Fornara F, de Montaigu A, Coupland G. SnapShot: Control of flowering in Arabidopsis. Cell. 2010;141(3):550. doi:10.1016/j.cell.2010.04.024.
Article
PubMed
Google Scholar
Brachi B, Faure N, Horton M, Flahauw E, Vazquez A, Nordborg M, et al. Linkage and association mapping of Arabidopsis thaliana flowering time in nature. PLoS Genet. 2010;6(5):e1000940. doi:10.1371/journal.pgen.1000940.
Article
PubMed
PubMed Central
Google Scholar
Higgins JA, Bailey PC, Laurie DA. Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS One. 2010;5(4):e10065. doi:10.1371/journal.pone.0010065.
Article
PubMed
PubMed Central
Google Scholar
Peng FY, Hu Z, Yang R-C. Genome-wide comparative analysis of flowering-related genes in Arabidopsis, wheat, and barley. Int J Plant Genomics. 2015;2015:874361. doi:10.1155/2015/874361.
Article
PubMed
PubMed Central
Google Scholar
Distelfeld A, Li C, Dubcovsky J. Regulation of flowering in temperate cereals. Curr Opin Plant Biol. 2009;12(2):178–84. http://dx.doi.org/10.1016/j.pbi.2008.12.010.
Article
CAS
PubMed
Google Scholar
Andres F, Coupland G. The genetic basis of flowering responses to seasonal cues. Nat Rev Genet. 2012;13(9):627–39. doi:10.1038/Nrg3291.
Article
CAS
PubMed
Google Scholar
Shrestha R, Gomez-Ariza J, Brambilla V, Fornara F. Molecular control of seasonal flowering in rice, arabidopsis and temperate cereals. Ann Bot-London. 2014;114(7):1445–58. doi:10.1093/aob/mcu032.
Article
Google Scholar
Blumel M, Dally N, Jung C. Flowering time regulation in crops-what did we learn from Arabidopsis? Curr Opin Biotechnol. 2015;32:121–9. doi:10.1016/j.copbio.2014.11.023.
Article
PubMed
Google Scholar
Fjellheim S, Boden S, Trevaskis B. The role of seasonal flowering responses in adaptation of grasses to temperate climates. Front Plant Sci. 2014;5:431. doi:10.3389/Fpls.2014.00431.
Article
PubMed
PubMed Central
Google Scholar
Song YH, Ito S, Imaizumi T. Similarities in the circadian clock and photoperiodism in plants. Curr Opin Plant Biol. 2010;13(5):594–603. doi:10.1016/j.pbi.2010.05.004.
Article
PubMed
PubMed Central
Google Scholar
Calixto CPG, Waugh R, Brown JWS. Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes. J Mol Evol. 2015;80(2):108–19. doi:10.1007/s00239-015-9665-0.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wittkopp PJ, Kalay G. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet. 2012;13(1):59–69. http://www.nature.com/nrg/journal/v13/n1/full/nrg3095.html.
Article
CAS
Google Scholar
Beales J, Turner A, GriYths S, Snape JW, Laurie DA. A Pseudo-Response Regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet. 2007;115(5):721–33. doi:10.1007/s00122-007-0603-4.
Article
CAS
PubMed
Google Scholar
Wilhelm EP, Turner AS, Laurie DA. Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theor Appl Genet. 2009;118(2):285–94. doi:10.1007/s00122-008-0898-9.
Article
CAS
PubMed
Google Scholar
Shaw LM, Turner AS, Herry L, Griffiths S, Laurie DA. Mutant alleles of Photoperiod-1 in wheat (Triticum aestivum L.) that confer a late flowering phenotype in long days. PLoS One. 2013;8(11):e79459. doi:10.1371/journal.pone.0079459.
Article
PubMed
PubMed Central
Google Scholar
Nishida H, Yoshida T, Kawakami K, Fujita M, Long B, Akashi Y, et al. Structural variation in the 5’ upstream region of photoperiod-insensitive alleles Ppd-A1a and Ppd-B1a identified in hexaploid wheat (Triticum aestivum L.), and their effect on heading time. Mol Breed. 2013;31(1):27–37. doi:10.1007/s11032-012-9765-0.
Article
CAS
Google Scholar
Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J. Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci U S A. 2003;100(10):6263–8. doi:10.1073/pnas.0937399100.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Wang YY, Wu SW, Yang JP, Liu HW, Zhou Y. A single nucleotide polymorphism at the Vrn-D1 promoter region in common wheat is associated with vernalization response. Theor Appl Genet. 2012;125(8):1697–704. doi:10.1007/s00122-012-1946-z.
