title: Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region.
abstract: BACKGROUND
  In wheat, the vernalization requirement is mainly controlled by the VRN genes. Different species of hexaploid and tetraploid wheat are widely used as genetic source for new mutant variants and alleles for fundamental investigations and practical breeding programs. In this study, VRN-A1 and VRN-B1 were analysed for 178 accessions representing six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and five hexaploid species (T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii).
  
  
  RESULTS
  Novel allelic variants in the promoter region of VRN-A1 and VRN-B1 were identified based on the change in curvature and flexibility of the DNA molecules. The new variants of VRN-A1 (designated as Vrn-A1a.2, Vrn-A1b.2 - Vrn-A1b.6 and Vrn-A1i) were found to be widely distributed in hexaploid and tetraploid wheat, and in fact were predominant over the known VRN-A1 alleles. The greatest diversity of the new variants of VRN-B1 (designated as VRN-B1.f, VRN-B1.s and VRN-B1.m) was found in the tetraploid and some hexaploid wheat species. For the first time, minor differences within the sequence motif known as the VRN-box of VRN1 were correlated with wheat growth habit. Thus, vrn-A1b.3 and vrn-A1b.4 were revealed in winter wheat in contrast to Vrn-A1b.2, Vrn-A1b.5, Vrn-A1b.6 and Vrn-A1i. It was found that single nucleotide mutation in the VRN-box can influence the vernalization requirement and growth habit of wheat. Our data suggest that both the A-tract and C-rich segment within the VRN-box contribute to its functionality, and provide a new view of the hypothesised role of the VRN-box in regulating transcription of the VRN1 genes. Specifically, it is proposed that combination of mutations in this region can modulate vernalization sensitivity and flowering time of wheat.
  
  
  CONCLUSIONS
  New allelic variants of the VRN-A1 and VRN-B1 genes were identified in hexaploid and tetraploid wheat. Mutations in A-tract and C-rich segments within the VRN-box of VRN-A1 are associated with modulation of the vernalization requirement and flowering time. New allelic variants will be useful in fundamental investigations into the regulation of VRN1 expression, and provide a valuable genetic resource for practical breeding of wheat.
authors.affiliation: Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal Research Center Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation. muterko@gmail.com.|Department of Common and Molecular Genetics, Plant Breeding and Genetics Institute - National Center of Seed and Cultivar Investigation, Ovidiopolskaya Road 3, Odessa, 65036, Ukraine. muterko@gmail.com.
authors.forename: Alexandr
authors.initials: A
authors.lastname: Muterko
authors.affiliation: Laboratory of Plant Genomics and Bioinformatics, RSE "National Center for Biotechnology", Sh. Valikhanov 13/1, Astana, 010000, Kazakhstan.|University of Helsinki, Institute of Biotechnology, MTT Plant Genomics Laboratory, Biocentre 3, P.O. Box 65, Viikinkaari 1, Helsinki, 00014, Finland.
authors.forename: Ruslan
authors.initials: R
authors.lastname: Kalendar
authors.affiliation: Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal Research Center Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation.
authors.forename: Elena
authors.initials: E
authors.lastname: Salina
mesh_terms: D000483:Alleles; D018744:DNA, Plant / Q000737:chemistry; D017343:Genes, Plant; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012621:Seasons; D013696:Temperature; D014908:Triticum / Q000235:genetics* / Q000254:growth & development
chemical_list: D018744:DNA, Plant
references.citation: Nucleic Acids Res. 2007;35(13):4409-19
references.pmid: 17576671
references.citation: Genes Dev. 2004 Sep 15;18(18):2237-42
references.pmid: 15371337
references.citation: Biophys J. 2009 Aug 19;97(4):1138-47
references.pmid: 19686662
references.citation: Methods Mol Biol. 2010;674:57-83
references.pmid: 20827586
references.citation: Nucleic Acids Res. 2014 Feb;42(4):2138-46
references.pmid: 24275492
references.citation: Science. 2004 Mar 12;303(5664):1640-4
references.pmid: 15016992
references.citation: Plant Mol Biol. 2006 Mar;60(4):469-80
references.pmid: 16525885
references.citation: Am J Hum Genet. 1991 Jan;48(1):137-44
references.pmid: 1670750
references.citation: Genes Dev. 1999 Dec 15;13(24):3217-30
references.pmid: 10617571
references.citation: Mol Genet Genomics. 2012 Jul;287(7):575-90
references.pmid: 22684814
references.citation: Plant J. 2013 Dec;76(5):742-53
references.pmid: 24033823
references.citation: PLoS Genet. 2012;8(12):e1003134
