Skip to main content

Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice

Abstract

Vernalization, a period of low temperature to induce transition from vegetative to reproductive state, is an important environmental stimulus for many cool season grasses. A key gene in the vernalization pathway in grasses is the VRN1 gene. The objective of this study was to identify causative polymorphism(s) at the VRN1 locus in perennial ryegrass (Lolium perenne) for variation in vernalization requirement. Two allelic Bacterial Artificial Chromosome clones of the VRN1 locus from the two genotypes Veyo and Falster with contrasting vernalization requirements were identified, sequenced, and characterized. Analysis of the allelic sequences identified an 8.6-kb deletion in the first intron of the VRN1 gene in the Veyo genotype which has low vernalization requirement. This deletion was in a divergent recurrent selection experiment confirmed to be associated with genotypes with low vernalization requirement. The region surrounding the VRN1 locus in perennial ryegrass showed microcolinearity to the corresponding region on chromosome 3 in Oryza sativa with conserved gene order and orientation, while the micro-colinearity to the corresponding region in Triticum monococcum was less conserved. Our study indicates that the first intron of the VRN1 gene, and in particular the identified 8.6 kb region, is an important regulatory region for vernalization response in perennial ryegrass.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  • Aamlid TS, Heide OM, Boelt B (2000) Primary and secondary induction requirements for flowering of contrasting European varieties of Lolium perenne. Ann Bot 86:1087–1095

    Article  Google Scholar 

  • Andersen JR, Jensen LB, Asp T, Lübberstedt T (2006) Vernalization response in perennial ryegrass (Lolium perenne L.) involves orthologues of diploid wheat (Triticum monococcum) VRN1 and rice (Oryza sativa) Hd1. Plant Mol Biol 60:481–494

    PubMed  Article  CAS  Google Scholar 

  • Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167

    PubMed  Article  CAS  Google Scholar 

  • Bennett MD, Smith JB (1976) Nuclear DNA amounts in angiosperms. Phil Transac Royal Soc London Series B-Biol Sci 334:309–345

    Article  Google Scholar 

  • Bennetzen JL (2000) Transposable element contributions to plant genome evolution. Plant Mol Biol 42:251–269

    PubMed  Article  CAS  Google Scholar 

  • Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C et al (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res 16:1241–1251

    PubMed  Article  CAS  Google Scholar 

  • Burn JE, Smyth DR, Peacock WJ, Dennis ES (1993) Genes conferring late flowering in Arabidopsis thaliana. Genetica 90:147–155

    Article  Google Scholar 

  • Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611–622

    PubMed  Article  CAS  Google Scholar 

  • Choudhuri JV, Schleiermacher C, Kurtz S, Giegerich R (2004) Genalyzer: interactive visualization of sequence similarities between entire genomes. Bioinformatics 20:1964–1965

    PubMed  Article  CAS  Google Scholar 

  • Clarke JH, Dean C (1994) Mapping FRI, a locus controlling flowering time and vernalization response in Arabidopsis thaliana. Mol Gen Genet 242:81–89

    PubMed  CAS  Google Scholar 

  • Cooper JP (1960) Short-day and low-temperature induction in Lolium. Ann Bot 24:232–246

    Google Scholar 

  • Corbesier L, Vincent C, Jang SH, Fornara F, Fan QZ, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C (2007) FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316:1030–1033

    PubMed  Article  CAS  Google Scholar 

  • Danyluk J, Kane NA, Breton G, Limin AE, Fowler DB, Sarhan F (2003) TaVRT-1, a putative transcription factor associated with vegetative to reproductive transition in cereals. Plant Physiol 132:1849–1860

    PubMed  Article  CAS  Google Scholar 

  • Dubcovsky J, Loukoianov A, Fu D, Valarik M, Sanchez A, Yan L (2006) Effect of photoperiod on the regulation of wheat vernalization genes VRN1 and VRN2. Plant Mol Biol 60:469–480

    PubMed  Article  CAS  Google Scholar 

  • Evans GM, Rees H, Snell CL, Sun S (1972) The relationship between nuclear DNA amount and the duration of the mitotic cycle. Chromosom Today 3:24–31

    CAS  Google Scholar 

  • Ewing B, Green P (1998) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8:186–194

    PubMed  CAS  Google Scholar 

  • Farrar K, Asp T, Lübberstedt T, Xu M, Thomas AM, Christiansen C, Humphreys MO, Donnison IS (2007) Construction of two Lolium perenne BAC libraries and identification of BACs containing candidate genes for disease resistance and forage quality. Plant Breed 19:15–23

