Wheat CBF gene family: Identification of polymorphisms in the CBF coding sequence

Genome

Volumn 55, Issue 12, 2012, Pages 865-881

  Mohseni, Sara ^a   Che, Hua ^a   Djillali, Zakia ^a   Dumont, Estelle ^a   Nankeu, Joseph ^a   Danyluk, Jean ^a  

^a UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

Author keywords

CBF transcription factors; Cold acclimation; Freezing tolerance; Polymorphisms

Indexed keywords

TRANSACTIVATOR PROTEIN; VEGETABLE PROTEIN;

ACCLIMATIZATION; ALLELE; ARTICLE; BREEDING; CHEMISTRY; COLD; GENETIC POLYMORPHISM; GENETICS; MULTIGENE FAMILY; OPEN READING FRAME; PLANT GENE; POLYPLOIDY; PROTEIN TERTIARY STRUCTURE; PSEUDOGENE; WHEAT;

ACCLIMATIZATION; ALLELES; BREEDING; COLD TEMPERATURE; GENES, PLANT; MULTIGENE FAMILY; OPEN READING FRAMES; PLANT PROTEINS; POLYMORPHISM, GENETIC; POLYPLOIDY; PROTEIN STRUCTURE, TERTIARY; PSEUDOGENES; TRANS-ACTIVATORS; TRITICUM;

TRITICEAE; TRITICUM AESTIVUM;

EID: 84870948617     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2012-0112     Document Type: Article

References (48)