Article
PubMed
Google Scholar
Cockram J, Chiapparino E, Taylor SA, Stamati K, Donini P, Laurie DA, et al. Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype. Theor Appl Genet. 2007;115(7):993–1001. doi:10.1007/s00122-007-0626-x.
Article
CAS
PubMed
Google Scholar
Fu DL, Szucs P, Yan LL, Helguera M, Skinner JS, von Zitzewitz J, et al. Large deletions within the first intron in VRN-1 are associated with spring growth habit in barley and wheat (vol 273, pg 54, 2005). Mol Genet Genomics. 2005;274(4):442–3. doi:10.1007/s00438-005-0045-0.
Article
CAS
Google Scholar
Oliver SN, Deng WW, Casao MC, Trevaskis B. Low temperatures induce rapid changes in chromatin state and transcript levels of the cereal VERNALIZATION1 gene. J Exp Bot. 2013;64(8):2413–22. doi:10.1093/jxb/ert095.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kippes N, Debernardi JM, Vasquez-Gross HA, Akpinar BA, Budak H, Kato K, et al. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. Proc Natl Acad Sci U S A. 2015;112(39):E5401–10. doi:10.1073/pnas.1514883112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Park SG, Hannenhalli S, Choi SS. Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals. BMC Genomics. 2014;15:526. doi:10.1186/1471-2164-15-526.
Article
PubMed
PubMed Central
Google Scholar
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, et al. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014;158(6):1431–43. doi:10.1016/j.cell.2014.08.009.
Article
CAS
PubMed
PubMed Central
Google Scholar
Franco-Zorrilla JM, Lopez-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A. 2014;111(6):2367–72. doi:10.1073/pnas.1316278111.
Article
CAS
PubMed
PubMed Central
Google Scholar
Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009;10(9):605–16. doi:10.1038/nrg2636.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mathelier A, Wasserman WW. The next generation of transcription factor binding site prediction. PLoS Comput Biol. 2013;9(9):e1003214. doi:10.1371/journal.pcbi.1003214.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grant CE, Bailey TL, Noble WS. FIMO: scanning for occurrences of a given motif. Bioinformatics. 2011;27(7):1017–8. doi:10.1093/bioinformatics/btr064.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stormo GD. Modeling the specificity of protein-DNA interactions. Quant Biol. 2013;1(2):115–30. doi:10.1007/s40484-013-0012-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mathelier A, Zhao XB, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014;42:D142–7. doi:10.1093/nar/gkt997.
Article
CAS
PubMed
Google Scholar
Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 2006;34:D108–10. doi:10.1093/nar/gkj143.
Article
CAS
PubMed
Google Scholar
Kumari S, Ware D. Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PLoS One. 2013;8(10):e79011. doi:10.1371/journal.pone.0079011.
Article
CAS
PubMed
PubMed Central
Google Scholar
Morey C, Mookherjee S, Rajasekaran G, Bansal M. DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes. Plant Physiol. 2011;156(3):1300–15. doi:10.1104/pp.110.167809.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yilmaz A, Mejia-Guerra MK, Kurz K, Liang XY, Welch L, Grotewold E. AGRIS: the Arabidopsis gene regulatory information server, an update. Nucleic Acids Res. 2011;39:D1118–22. doi:10.1093/nar/gkq1120.
Article
CAS
PubMed
Google Scholar
Kaufmann K, Pajoro A, Angenent GC. Regulation of transcription in plants: mechanisms controlling developmental switches. Nat Rev Genet. 2010;11(12):830–42. doi:10.1038/nrg2885.
Article
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389–402. doi:10.1093/nar/25.17.3389.
Article
CAS
PubMed
PubMed Central
Google Scholar
Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, et al. RSAT 2015: regulatory sequence analysis tools. Nucleic Acids Res. 2015;43:W50–6. doi:10.1093/nar/gkv362.
Article
PubMed
PubMed Central
Google Scholar
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2015. Nucleic Acids Res. 2015;43:D662–9. doi:10.1093/Nar/Gku1010.
Article
PubMed
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8. doi:10.1093/nar/gkp335.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berger MF, Bulyk ML. Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors. Nat Protoc. 2009;4(3):393–411. doi:10.1038/nprot.2008.195.
Article
CAS
PubMed
PubMed Central
Google Scholar
R Core Team. R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2014.
Google Scholar
Storey JD. The positive false discovery rate: A Bayesian interpretation and the q-value. Ann Stat. 2003;31(6):2013–35. doi:10.1214/aos/1074290335.
