Functional & Integrative Genomics

, Volume 13, Issue 1, pp 57–65 | Cite as

Induction of DREB2A pathway with repression of E2F, jasmonic acid biosynthetic and photosynthesis pathways in cold acclimation-specific freeze-resistant wheat crown

  • Amrit Karki
  • David P. Horvath
  • Fedora Sutton
Original Paper


Winter wheat lines can achieve cold acclimation (development of tolerance to freezing temperatures) and vernalization (delay in transition from vegetative to reproductive phase) in response to low non-freezing temperatures. To describe cold-acclimation-specific processes and pathways, we utilized cold acclimation transcriptomic data from two lines varying in freeze survival but not vernalization. These lines, designated freeze-resistant (FR) and freeze-susceptible (FS), were the source of crown tissue RNA. Well-annotated differentially expressed genes (p ≤ 0.005 and fold change ≥ 2 in response to 4 weeks cold acclimation) were used for gene ontology and pathway analysis. “Abiotic stimuli” was identified as the most enriched and unique for FR. Unique to FS was “cytoplasmic components.” Pathway analysis revealed the “triacylglycerol degradation” pathway as significantly downregulated and common to both FR and FS. The most enriched of FR pathways was “neighbors of DREB2A,” with the highest positive median fold change. The “13-LOX and 13-HPL” and the “E2F” pathways were enriched in FR only with a negative median fold change. The “jasmonic acid biosynthesis” pathway and four “photosynthetic-associated” pathways were enriched in both FR and FS but with a more negative median fold change in FR than in FS. A pathway unique to FS was “binding partners of LHCA1,” which was enriched only in FS with a significant negative median fold change. We propose that the DREB2A, E2F, jasmonic acid biosynthesis, and photosynthetic pathways are critical for discrimination between cold-acclimated lines varying in freeze survival.


Gene ontology (GO) Pathway Cold acclimation Vernalization Freeze survival Winter wheat DREB2A Jasmonic acid E2F. 



This work was part of the Ph.D. training program of A.K and was made possible by support from the Sutton Laboratory, the SDSU Plant Science Dept., the Mathematics and Statistics Dept., the SDSU Experiment Station, and the Horvath Laboratory at USDA, Fargo, ND.

