowering time evaluation
To characterize the natural variation of flowering time in B. rapa, we measured 159 accessions belonging to 11 cultivar groups (Table 1, Additional file 1). We investigated flowering time for this germplasm collection under open field conditions in Kunming, Yunnan Province, southern China, from 12 October 2009 to 1 April 2010, as well as in a greenhouse in Beijing, northern China, from 23 October 2010 to 20 March 2011. The lowest mean daily temperature in Kunming is in December and January (average, 8.2°C). The day length varied between 142.7 h in October and 244.8 h in April. The day length in Beijing is 2,562–2,744 h per year on average. The shortest days are in winter (581.6 h in total during December to February), and the longest days are in spring (778.8 h in total from March to May). The temperature in the greenhouse varied between 15 to 25°C day/night, and no additional lighting was supplied.
Nine B. rapa accessions (Table 2) with a wide range of flowering times were used to screen for BrFLC2 sequence variations. The accessions were grown in a greenhouse in Beijing in the fall of both 2008 and 2009 to investigate variations in flowering times.
A BC2DH population with 120 lines derived from a cross between the yellow sarson line L143 (R500 from Wisconsin University) and the Chinese cabbage line Z16, using Z16 as the recurrent parent, were screened for polymorphisms of the BrFLC2Indel marker. We selected five lines with the insertion allele and three lines with the deletion allele and grew them in the greenhouse in Beijing from 20 August 2010 to investigate flowering time. Five replicates were grown for each line. Flowering time was scored as the number of days from sowing to the opening of the first flower (DTF). For the nine B. rapa accessions that were used to sequence BrFLC2, DTF was recorded as described above until 90 d and then those plants with no open flowers were transferred to a cold treatment. For the germplasm collection of 159 accessions grown in the open field, DTF was recorded until 155 DTF, while in the greenhouse flowering time was recorded until 150 DTF. Plants that did not have open flowers at the end of the experiment were assigned a value of 90 DTF, 155 DTF, and 150 DTF in the three respective experiments.
Genomic DNA was isolated from leaf samples using the CTAB method . Specific primers were designed for BrFLC2 (AY205317S1, AY205317S2). BrFLC2 was amplified by nested PCR. The outside forward primer was FLC012F1 (5′- CCTTGATCGATATGGGAAACAAC -3′) located in exon 2 and the outside reverse primer was FLCR5 (5′- TAATTAAGYAGYGGGAGAGTYAC-3′) located in exon 7. The inside forward primer was FLC2F8 (5′-GGAATCAAATTCTGATGTAAGCGTC -3′) located in exon 4 and the inside reverse primer was FLC2R6 (5′-TTTGTCCAGGTGACATCTCCATT-3′) located in exon 7 (Figures 1). The amplified fragment covered the region of exons 4–7 and the intervening introns between these exons. PCR was carried out in a total volume of 20 μl containing 50 ng template DNA, 0.5 μM each primer, 200 μM dNTPs, 1× PCR reaction buffer, and 1 U Taq polymerase. PCR was performed under the following conditions: the template was denatured at 94°C for 5 min, followed by 35 cycles of amplification (94°C for 1 min, 56°C for 1 min, 72°C for 1 min 30 s), and a final extension at 72°C for 10 min. PCR products from the nine accessions listed in Table 2 were purified by ethanol and NaAc (3 M, pH = 5.4) and then cloned into the PMD-18 T vectors (Promega, http://www.promega.com) for sequencing.
InDel marker analysis and CAPS marker analysis
The forward primer FLC2IndelF (5′-GTCGACTCCCTCGTTCAGC -3′) in exon 4 and the reverse primer FLC2IndelR (5′-AGGGAAACTAATACAATACGCAA -3′) in intron 5 were designed to develop an InDel marker for BrFLC2. PCR was performed under the following conditions: denaturation at 94°C for 3 min, followed by 35 cycles of amplification (94°C for 45 s, 55°C for 45 s, 72°C for 1 min), and a final extension at 72°C for 10 min. The PCR products were fractionated on an 8.0% polyacrylamide gel to determine the genotype of the InDel marker. We used the CAPS marker for BrFLC1, FLC1-MvaI, to screen the 159 accessions as described by Yuan et al. .
RNA extraction and reverse-transcriptase PCR (RT-PCR)
Germinated seeds from the yellow sarson accession L143 were planted in pots in a growth chamber at 25/20°C (day/night) with a 16-h light/8-h dark photoperiod. Young leaves were collected from plants 14 days after sowing. Total RNA was extracted using TRIplant Reagent (BioTeke, http://www.bioteke.com/). First-strand cDNA was synthesized from 1 μg total RNA using a cDNA synthesis kit (MBI Fermentas, http://www.fermentas.com) according to the manufacturer’s instructions. Because there are four homologs of FLC in B. rapa, we designed specific primers to amplify to amplify the cDNA of BrFLC2, based on the B. rapa genome sequence (http://brassicadb.org/brad/). The specific primers were as follows: forward, BrCFLC2F (5′-CCGAACCTCAGGATCAAATT -3′) located in the 5′UTR, and reverse, BrCFLC2R (5′ -TTCACCCTTATAGGGGAATAGTT -3′) located in the 3′UTR. We carried out RT-PCR under the following conditions: denaturation at 94°C for 4 min, followed by 35 cycles of amplification (94°C for 45 s, 60°C for 45 s, 72°C for 1 min), and a final extension at 72°C for 10 min. The amplified products were separated on SYBR green-stained 2.0% agarose gels. RT-PCR products were precipitated using ethanol and then dissolved in ddH2O. The purified RT-PCR product was cloned into pEASY-T1 vectors (TransGen Biotech, http://www.transgen.com) for sequencing. Escherichia coli strain DH5a (Tiangen Biotech, http://www.tiangen.com/) was transformed with these constructs and the positive colonies were selected. Plasmid DNA was isolated and sequenced using corresponding primers.
The BrFLC2 gene was sequenced using an ABI3730XL DNA analyzer (Perkin-Elmer, USA). All sequences were aligned against the published BrFLC2 sequence. Sequence alignment and analysis were conducted using MegAlign of DNASTAR.
Analysis of variance (ANOVA) and analysis of association were tested by one-way ANOVA and one-tailed Pearson correlation in SPSS version 12.0.1 (SPSS Inc., Chicago, IL, USA). ANOVA was performed with marker genotype as a factor.
flowering locus C
days to flowering.
This work was supported by grants from the National Natural Science Foundation of China (30800753). The research was conducted in the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China and the Sino-Dutch Joint Lab of Horticultural Genomics Technology, Beijing. The authors gratefully acknowledge funding from the European Community financial participation under the Seventh Framework Programme for Research, Technological Development and Demonstration Activities, for the Integrated Project NUE-CROPS FP7-CP-IP 222645. The views expressed in this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of the information contained herein.
- Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, Koenig D, Lanz C, Stegle O, Lippert C, Wang X, Ott F, Muller J, Alonso-Blanco C, Borgwardt K, Schmid KJ, Weigel D: Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011, 43: 956-963. 10.1038/ng.911.PubMedView ArticleGoogle Scholar
- Koornneef M, Alonso-Blanco C, Blankestijn-de Vries H, Hanhart CJ, Peeters AJM: Genetic Interactions Among Late-Flowering Mutants of Arabidopsis. Genetics. 1998, 148: 885-892.PubMedPubMed CentralGoogle Scholar
- Koornneef M, Blankestijn-de Vries H, Hanhart C, Soppe W, Peeters T: The phenotype of some late-flowering mutants is enhanced by a locus on chromosome 5 that is not effective in the Landsberg erecta wild-type. Plant J. 1994, 6: 911-919. 10.1046/j.1365-313X.1994.6060911.x.View ArticleGoogle Scholar
- Michaels SD, Amasino RM: Loss of FLOWERING LOCUS C activity eliminates the late-flowering phenotype of FRIGIDA and autonomous pathway mutations but not responsiveness to vernalization. Plant Cell. 2001, 13: 935-942.PubMedPubMed CentralView ArticleGoogle Scholar
- Fornara F, de Montaigu A, Coupland G: SnapShot: Control of Flowering in Arabidopsis. Cell. 2010, 141: 550-550. 10.1016/j.cell.2010.04.024. e552PubMedView ArticleGoogle Scholar
- Helliwell CA, Wood CC, Robertson M, James Peacock W, Dennis ES: The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J. 2006, 46: 183-192. 10.1111/j.1365-313X.2006.02686.x.PubMedView ArticleGoogle Scholar
- Michaels SD, Amasino RM: FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell. 1999, 11: 949-956.PubMedPubMed CentralView ArticleGoogle Scholar
- Searle I, He Y, Turck F, Vincent C, Fornara F, Krober S, Amasino RA, Coupland G: The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes & Dev. 2006, 20: 898-912. 10.1101/gad.373506.View ArticleGoogle Scholar
- Sheldon CC, Rouse DT, Finnegan EJ, Peacock WJ, Dennis ES: The molecular basis of vernalization: The central role of FLOWERING LOCUS C (FLC). PNAS. 2000, 97: 3753-3758. 10.1073/pnas.97.7.3753.PubMedPubMed CentralView ArticleGoogle Scholar
- Helliwell CA, Robertson M, Finnegan EJ, Buzas DM, Dennis ES: Vernalization-repression of Arabidopsis FLC requires promoter sequences but not antisense transcripts. PLoS ONE. 2011, 6 (6): e21513-10.1371/journal.pone.0021513.PubMedPubMed CentralView ArticleGoogle Scholar
- Kim S-Y, Park B-S, Kwon S-J, Kim J, Lim M-H, Park Y-D, Kim DY, Suh S-C, Jin Y-M, Ahn JH, Lee Y-H: Delayed flowering time in Arabidopsis and Brassica rapa by the overexpression of FLOWERING LOCUS C (FLC) homologs isolated from Chinese cabbage (Brassica rapa L. ssp. pekinensis). Plant Cell Rep. 2007, 26: 327-336. 10.1007/s00299-006-0243-1.PubMedView ArticleGoogle Scholar
- Schranz ME, Quijada P, Sung S-B, Lukens L, Amasino R, Osborn TC: Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics. 2002, 162: 1457-1468.PubMedPubMed CentralGoogle Scholar
- Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J-H, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park B-S, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim J-S, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon S-J, Choi S-R, Lee T-H, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z: The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011, 43: 1035-1039. 10.1038/ng.919.PubMedView ArticleGoogle Scholar
- Yang T-J, Kim JS, Kwon S-J, Lim K-B, Choi B-S, Kim J-A, Jin M, Park JY, Lim M-H, Kim H-I, Lim YP, Kang JJ, Hong J-H, Kim C-B, Bhak J, Bancroft I, Park B-S: Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell. 2006, 18: 1339-1347. 10.1105/tpc.105.040535.PubMedPubMed CentralView ArticleGoogle Scholar
- Osborn TC, Kole C, Parkin IAP, Sharpe AG, Kuiper M, Lydiate DJ, Trick M: Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana. Genetics. 1997, 146: 1123-1129.PubMedPubMed CentralGoogle Scholar
- Feng C, Shengyi L, Jian W, Lu F, Silong S, Bo L, Pingxia L, Wei H, Xiaowu W: BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biology. 2011, 11: 136-10.1186/1471-2229-11-136.View ArticleGoogle Scholar
- Osborn TC: The contribution of polyploidy to variation in Brassica species. Physiol Plantarum. 2004, 121: 531-536. 10.1111/j.1399-3054.2004.00360.x.View ArticleGoogle Scholar
- Yuan Y-X, Wu J, Sun R-F, Zhang X-W, Xu D-H, Bonnema G, Wang X-W: A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time. J Exp Bot. 2009, 60: 1299-1308. 10.1093/jxb/erp010.PubMedPubMed CentralView ArticleGoogle Scholar
- Zhao J, Kulkarni V, Liu N, Pino Del Carpio D, Bucher J, Bonnema G: BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa. J Exp Bot. 2010, 61: 1817-1825. 10.1093/jxb/erq048.PubMedPubMed CentralView ArticleGoogle Scholar
- Zhao J, Wang X, Deng B, Lou P, Wu J, Sun R, Xu Z, Vromans J, Koornneef M, Bonnema G: Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor Appl Genet. 2005, 110: 1301-1314. 10.1007/s00122-005-1967-y.PubMedView ArticleGoogle Scholar
- Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C: Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science. 2000, 290: 344-347. 10.1126/science.290.5490.344.PubMedView ArticleGoogle Scholar
- Shindo C, Aranzana MJ, Lister C, Baxter C, Nicholls C, Nordborg M, Dean C: Role of FRIGIDA and FLOWERING LOCUS C in Determining Variation in Flowering Time of Arabidopsis. Plant Physiology. 2005, 138: 1163-1173. 10.1104/pp.105.061309.PubMedPubMed CentralView ArticleGoogle Scholar
- Osterberg MK, Shavorskaya O, Lascoux M, Lagercrantz U: Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time. Genetics. 2002, 161: 299-306.PubMedPubMed CentralGoogle Scholar
- Caicedo AL, Stinchcombe JR, Olsen KM, Schmitt J, Purugganan MD: Epistatic interaction between Arabidopsis FRI and FLC flowering time genes generates a latitudinal cline in a life history trait. PNAS. 2004, 101: 15670-15675. 10.1073/pnas.0406232101.PubMedPubMed CentralView ArticleGoogle Scholar
- Slotte T, Huang H-R, Holm K, Ceplitis A, Onge KS, Chen J, Lagercrantz U, Lascoux M: Splicing variation at a FLOWERING LOCUS C homolog is Associated with flowering time variation in the tetraploid Capsella bursa-pastoris. Genetics. 2009, 183: 337-345. 10.1534/genetics.109.103705.PubMedPubMed CentralView ArticleGoogle Scholar
- Brenton RG: Alternative splicing: increasing diversity in the proteomic world. Trends Genet. 2001, 17: 100-107. 10.1016/S0168-9525(00)02176-4.View ArticleGoogle Scholar
- Lou P, Wu J, Cheng F, Cressman LG, Wang X, McClung CR: Preferential Retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell. 2012, 24: 2415-2426. 10.1105/tpc.112.099499.PubMedPubMed CentralView ArticleGoogle Scholar
- Wang X, Lou P, Bonnema G, Yang B, He H, Zhang Y, Fang Z: Linkage mapping of a dominant male sterility gene Ms-cd1 in Brassica oleracea. Genome. 2005, 48: 848-854. 10.1139/g05-044.PubMedView ArticleGoogle Scholar