Article
Google Scholar
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80. doi:10.1186/Gb-2004-5-10-R80.
Article
PubMed
PubMed Central
Google Scholar
Zhao S, Fung-Leung W-P, Bittner A, Ngo K, Liu X. Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells. PLoS One. 2014;9(1):e78644. doi:10.1371/journal.pone.0078644.
Article
PubMed
PubMed Central
Google Scholar
Chen F, Mackey AJ, Stoeckert CJ, Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 2006;34:D363–8. doi:10.1093/Nar/Gkj123.
Article
CAS
PubMed
Google Scholar
Li L, Stoeckert CJ, Roos DS. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178–89. doi:10.1101/Gr.1224503.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tajima F. Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics. 1989;123(3):585–95.
CAS
PubMed
PubMed Central
Google Scholar
Vilella AJ, Blanco-Garcia A, Hutter S, Rozas J. VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics. 2005;21(11):2791–3. doi:10.1093/bioinformatics/bti403.
Article
CAS
PubMed
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–8. doi:10.1093/bioinformatics/btm404.
Article
CAS
PubMed
Google Scholar
Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, Evelo CT, et al. WikiPathways: building research communities on biological pathways. Nucleic Acids Res. 2012;40:D1301–7. doi:10.1093/nar/gkr1074.
Article
CAS
PubMed
Google Scholar
Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, et al. PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput Biol. 2015;11(2):e1004085. doi:10.1371/journal.pcbi.1004085.
Article
PubMed
PubMed Central
Google Scholar
Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D/’Amore R, Allen AM, et al. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012;491(7426):705–10. http://www.nature.com/nature/journal/v491/n7426/full/nature11650.html.
Article
CAS
PubMed
PubMed Central
Google Scholar
Riechmann JL, Ratcliffe OJ. A genomic perspective on plant transcription factors. Curr Opin Plant Biol. 2000;3(5):423–34.
Article
CAS
PubMed
Google Scholar
Ream TS, Woods DP, Schwartz CJ, Sanabria CP, Mahoy JA, Walters EM, et al. Interaction of photoperiod and vernalization determines flowering time of Brachypodium distachyon. Plant Physiol. 2014;164(2):694–709. doi:10.1104/pp.113.232678.
Article
CAS
PubMed
Google Scholar
The International Barley Genome Sequencing Consortium. A physical, genetic and functional sequence assembly of the barley genome. Nature. 2012;491(7426):711–6. http://www.nature.com/nature/journal/v491/n7426/full/nature11543.html.
Google Scholar
The International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014;345(6194):1251788. doi:10.1126/science.1251788.
Article
Google Scholar
Zhu B, Zhang W, Zhang T, Liu B, Jiang J. Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures. Plant Cell. 2015;27:2415–26. doi:10.1105/tpc.15.00537.
Article
CAS
PubMed
PubMed Central
Google Scholar
Stewart AJ, Hannenhalli S, Plotkin JB. Why transcription factor binding sites are ten nucleotides long. Genetics. 2012;192(3):973–85. doi:10.1534/genetics.112.143370.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doniger SW, Huh J, Fay JC. Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Res. 2005;15(5):701–9. doi:10.1101/gr.3578205.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oh YM, Kim JK, Choi S, Yoo JY. Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. Nucleic Acids Res. 2012;40(5):e38. doi:10.1093/nar/gkr1252.
Article
CAS
PubMed
Google Scholar
Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, et al. Diversity and complexity in DNA recognition by transcription factors. Science. 2009;324(5935):1720–3. doi:10.1126/science.1162327.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kielbasa SM, Gonze D, Herzel H. Measuring similarities between transcription factor binding sites. BMC Bioinformatics. 2005;6:237. doi:10.1186/1471-2105-6-237.
Article
PubMed
PubMed Central
Google Scholar
Erill I, O’Neill MC. A reexamination of information theory-based methods for DNA-binding site identification. BMC Bioinformatics. 2009;10:57. doi:10.1186/1471-2105-10-57.
Article
PubMed
PubMed Central
Google Scholar
Becker A, Theissen G. The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol. 2003;29(3):464–89. doi:10.1016/S1055-7903(03)00207-0.
Article
CAS
PubMed
Google Scholar
Dorca-Fornell C, Gregis V, Grandi V, Coupland G, Colombo L, Kater MM. The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems. Plant J. 2011;67(6):1006–17. doi:10.1111/j.1365-313X.2011.04653.x.