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  1. Beißbarth T, Speed TP (2004) GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics 20(9):1464–1465PubMedCrossRefGoogle Scholar
  2. Bogner V, Leidel BA, Kanz KG, Mutschler W, Neugebauer EA, Biberthaler P (2011) Pathway analysis in microarray data: a comparison of two different pathway analysis devices in the same data set. Shock 35(3):245–251PubMedCrossRefGoogle Scholar
  3. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19(2):185–193PubMedCrossRefGoogle Scholar
  4. Chauvin LP, Houd M, Sarhan F (1993) A leaf-specific gene stimulated by light during wheat acclimation to low temperatures. Plant Mol Biol 23:255–265PubMedCrossRefGoogle Scholar
  5. Chen T-H, Gusta L, Fowler DB (1983) Freezing injury and root development in winter cereals. Plant Physiol 73(3):773–777PubMedCrossRefGoogle Scholar
  6. Christova PK, Christov NK, Imai R (2006) A cold inducible multidomain cystatin from winter wheat inhibits growth of the snow mold fungus, Microdochium nivale. Planta 223(6):1207PubMedCrossRefGoogle Scholar
  7. Danyluk J, Houde M, Rassart E, Sarhan F (1994) Differential expression of a gene encoding an acidic dehydrin in chilling sensitive and freezing tolerant Gramineae species. FEBS Lett 344(1):20–24PubMedCrossRefGoogle Scholar
  8. de Jager SM, Menges M, Bauer U-M, Murray JAH (2001) Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol Biol 47(4):555–568PubMedCrossRefGoogle Scholar
  9. Dhillon T, Pearce SP, Stockinger EJ, Distelfeld A, Li C, Knox AK, Vashegyi I, Vágújfalvi A, Galiba G, Dubcovsky J (2010a) Regulation of freezing tolerance and flowering in temperate cereals: the VRN-1 connection. Plant Phys 153(4):1846–1858CrossRefGoogle Scholar
  10. del Pozo JC, Boniotti MB, Gutierrez C (2002) Arabidopsis E2F2 functions in cell division and is degraded by the ubiquitin-SCFAtSKP2 pathway in response to light. Plant Cell 14:3057–3071PubMedCrossRefGoogle Scholar
  11. Dhillon T, Pearce SP, Stockinger EJ, Distelfeld A, Li C, Knox AK, Vashegyi I, Vágújfalvi A, Galiba G, Dubcovsky J (2010b) Regulation of freezing tolerance and flowering in temperate cereals: the VRN-1 connection. Plant Phys 153(4):1846–1858CrossRefGoogle Scholar
  12. Egawa C, Kobayashi F, Ishibashi M, Nakamura T, Nakamura C, Takumi S (2006) Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat. Genes Genet Syst 81(2):77–91PubMedCrossRefGoogle Scholar
  13. Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. The Plant Cell 14(8):1675–1690PubMedCrossRefGoogle Scholar
  14. Gana JA, Sutton F, Kenefick DG (1997) cDNA structure and expression patterns of a low-temperature-specific wheat gene tacr7. Plant Mol Biol 34(4):643–650PubMedCrossRefGoogle Scholar
  15. Ganeshan S, Sharma P, Young L, Kumar A, Fowler DB, Chibbar RN (2011) Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance. Plant Mol Biol 75(4–5):379–398PubMedCrossRefGoogle Scholar
  16. Gong Z, Dong C-H, Lee H, Zhu J, Xiong L (2005) A DEAD box RNA helicase is essential for mRNA export and important for development and stress response in Arabidopsis. Plant Cell 17(1):256–267PubMedCrossRefGoogle Scholar
  17. Gray GR, Chauvin LP, Sarhan F, Huner NPA (1997) Cold acclimation and freezing tolerance. Plant Physiol 114(2):467–474PubMedGoogle Scholar
  18. Gulick PJ, Drouin S, Yu Z, Danyluk J, Poisson G, Monroy AF, Sarhan F (2005) Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48(5):913–923PubMedCrossRefGoogle Scholar
  19. Gusta LV, Weiser CI (1972) Nucleic acid and protein changes in relation to cold acclimation and freezing injury of Korean boxwood leaves. Plant Physiol 49(1):9l–96lCrossRefGoogle Scholar
  20. Gusta LV, Trischuk R, Weiser CJ (2005) Plant cold acclimation: the role of abscisic acid. J Plant growth Regul 24:308–318CrossRefGoogle Scholar
  21. Guy CL (1990) Cold acclimation and freezing stress tolerance: role of protein metabolism. Annu Rev Plant Physiol Plant Mol Biol 41:187–223CrossRefGoogle Scholar