    CAS  Google Scholar 

  • Frohman MA, Dush MK, Martin GR (1998) Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer. Proc Natl Acad Sci USA 85:8998–9002

    Article  Google Scholar 

  • Fu D, Szücs P, Yan L, Helguera M, Skinner JS, von Zitzewitz J, Hayes PM, Dubcovsky J (2005) Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat. Mol Gen Genomics 273:54–65

    Article  CAS  Google Scholar 

  • 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

    PubMed  Article  CAS  Google Scholar 

  • Gierl A, Saedler H, Peterson PA (1989) Maize transposable elements. Annu Rev Genet 23:71–85

    PubMed  Article  CAS  Google Scholar 

  • Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202

    PubMed  CAS  Google Scholar 

  • Gremme G, Brendel V, Sparks ME, Kurtz S (2005) Engineering a software tool for gene structure prediction in higher organisms. Inf Softw Technol 47:965–978

    Article  Google Scholar 

  • Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612–1624

    PubMed  Article  CAS  Google Scholar 

  • Heide OM (1994) Control of flowering and reproduction in temperate grasses. New Phytol 128:347–362

    Article  CAS  Google Scholar 

  • Higgins JA, Bailey PC, Laurie DA (2010) Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS ONE 5(4):e10065

    PubMed  Article  Google Scholar 

  • Jensen LB, Andersen JR, Frei U, Xing Y, Taylor C, Holm PB, Lübberstedt T (2005) QTL mapping of vernalization response in perennial ryegrass (Lolium perenne L.) reveals co-location with an orthologue of wheat VRN1. Theor Appl Genet 110:527–536

    PubMed  Article  CAS  Google Scholar 

  • Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C (2000) Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science 290:344–347

    PubMed  Article  CAS  Google Scholar 

  • Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5:246–251

    PubMed  Article  CAS  Google Scholar 

  • Koornneef M, Blankestijn-de Vries H, Hanhart C, Soppe W, Peeters T (1994) The phenotype of some late-flowering mutants is enhanced by a locus on chromosome 5 that is not effective in the Lansberg erecta wild-type. Plant J 6:911–919

    Article  CAS  Google Scholar 

  • Lee I, Bleecker A, Amasino R (1993) Analysis of naturally occurring late flowering in Arabidopsis thaliana. Mol Gen Genet 237:171–176

    PubMed  Article  CAS  Google Scholar 

  • Lee I, Michaels SD, Masshardt AS, Amasino RM (1994) The late-flowering phenotype of FRIGIDA and LUMINIDEPENDENS is suppressed in the Lansberg erecta strain of Arabidopsis. Plant J 6:903–909

    Article  CAS  Google Scholar 

  • Levy YY, Mesnage S, Mylne JS, Gendall AR, Dean C (2002) Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297:243–246

    PubMed  Article  CAS  Google Scholar 

  • Lewin B (1997) Transposons. In: Lewin B (ed) Genes VI. Oxford University Press, New York, pp 563–595

    Google Scholar 

  • Li C, Dubcovsky J (2008) Wheat FT protein regulates VRN1 transcription through interactions with FDL2. Plant J 55:543–554

    PubMed  Article  CAS  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene Expression data using real-time quantitative PCR and the 2 Δ Δ CT method. Methods 25:402–408

    PubMed  Article  CAS  Google Scholar 

  • Lübberstedt T, Andreasen BS, Holm PB et al (2003) Development of ryegrass allele-specific (GRASP) markers for sustainable grassland improvement—a new framework V project. Czech J Genet Plant Breed 39:125–128

    Google Scholar 

  • Lukashin AV, Borodovsky M (1998) GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 26:1107–1115

    PubMed  Article  CAS  Google Scholar 

  • McCarthy EM, McDonald JF (2003) LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19:362–367

    PubMed  Article  CAS  Google Scholar 

  • Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956

    PubMed  Article  CAS  Google Scholar 

  • Napp-Zinn K (1987) Vernalization: environmental and genetic regulation. In: Atherton JG (ed) Manipulation of flowering. Butterworths, London, pp 123–132

    Google Scholar 

  • Osborn TC, Kole C, Parkin IAP, Sharpe AG, Kuiper M, Lydiate DJ, Trick M (1997) Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana. Genet Soc Am 146:1123–1129

    CAS  Google Scholar 

  • Pereira A, Cuypers H, Gierl A, Sommer ZS, Saedler H (1986) Molecular analysis of the En/Spm transposable element system in Zea mays. EMBO J 5:835–841

    PubMed  CAS  Google Scholar 

  • Salamov A, Solovyev V (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516–522

