Article | 02. 2015 Vol. 33, Issue. 1
Time-based Expression Networks of Genes Related to Cold Stress in Brassica rapa ssp. pekinensis



Department of Horticultural Biotechnology, Kyunghee University1




2015.02. 114:123


PDF XML




Plants can respond and adapt to cold stress through regulation of gene expression in various biochemical and physiological processes. Cold stress triggers decreased rates of metabolism, modification of cell walls, and loss of membrane function. Hence, this study was conducted to construct coexpression networks for time-based expression pattern analysis of genes related to cold stress in Chinese cabbage (Brassica rapa ssp. pekinensis). B. rapa cold stress networks were constructed with 2,030 nodes, 20,235 edges, and 34 connected components. The analysis suggests that similar genes responding to cold stress may also regulate development of Chinese cabbage. Using this network model, it is surmised that cold tolerance is strongly related to activation of chitinase antifreeze proteins by WRKY transcription factors and salicylic acid signaling, and to regulation of stomatal movement and starch metabolic processes for systemic acquired resistance in Chinese cabbage. Moreover, within 48 h, cold stress triggered transition from vegetative to reproductive phase and meristematic phase transition. In this study, we demonstrated that this network model could be used to precisely predict the functions of cold resistance genes in Chinese cabbage.



1. Alonso-Blanco, C., M.G. Aarts, L. Bentsink, J.J. Keurentjes, M. Reymond, D. Vreugdenhil, and M. Koornneef. 2009. What has natural variation taught us about plant development, physiology, and adaptation? Plant Cell 21:1877–1896.  

2. Ananga, A.O., E. Cebert, J.W. Ochieng, S. Kumar, D. Kambiranda, H. Vasanthaiah, V. Tsolova, Z. Senwo, K. Konan, and F.N. Anike. 2012. Prospects for transgenic and molecular breeding for cold tolerance in canola (Brassica napus L.), p. 1-32. In: U.G. Akpan (ed.). Oilseeds. InTech Press, Rijeka, Hrv.  

3. Barah, P., N.D. Jayavelu, S. Rasmussen, H.B. Nielsen, J. Mundy, and A.M. Bones. 2013. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. BMC Genomics 14:722.  

4. Barnes, J. and P. Hut. 1986. A hierarchical O (N log N) force- calculation algorithm. Nature 324:446-449.  

5. Bindea, G., B. Mlecnik, H. Hackl, P. Charoentong, M. Tosolini, A. Kirilovsky, W.H. Fridman, F. Pagès, Z. Trajanoski, and J. Galon. 2009. ClueGO: A cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091-1093.  

6. Brassica rapa Genome Sequencing Project Consortium. 2011. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 43:1035-1039.  

7. Chawade, A., M. Bräutigam, A. Lindlöf, O. Olsson, and B. Olsson. 2007. Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co- expression patterns, promoter motifs and transcription factors. BMC Genomics 8:304.  

8. Chinnusamy, V., J. Zhu, and J.K. Zhu. 2007. Cold stress regulation of gene expression in plants. Trends Plant Sci. 12:444-451.   

9. Cho, H.Y., S.G. Hwang, D.S. Kim, and C.S Jang. 2012. Genome- wide transcriptome analysis of rice genes responsive to chilling stress. Can. J. Plant Sci. 92:447-460.  

10. Ding, C.K., C.Y. Wang, K.C. Gross, and D.L. Smith. 2002. Jasmonate and salicylate induce the expression of pathogenesis- related-protein genes and increase resistance to chilling injury in tomato fruit. Planta 214:895-901.  

11. Eulgem, T., P.J. Rushton, S. Robatzek, and I.E. Somssich. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5:199-206.  

12. Fujimoto, S.Y., M. Ohta, A. Usui, H. Shinshi, and M. Ohme- Takagi. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12:393-404.  

13. Grene, R., C. Klumas, H. Suren, K. Yang, E. Collakova, E. Myers, L.S. Heath, and J.A. Holliday. 2012. Mining and visualization of microarray and metabolomic data reveal extensive cell wall remodeling during winter hardening in Sitka spruce (Picea sitchensis). Front. Plant Sci. 3:241.  

14. Griffith, M., P. Ala, D.S. Yang, W.C. Hon, and B.A. Moffatt. 1992. Antifreeze protein produced endogenously in winter rye leaves. Plant Physiol. 100:593-596.  

15. Hara, M., K. Oki, K. Hoshino, and T. Kuboi. 2004. Effects of sucrose on anthocyanin production in hypocotyl of two radish (Raphanus sativus) varieties. Plant Biotechnol. 21:401-405.  