Article
CAS
PubMed
Google Scholar
Gu XF, Le C, Wang YZ, Li ZC, Jiang DH, Wang YQ, et al. Arabidopsis FLC clade members form flowering-repressor complexes coordinating responses to endogenous and environmental cues. Nat Commun. 2013;4:1947. doi:10.1038/Ncomms2947.
PubMed
PubMed Central
Google Scholar
Trevaskis B, Hemming MN, Peacock WJ, Dennis ES. HvVRN2 responds to daylength, whereas HvVRN1 is regulated by vernalization and developmental status. Plant Physiol. 2006;140(4):1397–405. doi:10.1104/pp.105.073486.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wei B, Zhang RZ, Guo JJ, Liu DM, Li AL, Fan RC, et al. Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. PLoS One. 2014;9(1):e84781. doi:10.1371/journal.pone.0084781.
Article
PubMed
PubMed Central
Google Scholar
Mihailovich M, Militti C, Gabaldon T, Gebauer F. Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression. Bioessays. 2010;32(2):109–18. doi:10.1002/bies.200900122.
Article
CAS
PubMed
Google Scholar
Sasaki K, Imai R. Pleiotropic roles of cold shock domain proteins in plants. Front Plant Sci. 2012;2:116. doi:10.3389/fpls.2011.00116.
Article
PubMed
PubMed Central
Google Scholar
Girin T, David LC, Chardin C, Sibout R, Krapp A, Ferrario-Mery S, et al. Brachypodium: a promising hub between model species and cereals. J Exp Bot. 2014;65(19):5683–96. doi:10.1093/jxb/eru376.
Article
CAS
PubMed
Google Scholar
Dror I, Golan T, Levy C, Rohs R, Mandel-Gutfreund Y. A widespread role of the motif environment in transcription factor binding across diverse protein families. Genome Res. 2015;25(9):1268–80. doi:10.1101/gr.184671.114.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature. 2004;427(6970):164–7. doi:10.1038/nature02269.
Article
CAS
PubMed
Google Scholar
Pajoro A, Madrigal P, Muino JM, Matus JT, Jin J, Mecchia MA, et al. Dynamics of chromatin accessibility and gene regulation by MADS-domain transcription factors in flower development. Genome Biol. 2014;15(3):R41. doi:10.1186/gb-2014-15-3-r41.
Article
PubMed
PubMed Central
Google Scholar
Shi J, Dong A, Shen WH. Epigenetic regulation of rice flowering and reproduction. Front Plant Sci. 2015;5:803. doi:10.3389/fpls.2014.00803.
Article
PubMed
PubMed Central
Google Scholar
Palme AE, Wright M, Savolainen O. Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps. Mol Biol Evol. 2008;25(12):2567–77. doi:10.1093/molbev/msn194.
Article
CAS
PubMed
Google Scholar
Borneman AR, Gianoulis TA, Zhang ZDD, Yu HY, Rozowsky J, Seringhaus MR, et al. Divergence of transcription factor binding sites across related yeast species. Science. 2007;317(5839):815–9. doi:10.1126/science.1140748.
Article
CAS
PubMed
Google Scholar
Szucs P, Skinner JS, Karsai I, Cuesta-Marcos A, Haggard KG, Corey AE, et al. Validation of the VRN-H2/VRN-H1 epistatic model in barley reveals that intron length variation in VRN-H1 may account for a continuum of vernalization sensitivity. Mol Genet Genomics. 2007;277(3):249–61. doi:10.1007/s00438-006-0195-8.
Article
CAS
PubMed
Google Scholar
Schauer SE, Schluter PM, Baskar R, Gheyselinck J, Bolanos A, Curtis MD, et al. Intronic regulatory elements determine the divergent expression patterns of AGAMOUS-LIKE6 subfamily members in Arabidopsis. Plant J. 2009;59(6):987–1000. doi:10.1111/j.1365-313X.2009.03928.x.
Article
CAS
PubMed
Google Scholar
Ma Q, Liu B, Zhou C, Yin Y, Li G, Xu Y. An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale. Bioinformatics. 2013;29(18):2261–8. doi:10.1093/bioinformatics/btt397.
Article
CAS
PubMed
Google Scholar
Altarawy D, Ismail MA, Ghanem SM. MProfiler: A Profile-Based Method for DNA Motif Discovery. In: Kadirkamanathan V, Sanguinetti G, Girolami M, Niranjan M, Noirel J, editors. Pattern Recognition in Bioinformatics: 4th IAPR International Conference, PRIB 2009, Sheffield, UK, September 7-9, 2009. Proceedings. Berlin, Heidelberg: Springer Berlin Heidelberg; 2009. p. 13–23.
Chapter
Google Scholar