  22. Han K (1997) Partial cDNA of freeze resistance-related gene in wheat isolated by differential display. In Master of Science Thesis South Dakota State. University, Plant ScienceGoogle Scholar
  23. Hannah MA, Heyer AG, Hincha DK (2005) A global survey of gene regulation during cold acclimation in Arabidopsis thaliana. PLoS Genet 1(2):e26PubMedCrossRefGoogle Scholar
  24. Houde M, Danyluk J, Laliberts JF, Rassart E, Dhindsa RS, Sarhan F (1992) Cloning, characterization and expression of a cDNA encoding a 50 kilodalton protein specifically induced by cold acclimation in wheat. Plant Physiol 99(4):1381–1387PubMedCrossRefGoogle Scholar
  25. Houde M, Belcaid M, Ouellet F, Danyluk J, Monroy AF, Dryanova A, Gulick P, Bergeron A, Laroche A, Links MG, MacCarthy L, Crosby WL, Sarhan F (2006) Wheat EST resources for functional genomics of abiotic stress. BMC Genomics 7:149PubMedCrossRefGoogle Scholar
  26. Hughes MA, Dunn MA (1996) The molecular biology of plant acclimation to low temperature. J Exp Bot 47(3):291–305CrossRefGoogle Scholar
  27. Irizarry RA, Bolstad BM, Collins F, Cope LM, Hobbs B, Speed TP (2003) Summaries of Affymetrix gene chip probe level data. Nucleic Acids Res 31(4):e15PubMedCrossRefGoogle Scholar
  28. Janská A, Aprile A, Zamecnik J (2011) Transcriptional responses of winter barley to cold indicate nucleosome remodelling as a specific feature of crown tissues. Funct Integr Genomics 11(2):307–325PubMedCrossRefGoogle Scholar
  29. Kenefick DG, Koepke JA, Sutton F (2002) Plant water uptake by hard red winter wheat (Triticum aestivum L.) genotypes at 2 degrees C and low light intensity. BMC Plant Biol 2:8PubMedCrossRefGoogle Scholar
  30. Kosmala A, Bocian A, Rapacz M, Jurczyk B, Zwierzykowski Z (2009) Identification of leaf proteins differentially accumulated during cold acclimation between Festuca pratensis plants with distinct levels of frost tolerance. J Exp Bot 60(12):3595–3609PubMedCrossRefGoogle Scholar
  31. Kume S, Kobayashi F, Ishibashi M, Ohno R, Nakamura C, Takumi S (2005) Differential and coordinated expression of Cbf and Cor/Lea genes during long-term cold acclimation in two wheat cultivars showing distinct levels of freezing tolerance. Genes Genet Syst 80(3):185–197PubMedCrossRefGoogle Scholar
  32. Kwon C, Bednarek P, Schulze-Lefert P (2008) Secretory pathways in plant immune responses. Plant Physiol 147(4):1575–1583PubMedCrossRefGoogle Scholar
  33. Laudencia-Chingcuanco D, Ganeshan S, You F, Fowler B, Chibbar R, Anderson O (2011) Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.). BMC Genomics 12:299PubMedCrossRefGoogle Scholar
  34. Lee B, Lee H, Xiong L, Zhu J-K (2002) A mitochondrial complex I defect impairs cold-regulated nuclear gene expression. The Plant Cell 14(6):1235–1251PubMedCrossRefGoogle Scholar
  35. Liu Q, Sakuma Y, Abe H, Kasuga M, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an ERF/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):1391–1406PubMedGoogle Scholar
  36. Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D (2002) The E2F family of transcription factors from Arabidopsis thaliana. J Biol Chem 277(12):9911–9919PubMedCrossRefGoogle Scholar
  37. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res., 33 (dtabase issue): D284–D288Google Scholar
  38. Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Research 38 (Database issue): D204-D210.Google Scholar
  39. Monroy AF, Dryanova A, Malette B, Oren DH, Ridha Farajalla M, Liu W, Danyluk J, Ubayasena LW, Kane K, Scoles GJ, Sarhan F, Gulick PJ (2007) Regulatory gene candidates and gene expression analysis of cold acclimation in winter and spring wheat. Plant Mol Biol 64(4):409–423PubMedCrossRefGoogle Scholar
  40. Olien CR (1967) Freezing stress and survival. Annu Rev Plant Physiol 18:387–408CrossRefGoogle Scholar
  41. Olien CR, Clark JL (1993) Changes in soluble carbohydrate composition of barley, wheat, and rye during winter. Crop Sci 85(1):21–29Google Scholar