1. Akhunov E.D. Akhunova A.R. Linkiewicz A.M. Dubcovsky J. Hummel D. Lazo G. et al. 2003. Synteny perturbations between wheat homoeologous chromosomes caused by locus duplications and deletions correlate with recombination rates. Proc. Natl. Acad. Sci. U.S.A. 100 (19): 10836-10841. 10.1073/pnas.1934431100 12960374
2. Allen M.D. Yamasaki K. Ohme-Takagi M. Tateno M. Suzuki M. 1998. A novel mode of DNA recognition by a β-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J. 17 (18): 5484-5496. 10.1093/emboj/17.18.5484 9736626
3. Badawi M. Danyluk J. Boucho B. Houde M. Sarhan F. 2007. The CBF gene family in hexaploid wheat and its relationship to the phylogenetic complexity of cereal CBF s. Mol. Genet. Genomics, 277 (5): 533-554. 10.1007/s00438-006-0206-9 17285309
4. Båga M. Chodaparambil S.V. Limin A.E. Pecar M. Fowler D.B. Chibbar R.N. 2007. Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat. Funct. Integr. Genomics, 7 (1): 53-68. 10.1007/s10142-006-0030-7 16775685
5. Callebaut I. Labesse G. Durand P. Poupon A. Canard L. Chomilier J. et al. 1997. Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell. Mol. Life Sci. 53 (8): 621-645. 10.1007/s000180050082 9351466
6. Canella D. Gilmour S.J. Kuhn L.A. Thomashow M.F. 2010. DNA binding by the Arabidopsis CBF1 transcription factor requires the PKKP/RAGRxKFxETRHP signature sequence. Biochim. Biophys. Acta, 1799 (5-6): 454-462. 10.1016/j.bbagrm.2009. 11.017 19948259
7. Chandler J.W. Cole M. Flier A. Grewe B. Werr W. 2007. The AP2 transcription factors DORNRÖSCHEN and DORNRÖSCHEN-LIKE redundantly control Arabidopsis embryo patterning via interaction with PHAVOLUTA. Development, 134 (9): 1653-1662. 10.1242/dev.001016 17376809
8. Chinnusamy V. Zhu J. Zhu J.K. 2007. Cold stress regulation of gene expression in plants. Trends Plant Sci. 12 (10): 444-451. 10.1016/j.tplants. 2007.07.002 17855156
9. Comai L. 2005. The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6 (11): 836-846. 10.1038/nrg1711 16304599
10. den Dunnen J.T. Antonarakis S.E. 2000. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat. 15 (1): 7-12. 10612815
11. Francia E. Rizza F. Cattivelli L. Stanca A.M. Galiba G. Tóth B. et al. 2004. Two loci on chromosome 5H determine low-temperature tolerance in a 'Nure' (winter) × 'Tremois' (spring) barley map. Theor. Appl. Genet. 108 (4): 670-680. 10.1007/s00122-003-1468-9 14576984
12. Francia E. Barabaschi D. Tondelli A. Laidò G. Rizza F. Stanca A.M. et al. 2007. Fine mapping of a Hv CBF gene cluster at the frost resistance locus Fr-H2 in barley. Theor. Appl. Genet. 115 (8): 1083-1091. 10.1007/s00122-007-0634-x 17763839
13. Fricano A. Rizza F. Faccioli P. Pagani D. Pavan P. Stella A. et al. 2009. Genetic variants of HvCbf14 are statistically associated with frost tolerance in a European germplasm collection of Hordeum vulgare. Theor. Appl. Genet. 119 (7): 1335-1348. 10.1007/s00122-009-1138-7 19756475
14. Gaboriaud C. Bissery V. Benchetrit T. Mornon J.P. 1987. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Lett. 224 (1): 149-155. 10.1016/0014-5793(87)80439-8 3678489
15. Galiba G. Quarrie S.A. Sutka J. Morgounov A. Snape J.W. 1995. RFLP mapping of the vernalization (Vrn1) and frost resistance (Fr1) genes on chromosome 5A of wheat. Theor. Appl. Genet. 90 (7-8): 1174-1179. 10.1007/BF00222940
16. Galiba G. Vágújfalvi A. Li C. Soltész A. Dubcovsky J. 2009. Regulatory genes involved in the determination of frost tolerance in temperate cereals. Plant Sci. 176 (1): 12-19. 10.1016/j.plantsci.2008.09.016
17. Gill B.S. Appels R. Botha-Oberholster A.-M. Buell C.R. Bennetzen J.L. Chalhoub B. et al. 2004. A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics, 168 (2): 1087-1096. 10.1534/genetics.104.034769 15514080
18. Hahn M.W. 2009. Distinguishing among evolutionary models for the maintenance of gene duplicates. J. Hered. 100 (5): 605-617. 10.1093/jhered/ esp047
19. Houde M. Belcaid M. Ouellet F. Danyluk J. Monroy A. Dryanova A. et al. 2006. Wheat EST resources for functional genomics of abiotic stress. BMC Genomics, 7: 149. 10.1186/1471-2164-7-149 16772040
20. Huang X. Madan A. 1999. CAP3: a DNA sequence assembly program. Genome Res. 9 (9): 868-877. 10.1101/gr.9.9.868 10508846
21. Huang S. Sirikhachornkit A. Faris J. Su X. Gill B. Haselkorn R. Gornicki P. 2002 a. Phylogenetic analysis of the acetyl-CoA carboxylase and 3-phosphoglycerate kinase loci in wheat and other grasses. Plant Mol. Biol. 48 (5-6): 805-820. 10.1023/A:1014868320552 11999851
22. Huang S. Sirikhachornkit A. Su X. Faris J. Gill B. Haselkorn R. Gornicki P. 2002 b. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum / Aegilops complex and the evolutionary history of polyploid wheat. Proc. Natl. Acad. Sci. U.S.A. 99 (12): 8133-8138. 10.1073/pnas.072223799 12060759
23. Jaglo K.R. Kleff S. Amundsen K.L. Zhang X. Haake V. Zhang J.Z. et al. 2001. Components of the Arabidopsis C-repeat/dehydration-responsive element binding factor cold-response pathway are conserved in Brassica napus and other plant species. Plant Physiol. 127 (3): 910-917. 10.1104/pp.010548 11706173
24. Jaglo-Ottosen K.R. Gilmour S.J. Zarka D.G. Schabenberger O. Thomashow M.F. 1998. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science, 280 (5360): 104-106. 10.1126/science.280.5360.104 9525853