    PubMed  Article  CAS  Google Scholar 

  • SanMiguel PJ, RamaKrishna W, Bennetzen JL, Busso C, Dubovsky J (2002) Transposable elements, genes and recombination in a 215-kb contig from wheat chromosome 5Am. Funct Integr Genomics 2:70–80

    PubMed  Article  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W (2000) PipMaker—a web server for aligning two genomic DNA sequences. Genome Res 10:577–586

    PubMed  Article  CAS  Google Scholar 

  • Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards JA, Peacock WJ, Dennis ES (1999) The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458

    PubMed  Article  CAS  Google Scholar 

  • Shirasu K, Schulman AH, Lahaye T, Schulze-Lefert P (2000) A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res 10:908–915

    PubMed  Article  CAS  Google Scholar 

  • Skøt L, Humphreys MO, Armstead I, Heywood S, Skøt KP, Sanderson R, Thomas ID, Chorlton KH, Sackville Hamilton NR (2005) An association mapping approach to identify flowering time genes in natural populations of Lolium perenne (L.). Mol Breed 15:233–245

    Article  Google Scholar 

  • Sung S, Amasino RM (2004a) Vernalization and epigenetics: how plants remember winter. Cur Opin Plant Biol 7:4–10

    Article  CAS  Google Scholar 

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

    PubMed  Article  CAS  Google Scholar 

  • Sung S, Amasino RM (2005) Remembering winter: toward a molecular understanding of vernalization. Annu Rev Plant Biol 56:491–508

    PubMed  Article  CAS  Google Scholar 

  • Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K (2007) Hd3a protein is a mobile flowering signal in rice. Science 316:1033–1036

    PubMed  Article  CAS  Google Scholar 

  • Trevaskis B, Bagnall DJ, Ellis MH, Peacock WJ, Dennis ES (2003) MADS box genes control vernalization-induced flowering in cereals. Proc Natl Acad Sci USA 100:13099–13104

    PubMed  Article  CAS  Google Scholar 

  • Trevaskis B, Hemming MN, Peacock WJ, Dennis ES (2006) HvVRN2 responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status. Plant Physiol 140:1397–1405

    PubMed  Article  CAS  Google Scholar 

  • Turck F, Fornara F, Coupland G (2008) Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annu Rev Plant Biol 59:573–594

    PubMed  Article  CAS  Google Scholar 

  • von Zitzewitz J, Szucs P, Dubcovsky J, Yan L, Francia E, Pecchioni N, Casas A, Chen TH, Hayes PM, Skinner JS (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59:449–467

    Article  CAS  Google Scholar 

  • Xing Y, Frei U, Schejbel B, Asp T, Lübberstedt T (2007) Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC Plant Biol 7:43

    PubMed  Article  Google Scholar 

  • Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268

    PubMed  Article  CAS  Google Scholar 

  • Yan L, Helguera M, Kato K, Fukuyama S, Sherman J, Dubcovsky J (2004a) Allelic variation at the VRN-1 promoter region in polyploid wheat. Theor Appl Genet 109:1677–1686

    PubMed  Article  CAS  Google Scholar 

  • Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004b) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–1644

    PubMed  Article  CAS  Google Scholar 

  • Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA 103:19581–19586

    PubMed  Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by a grant from the framework “Biotechnology and applied plant genetics in plant breeding” from The Directorate for Food, Fisheries and Agricultural Business under the Danish Ministry of Food, Agriculture and Fisheries. Dorthe Strue Nielsen and Kirsten Vangsgaard are acknowledged for their excellent technical assistance.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Torben Asp.

Additional information

Communicated by Y. Van de Peer.

Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers JN969602 and JN969603 for the Veyo-GP and Falster-GP VRN1 alleles, respectively.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1. Percent Identity Plot output of the comparison of the VRN1 locus of Lolium perenne, H. vulgare, T. monococcum, T. aestivum, T. turgidum, Ae. tauschii, and the AP1 locus of O. sativa.

Supplementary Table 1. Germplasm evaluation for Veyo-GP and Falster-GP VRN1 alleles in 380 genotypes of L. perenne. 1: presence of allele; 0: absence of allele.

Supplementary material 1 (PDF 24 kb)

Supplementary material 2 (PDF 454 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Asp, T., Byrne, S., Gundlach, H. et al. Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley, wheat, and rice. Mol Genet Genomics 286, 433–447 (2011). https://doi.org/10.1007/s00438-011-0654-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-011-0654-8

Keywords

  • Lolium perenne
  • Perennial ryegrass
  • VRN1
  • Comparative genomics
  • Vernalization