  42. Pearce RS, Houlston CE, Atherton KM, Rixon JE, Harrison P, Hughes MA, Dunn MA (1998) Localization of expression of three cold-induced genes, blt101, blt4.9, and blt14, in different tissues of the crown and developing leaves of cold-acclimated cultivated barley. Plant Physiol 117(3):787–795PubMedCrossRefGoogle Scholar
  43. Ramirez-Parra E, Xie Q, Boniotti MB, Gutierrez C (1999) The cloning of plant E2F, a retinoblastoma-binding protein, reveals unique and conserved features with animal G(1)/S regulators. Nucleic Acids Res 27(17):3527–3533PubMedCrossRefGoogle Scholar
  44. Sakamoto H, Matsuda O, Iba K (2008) ITN1, a novel gene encoding an ankyrin-repeat protein that affects the ABA-mediated production of reactive oxygen species and is involved in salt-stress tolerance in Arabidopsis thaliana. Plant J 56(3):411–422PubMedCrossRefGoogle Scholar
  45. Seki M, Narusaka M, Ishida J, Nanjo T, Fujita M, Oono Y, Kamiya A, Nakajima M, Enju A, Sakurai T, Satou M, Akiyama K, Taji T, Yamaguchi-Shinozaki K, Carninci P, Kawai J, Hayashizaki Y, Shinozaki K (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. The Plant Journal 31(3):279–292PubMedCrossRefGoogle Scholar
  46. Sharma P, Sharma N, Deswal R (2005) The molecular biology of the low-temperature response in plants. Bioessays 27(10):1048–1059PubMedCrossRefGoogle Scholar
  47. Skinner DZ (2009) Post-acclimation transcriptome adjustment is a major factor in freezing tolerance of winter wheat. Funct Integr Genomics 9(4):513–523PubMedCrossRefGoogle Scholar
  48. Su C-F, Wang Y-C, Hsieh T-H, Lu C-A, Tseng TH, Yu SM (2010) A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiol 153(1):145–158PubMedCrossRefGoogle Scholar
  49. Sutton F, Ding X, Kenefick DG (1992) Group 3 LEA gene HVA1 regulation by cold acclimation and de-acclimation in two barley cultivars with varying freeze resistance. Plant Physiol 99(1):338–340PubMedCrossRefGoogle Scholar
  50. Sutton F, Chen D, Ge X, Kenefick D (2009) Cbf genes of the Fr-A2 allele are differentially regulated between long-term cold acclimated crown tissue of freeze-resistant and -susceptible, winter wheat mutant lines. BMC Plant Biology 9:34PubMedCrossRefGoogle Scholar
  51. Thomashow MF (1999) Plant cold acclimation: freezing tolerance, genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol 50:571–599PubMedCrossRefGoogle Scholar
  52. Wang Y, Gilbreath TM III, Kukutla P, Yan G, Xu J (2011) Dynamic gut microbiome across life history of the malaria mosquito Anopheles gambiae in Kenya. PLoS One 6(9):e24767. doi: 10.1371/journal.pone.0024767 PubMedCrossRefGoogle Scholar
  53. Wells DG, Lay CL, Buchenau GW, Johnson VA, Finney KF (1969) Registration of Winoka wheat. Crop Science 9(9):526CrossRefGoogle Scholar
  54. Winfield MO, Lu C, Wilson ID, Coghill JA, Edwards KJ (2010) Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol J 8(7):749–771PubMedCrossRefGoogle Scholar
  55. Wisniewski M, Bassett C, Gusta LV (2003) An overview of cold hardiness in woody plants: seeing the forest through the trees. Hort Science 38(5):952–959Google Scholar
  56. Xin Z, Browse J (2000) Cold comfort farm: the acclimation of plants to freezing temperatures. Plant Cell Environ 23(9):893–902CrossRefGoogle Scholar
  57. Young MD, Oshlk A, Wakefield MJ, Smyth GK (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:14CrossRefGoogle Scholar
  58. Zhang L, Dunn MA, Pearce RS, Hughes MA (1993) Analysis of organ specificity of a low-temperature-responsive gene family in rye (Secale cereale L). J Exp Bot 44(12):1787–1793CrossRefGoogle Scholar
  59. Zhu J, Jeong JC, Zhu Y, Sokolchik I, Miyazaki S, Zhu J-K, Hasegawa PM, Bohnert HJ, Shi H, Yun D-J, Bressan RA (2008) Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance. PNAS 105(12):4945–4950PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.South Dakota State UniversityBrookingsUSA
  2. 2.United States Department of AgricultureAgriculture Research Services, Bioscience Research LaboratoryFargoUSA
  3. 3.University of WisconsinMilwaukeeUSA

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