25. Kellogg E.A. 2001. Evolutionary history of the grasses. Plant Physiol. 125 (3): 1198-1205. 10.1104/pp.125.3.1198 11244101
26. m2 in Triticum monococcum. Plant Mol. Biol. 67 (3): 257-270. 10.1007/s11103-008-9316-6 18317935
27. Knox A.K. Dhillon T. Cheng H. Tondelli A. Pecchioni N. Stockinger E.J. 2010. CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor. Appl. Genet. 121 (1): 21-35. 10.1007/s00122-010-1288-7 20213518
28. Limin A.E. Danyluk J. Chauvin L.P. Fowler D.B. Sarhan F. 1997. Chromosome mapping of low-temperature induced WCS120 family genes and regulation of cold-tolerance expression in wheat. Mol. Gen. Genet. 253 (6): 720-727. 10.1007/s004380050376 9079883
29. Liu Q. Kasuga M. Sakuma Y. Abe H. Miura S. Yamaguchi-Shinozaki K. Shinozaki K. 1998. Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought-and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell, 10 (8): 1391-1406. 9707537
30. Liu Y. Zhao T.-J. Liu J.-M. Liu W.-Q. Liu Q. Yan Y.-B. Zhou H.-M. 2006. The conserved Ala37 in the ERF/AP2 domain is essential for binding with the DRE element and the GCC box. FEBS Lett. 580 (5): 1303-1308. 10.1016/j.febslet.2006. 01.048 16457823
31. Mao Y. Pavangadkar K.A. Thomashow M.F. Triezenberg S.J. 2006. Physical and functional interactions of Arabidopsis ADA2 transcriptional coactivator proteins with the acetyltransferase GCN5 and with the cold-induced transcription factor CBF1. Biochim. Biophys. Acta, 1759 (1-2): 69-79. 10.1016/j.bbaexp.2006. 02.006 16603259
32. m2 in Triticum monococcum. Mol. Genet. Genomics, 275 (2): 193-203. 10.1007/s00438-005-0076-6 16362370
33. Nakano T. Suzuki K. Fujimura T. Shinshi H. 2006. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol. 140 (2): 411-432. 10.1104/pp.105.073783 16407444
34. Pavangadkar K. Thomashow M.F. Triezenberg S.J. 2010. Histone dynamics and roles of histone acetyltransferases during cold-induced gene regulation in Arabidopsis. Plant Mol. Biol. 74 (1-2): 183-200. 10.1007/s11103-010-9665-9 20661629
35. Qi L.L. Echalier B. Chao S. Lazo G.R. Butler G.E. Anderson O.D. et al. 2004. A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics, 168 (2): 701-712. 10.1534/genetics.104.034868 15514046
36. Rozen, S., and Skaletsky, H.J. 2000. Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols: methods in molecular biology. Edited by S. Krawetz and S. Misener. Humana Press, Totowa, N.J. pp. 365-386.
37. Sakuma Y. Liu Q. Dubouzet J.G. Abe H. Shinozaki K. Yamaguchi-Shinozaki K. 2002. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration-and cold-inducible gene expression. Biochem. Biophys. Res. Commun. 290 (3): 998-1009. 10.1006/bbrc.2001.6299 11798174
38. Sandve S.R. Fjellheim S. 2010. Did gene family expansions during the Eocene-Oligocene boundary climate cooling play a role in Pooideae adaptation to cool climates? Mol. Ecol. 19 (10): 2075-2088. 10.1111/j.1365-294X.2010.04629.x 20406386
39. Skinner J.S. von Zitzewitz J. Szucs P. Marquez-Cedillo L. Filichkin T. Amundsen K. et al. 2005. Structural, functional, and phylogenetic characterization of a large CBF gene family in barley. Plant Mol. Biol. 59 (4): 533-551. 10.1007/s11103-005-2498-2 16244905
40. Skinner J.S. Sz̈ucs P. von Zitzewitz J. Marquez-Cedillo L. Filichkin T. Stockinger E.J. et al. 2006. Mapping of barley homologs to genes that regulate low temperature tolerance in Arabidopsis. Theor. Appl. Genet. 112 (5): 832-842. 10.1007/s00122-005-0185-y 16365758
41. Snape J.W. Sarma R.N. Quarrie S.A. Fish L.J. Galiba G. Sutka J. 2001. Mapping genes for flowering time and frost tolerance in cereals using precise genetic stocks. Euphytica, 120 (3): 309-315. 10.1023/A:1017541505152
42. Stockinger E.J. Skinner J.S. Gardner K.G. Francia E. Pecchioni N. 2007. Expression levels of barley Cbf genes at the Frost resistance-H2 locus are dependent upon alleles at Fr-H1 and Fr-H2. Plant J. 51 (2): 308-321. 10.1111/j.1365-313X.2007.0141.x 17559507
43. Tamura K. Peterson D. Peterson N. Stecher G. Nei M. Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28 (10): 2731-2739. 10.1093/molbev/msr121 21546353
44. Thomashow M.F. 1999. Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu. Rev. Plant Physiol. Plant Mol. Biol. 50 (1): 571-599. 10.1146/annurev.arplant.50.1.571 15012220
45. Tóth B. Galiba G. Fehér E. Sutka J. Snape J.W. 2003. Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor. Appl. Genet. 107 (3): 509-514. 10.1007/s00122-003-1275-3 12734655
46. Wang Z. Triezenberg S.J. Thomashow M.F. Stockinger E.J. 2005. Multiple hydrophobic motifs in Arabidopsis CBF1 COOH-terminus provide functional redundancy in trans-activation. Plant Mol. Biol. 58 (4): 543-559. 10.1007/s11103-005-6760-4 16021338
47. Xue G.-P. 2002. Characterization of the DNA-binding profile of barley HvCBF1 using an enzymatic method for rapid, quantitative and high-throughput analysis of the DNA binding activity. Nucleic Acids Res. 30 (15): e77. 10.1093/nar/gnf076 12140339
48. Xue G.-P. 2003. The DNA-binding activity of an AP2 transcriptional activator HvCBF2 involved in regulation of low temperature responsive genes in barley is modulated by temperature. Plant J. 33 (2): 373-383. 10.1046/j.1365-313X.2003.01630.x 12535350