references.pmid: 23271982
references.citation: J Exp Bot. 2005 Jan;56(409):1-14
references.pmid: 15557293
references.citation: Electrophoresis. 1989 May-Jun;10(5-6):354-9
references.pmid: 2548838
references.citation: Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):E5401-10
references.pmid: 26324889
references.citation: BMC Bioinformatics. 2010 Mar 15;11:129
references.pmid: 20230624
references.citation: BMC Plant Biol. 2013 Dec 05;13:199
references.pmid: 24314021
references.citation: J Mol Biol. 2000 Jun 16;299(4):965-77
references.pmid: 10843851
references.citation: Proc Natl Acad Sci U S A. 2009 May 19;106(20):8386-91
references.pmid: 19416817
references.citation: Theor Appl Genet. 2004 Nov;109(8):1677-86
references.pmid: 15480533
references.citation: BMC Genet. 2015 Jul 29;16:96
references.pmid: 26219856
references.citation: Genome Res. 2008 Feb;18(2):233-41
references.pmid: 18096746
references.citation: Biochemistry. 1983 Dec 20;22(26):6186-93
references.pmid: 6318810
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):325-7
references.pmid: 11752327
references.citation: Genome. 2009 Mar;52(3):294-7
references.pmid: 19234558
references.citation: Plant Sci. 2014 Feb;215-216:117-23
references.pmid: 24388522
references.citation: Plant Mol Biol. 2015 May;88(1-2):149-64
references.pmid: 25851614
references.citation: BMC Plant Biol. 2010 Aug 11;10:168
references.pmid: 20699006
references.citation: Nat Genet. 2012 May 27;44(7):743-50
references.pmid: 22634752
references.citation: Nat Commun. 2014 Aug 05;5:4572
references.pmid: 25091017
references.citation: EMBO J. 1995 Jun 1;14(11):2570-9
references.pmid: 7781610
references.citation: Genome Biol. 2007;8(6):R96
references.pmid: 17543110
references.citation: G3 (Bethesda). 2011 Dec;1(7):637-45
references.pmid: 22384375
references.citation: Proc Natl Acad Sci U S A. 1996 May 14;93(10):4862-7
references.pmid: 8643494
references.citation: Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664-8
references.pmid: 16593261
references.citation: Proc Natl Acad Sci U S A. 2002 Sep 3;99(18):11593-8
references.pmid: 12195017
references.citation: J Mol Biol. 1996 Aug 16;261(2):239-54
references.pmid: 8757291
references.citation: Nucleic Acids Res. 2012 Jun;40(11):4727-41
references.pmid: 22351747
references.citation: PLoS One. 2012;7(3):e33234
references.pmid: 22457747
references.citation: Science. 2007 May 18;316(5827):1030-3
references.pmid: 17446353
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3540-5
references.pmid: 12824362
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 15;95(19):11163-8
references.pmid: 9736707
references.citation: Nucleic Acids Res. 2013 Aug;41(15):7453-61
references.pmid: 23771141
references.citation: Front Plant Sci. 2015 Jul 01;6:470
references.pmid: 26191066
references.citation: J Hered. 2009 May-Jun;100(3):355-64
references.pmid: 19251764
references.citation: Plant Physiol. 2005 Aug;138(4):2145-54
references.pmid: 16040653
references.citation: Nature. 1986 Apr 10-16;320(6062):501-6
references.pmid: 3960133
references.citation: Methods Enzymol. 1992;212:30-46
references.pmid: 1518451
references.citation: J Med Chem. 2008 Sep 25;51(18):5641-9
references.pmid: 18767830
references.citation: Trends Plant Sci. 2007 Aug;12(8):352-7
references.pmid: 17629542
references.citation: Proc Natl Acad Sci U S A. 2003 May 13;100(10):6263-8
references.pmid: 12730378
references.citation: Genetics. 2007 Dec;177(4):2535-9
references.pmid: 18073446
references.citation: Plant J. 2011 Sep;67(5):763-73
references.pmid: 21554456
references.citation: Plant Physiol. 2009 Jan;149(1):245-57
references.pmid: 19005084
references.citation: Mol Genet Genomics. 2005 Mar;273(1):54-65
references.pmid: 15690172
references.citation: Proc Natl Acad Sci U S A. 2006 Dec 19;103(51):19581-6
references.pmid: 17158798
references.citation: BMC Bioinformatics. 2009 Dec 15;10:421
references.pmid: 20003500
references.citation: Annu Rev Biochem. 1990;59:755-81
references.pmid: 2197990
references.citation: Comp Funct Genomics. 2012;2012:695827
references.pmid: 22474413
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: BMC Plant Biol. 2015 Mar 31;15:94
references.pmid: 25888295
references.citation: Nucleic Acids Res. 2007;35(18):6219-26
references.pmid: 17855401
references.citation: Plant J. 2008 Aug;55(4):543-54
references.pmid: 18433437
references.citation: J Mol Biol. 1990 Apr 20;212(4):563-78
references.pmid: 2329577
references.citation: J Mol Biol. 2000 Jan 7;295(1):85-103
references.pmid: 10623510
references.citation: Nature. 1993 Oct 7;365(6446):520-7
references.pmid: 8413605