16. He, Y. and R.M. Amasino. 2005. Role of chromatin modification in flowering-time control. Trends Plant Sci. 10:30-35.  

17. Hirose, T., N. Aoki, Y. Harada, M. Okamura, Y. Hashida, R. Ohsugi, M. Akio, H. Hirochika, and T. Terao. 2013. Disruption of a rice gene for α-glucan water dikinase, OsGWD1, leads to hyperaccumulation of starch in leaves but exhibits limited effects on growth. Front. Plant Sci. 4:147.   

18. Hon, W.C., M. Griffith, P. Chong, and D. Yang. 1994. Extraction and isolation of antifreeze proteins from winter rye (Secale cereale L.) leaves. Plant Physiol. 104:971-980.  

19. Hua, Y.J., G.L. Yuan, Y. Man, Q.X. Hua, and Z.M. Fang. 2008. Salicylic acid induced enhancement of cold tolerance through activation of antioxidative capacity in watermelon. Sci. Hortic. 118:200-205.  

20. Huang, D.W., B.T. Sherman, and R.A. Lempicki. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44-57.  

21. Janská, A., P. Marsík, S. Zelenková, and J. Ovesná. 2010. Cold stress and acclimation - What is important for metabolic adjustment? Plant Biol. 12:395-405.   

22. Kamata, T. and M. Uemura. 2004. Solute accumulation in heat seedlings during cold acclimation: Contribution to increased freezing tolerance. Cryo. Letters 5:311-322.  

23. Kanehisa, M., S. Goto, Y. Sato, M. Furumichi, and M. Tanabe. 2012. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic. Acids Res. 40:D109-114.  

24. Kang, H.M. and M.E. Saltveit. 2002. Chilling tolerance of maize, cucumber and rice seedling leaves and roots are differentially affected by salicylic acid. Physiol. Plant. 115:571-576.  

25. Kim, J.S., H.J. Jung, H.J. Lee, K.A. Kim, C.H. Goh, Y. Woo, S.H. Oh, Y.S. Han, and H. Kang. 2008. Glycine-rich RNA- binding protein 7 affects abiotic stress responses by regulating stomata opening and closing in Arabidopsis thaliana. Plant J. 55:455-466.  

26. Korn, M., S. Peterek, H.P. Mock, A.G. Heyer, and D.K. Hincha. 2008. Heterosis in the freezing tolerance, and sugar and flavonoid contents of crosses between Arabidopsis thaliana accessions of widely varying freezing tolerance. Plant Cell Environ. 31:813-827.  

27. Kreps, J.A., Y. Wu, H.S. Chang, T. Zhu, X. Wang, and J.F. Harper. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol. 130:2129-2141.  

28. Kunkel, B.N. and D.M. Brooks. 2002. Cross talk between signaling pathways in pathogen defense. Curr. Opin. Plant Biol. 5:325-331.  

29. Lee, B.H., H. Lee, L. Xiong, and J.K. Zhu. 2002. A mitochondrial complex I defect impairs cold-regulated nuclear gene expression. Plant Cell 14:1235-1251.  

30. Lee, S.C., M.H. Lim, J.A. Kim, S.I. Lee, J.S. Kim, M. Jin, S.J. Kwon, J.H. Mun, Y.K. Kim, H.U. Kim, Y. Hur, and B.S. Park. 2008. Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray. Mol. Cells 26:595-605.  

31. Leyva, A., J.A. Jarillo, J. Salinas, and J.M. Martinez-Zapater. 1995. Low temperature induces the accumulation of phenylalanine ammonia-lyase and chalcone synthase mRNAs of Arabidopsis thaliana in a light-dependent manner. Plant Physiol. 108:39-46.  

32. Luan, S. 2002. Signaling drought in guard cells. Plant Cell Environ. 25:229-237.  

33. Maruyama, K., M. Takeda, S. Kidokoro, K. Yamada, Y. Sakuma, K. Urano, M. Fujita, K. Yoshiwara, S. Matsukura, Y. Morishita, R. Sasaki, H. Suzuki, K. Saito, D. Shibata, K. Shinozaki, and K. Yamaguchi-Shinozaki. 2009. Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol. 150:1972-1980.  

34. Naika, M., K. Shameer, and R. Sowdhamini. 2013. Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics. Mol. Biosyst. 9:1888-1908.  

35. Penfield, S. 2008. Temperature perception and signal transduction in plants. New Phytol. 179:615-628.  

36. Pihakaski-Maunsbach, K., B. Moffatt, P. Testillano, M. Risueño, S. Yeh, M. Griffith, and A.B. