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A 215-bp indel at intron I of BoFLC2 affects flowering time in Brassica oleracea var. capitata during vernalization

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Abstract

Key message

In response to cold, a 215-bp deletion at intron I of BoFLC2 slows its silencing activity by feedback to the core genes of the PHD-PRC2 complex, resulting in late flowering in cabbage.

Abstract

Cabbage is a plant-vernalization-responsive flowering type. In response to cold, BoFLC2 is an important transcription factor, which allows cabbage plants to remain in the vegetative phase. However, there have been few reports on the detailed and functional effects of genetic variation in BoFLC2 on flowering time in cabbage. Herein, BoFLC2E and BoFLC2L, cloned from extremely early and extremely late flowering cabbages, respectively, exhibited a 215-bp indel at intron I, three non-synonymous SNPs and a 3-bp indel at exon II. BoFLC2L was found to be related to late flowering, as verified in 40 extremely early/late flowering accessions, a diverse set of cabbage inbred lines and two F2 generations by using indel-FLC2 marker. Among the genetic variation of BoFLC2, the 215-bp deletion at intron I was the main reason for the delayed flowering time, as verified in the transgenic progenies of seed-vernalization-responsive Arabidopsis thaliana (Col) and rapid cycler B. oleracea (TO1000, boflc2). This is the first report to show that the intron I indel of BoFLC2 affects the flowering time of cabbage. Although the intron I 215-bp indel between BoFLC2E and BoFLC2L did not cause alternative splicing, it slowed BoFLC2L silencing during vernalization and feedback to the core genes of the PHD-PRC2 complex, resulting in their lower transcription levels. Our study not only provides an effective molecular marker-assisted selective strategy for identifying bolting-resistant resources and breeding improved varieties in cabbage, but also provides an entry point for exploring the mechanisms of flowering time in plant-vernalization-responsive plants.

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All data generated or analyzed during this study are included in this published article [and its supplementary information files].

Abbreviations

bp:

Base pair

BRAD:

Brassica database

D:

Asp, aspartic acid

DTF:

Days to flower

E:

Glu, glutamic acid

I:

Ile, isoleucine

Indel:

Insertion/deletion

K:

Lys, lysine

lncRNA:

Long noncoding RNA

NCBI:

The national center for biotechnology

PCR:

Polymerase chain reaction

PHD:

Homologue plant homeodomain

PRC2:

Polycomb repressive complex 2

RT-qPCR:

Quantitative Real-time polymerase chain reaction

SNPs:

Single nucleic polymorphisms

V:

Val, valine

References

  • Abuyusuf M, Nath UK, Kim H-T, Islam MR, Park J-I, Nou I-S (2019) Molecular markers based on sequence variation in BoFLC1.C9 for characterizing early- and late-flowering cabbage genotypes. BMC Genet 20(1):42

  • Amasino RM, Michaels SD (2010) The timing of flowering. Plant Physiol 154(2):516–520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhalla PL, Singh MB (2008) Agrobacterium-mediated transformation of Brassica napus and Brassica oleracea. Nat Protoc 3:181–189

    Article  CAS  PubMed  Google Scholar 

  • Blázquez MA, Trénor M, Weigel D (2002) Independent control of gibberellin biosynthesis and flowering time by the circadian clock in Arabidopsis. Plant Physiol 130(4):1770–1775

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Callis J, Fromm M, Walbot V (1987) Introns increase gene expression in cultured maize cells. Genes Dev 1:1183–1200

    Article  CAS  PubMed  Google Scholar 

  • Capovilla G, Schmid M, Posé D (2015) Control of flowering by ambient temperature. J Exp Bot 66(1):59–69

    Article  CAS  PubMed  Google Scholar 

  • Castro-Mondragon JA, Riudavets-Puig R, Rauluseviciute I, Berhanu Lemma R, Turchi L, Blanc-Mathieu R, Lucas J, Boddie P, Khan A, Manosalva Pérez N, Fornes O, Leung TY, Aguirre A, Hammal F, Schmelter D, Baranasic D, Ballester B, Sandelin A, Lenhard B, Vandepoele K, Wasserman WW, Parcy F, and Mathelier A (2021) JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Res 1:gkab1113

  • Costa S, Dean C (2019) Storing memories: the distinct phases of Polycomb-mediated silencing of Arabidopsis FLC. Biochem Soc Trans 47(4):1187–1196

    Article  CAS  PubMed  Google Scholar 

  • Coustham V, Li P, Strange A, Lister C, Song J, Dean C (2012) Quantitative modulation of polycomb silencing underlines natural variation in vernalization. Science 337(6094):584–587

    Article  CAS  PubMed  Google Scholar 

  • Csorba T, Questa JI, Sun Q, Dean C (2014) Antisense COOLAIR mediates the coordinated switching of chromatin states at FLC during vernalization. Proc Natl Acad Sci 111(45):16160–16165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Lucia F, Crevillen P, Jones AME, Greb T, Dean C (2008) A PHD-Polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci 105(44):16831–16836

    Article  PubMed  PubMed Central  Google Scholar 

  • Finnegan EJ, Dennis ES (2007) Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr Biol 17(22):1978–1983

    Article  CAS  PubMed  Google Scholar 

  • Friend DJC (1985) Brassica. In: Halevy AH, eds. CRC Handbook of flowering. Boca Raton: CRC Press, Inc pp48–77

  • Gendall AR, Levy YY, Wilson A, Dean C (2001) The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107:525–535

    Article  CAS  PubMed  Google Scholar 

  • Golicz AA, Bayer PE, Barker GC, Edger PP, Kim HR, Martinez PA, Chan CKK, Severn-Ellis A, McCombie WR, Parkin IAP, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D (2016) The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo N, Wang S, Gao L, Liu Y, Wang X, Lai E, Duan M, Wang G, Li J, Yang M, Zong M, Han S, Pei Y, Borm T, Sun H, Miao L, Liu D, Yu F, Zhang W, Ji H, Zhu C, Xu Y, Bonnema G, Li J, Fei Z, Liu F (2021) Genome sequencing sheds light on the contribution of structural variants to Brassica oleracea diversification. BMC Biol 19:93

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Han X, Han F, Ren X, Si J, Li C, Song H (2013) Ssp DnaE splite-intein mediated split-Cre reconstitution in tobacco. Plant Cell Tiss Org 113(3):529–542

    Article  CAS  Google Scholar 

  • He Y, Amasino RM (2005) Role of chromatin modification in flowering-time control. Trends Plant Sci 10(1):30–35

    Article  CAS  PubMed  Google Scholar 

  • He Y, Michaels SD, Amasino RM (2003) Regulation of flowering time by histone acetylation in Arabidopsis. Science 302(5651):1751–1754

    Article  CAS  PubMed  Google Scholar 

  • Irwin JA, Soumpourou E, Lister C, Ligthart J-D, Kennedy S, Dean C (2016) Nucleotide polymorphism affecting FLC expression underpins heading date variation in horticultural brassicas. Plant J 87(6):597–605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ito H, Saito K (1962) Time and temperature factors for the flower formation in cabbage. Tohoku J Agric Res 12(4):297–316

    Google Scholar 

  • Kim D, Xi Y, Sung S (2017) Modular function of long noncoding RNA, COLDAIR, in the vernalization response. PLoS Genet 13(7):e1006939

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim D-H, Doyle MR, Sung S, Amasino RM (2009) Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 25:277–299

    Article  CAS  PubMed  Google Scholar 

  • Kitamoto N, Yui S, Nishikawa K, Takahata Y, Yokoi S (2014) A naturally occurring long insertion in the first intron in the Brassica rapa FLC2 gene causes delayed bolting. Euphytica 196:213–223

    Article  CAS  Google Scholar 

  • Li P, Filiault D, Box MS, Kerdaffrec E, van Oosterhout C, Wilczek AM, Schmitt J, McMullan M, Bergelson J, Nordborg M, Dean C (2014) Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana. Genes Dev 28:1635–1640

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li P, Tao Z, Dean C (2015) Phenotypic evolution through variation in splicing of the noncoding RNA COOLAIR. Genes Dev 29(7):696–701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin S-I, Wang J-G, Poon S-Y, Su C-I, Wang S-S, Chiou T-J (2005) Differential regulation of FLOWERING LOCUS C expression by vernalization in cabbage and Arabidopsis. Plant Physiol 137(3):1037–1048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin Y, Lee J, Tseng M, Lee C, Shen C, Wang C, Liou C, Shuang L, Paterson AH, Hwu K (2018) Subtropical adaptation of a temperate plant (Brassica oleracea var. italica) utilizes non-vernalization-responsive QTLs. Sci Rep 8:13609

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Okazaki K, Sakamoto K, Kikuchi R, Saito A, Togashi E, Kuqinuki Y, Matsumoto S, Hirai M (2007) Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea. Thero Appl Genet 114(4):595–608

    Article  CAS  Google Scholar 

  • Parra G, Bradnam K, Rose AB, Korf I (2011) Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Res 39(13):5328–5337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qüesta JI, Song J, Geraldo N, An H, Dean C (2016) Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science 353(6298):485–488

    Article  PubMed  CAS  Google Scholar 

  • Ridge S, Brown PH, Hecht V, Driessen RG, Weller JL (2015) The role of BoFLC2 in cauliflower (Brassica oleracea var botrytis L) reproductive development. J Exp Bot 66(1):125–135

    Article  CAS  PubMed  Google Scholar 

  • Rose AB (2019) Introns as gene regulators: a brick on the accelerator. Front Genet 9:672

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schranz ME, Quijada P, Sung S-B, Lukens L, Amasino R, Osborn TC (2002) Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162(3):1457–1468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Searle I, He Y, Turck F, Vincent C, Fornara F, Kröber S, Amasino RA, Coupland G (2006) The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev 20(7):898–912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sheldon CC, Rouse DT, Finnegan EJ, Peacock WJ, Dennis ES (2000) The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc Natl Acad Sci 97(7):3753–3758

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shindo C, Aranzana MJ, Lister C, Baxter C, Nicholls C, Nordborg M, Dean C (2005) Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis. Plant Physiol 138(2):1163–1173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shindo C, Lister C, Crevillen P, Nordborg M, Dean C (2006) Variation in the epigenetic silencing of FLC contributes to natural variation in Arabidopsis vernalization response. Genes Dev 20(22):3079–3083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song YH, Ito S, Imaizumi T (2013) Flowering time regulation: photoperiod- and temperature-sensing in leaves. Trends Plant Sci 18(10):575–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sung S, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427:159–164

    Article  CAS  PubMed  Google Scholar 

  • Tian Y, Zheng H, Zhang F, Wang S, Ji X, Xu C, He Y, Ding Y (2019) PRC2 recruitment and H3K27me3 deposition at FLC require FCA binding of COOLAIR. Sci Adv 5(4):eqqu2746

    Google Scholar 

  • Uptmoor R, Li J, Schrag T, Stützel H (2012) Prediction of flowering time in Brassica oleracea using a quantitative trait loci-based phenology model. Plant Biol 14(1):179–189

    CAS  PubMed  Google Scholar 

  • Wood CC, Robertson M, Tanner G, Peacock WJ, Dennis ES, Helliwell CA (2006) The Arabidopsis thaliana vernalization response requires a Polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci 103(39):14631–14636

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wu J, Wei K, Cheng F, Li S, Wang Q, Zhao J, Bonnema G, Wang X (2012) A naturally occurring InDel variation in Bra. A FLC. b (BrFLC2) associated with flowering time variation in Brassica rapa. BMC Plant Biol 12:151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang H, Berry S, Olsson TSG, Hartley M, Howard M, Dean C (2017) Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis. Science 357(6356):1142–1145

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We would like to thank the Grants of the National Natural Science Foundation of China (31801855), the Natural Science Foundation of Chongqing, China (cstc2018jcyjAX0039), and the Fundamental Research Funds for the Central Universities (SWU118063, XDJK2019B046); we were also supported by the Technology Innovation and Application Development Program of Chongqing (cstc2019.jscx-gksbX0117, cstc2019.jscx-gksbX0143, cstc2021jscx-cylh0001), and Sichuan Province Regional Innovation Cooperation Project (2022YFQ0031). We also thank the International Science Editing for the language editing.

Funding

The Grants of the National Natural Science Foundation of China (31801855), the Natural Science Foundation of Chongqing, China (cstc2018jcyjAX0039).

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Author notes

  1. Qinfei Li and Ao Peng have contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Horticulture Science for the Southern Mountains Regions, Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China

    Qinfei Li, Ao Peng, Jiaqin Yang, Sidi Zheng, Zhangping Li, Yinhui Mu, Jun Si, Xuesong Ren & Hongyuan Song

  2. Chongqing Academy of Agricultural Sciences, Chongqing Sanqian Seed Industry Co., Ltd, Chongqing, 400060, China

    Lei Chen

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  1. Qinfei Li
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Contributions

QL and HS conceived and designed the project. QL wrote and revised the manuscript. AP, SZ, ZL, JY and YM formulated the experiments. LC, JS and XR supplied the plant materials and collecting flowering time data. QL and AP contribute equally to this work. All authors approved and read the final manuscript.

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Correspondence to Xuesong Ren or Hongyuan Song.

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Communicated by Maria Laura Federico.

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Li, Q., Peng, A., Yang, J. et al. A 215-bp indel at intron I of BoFLC2 affects flowering time in Brassica oleracea var. capitata during vernalization. Theor Appl Genet 135, 2785–2797 (2022). https://doi.org/10.1007/s00122-022-04149-1

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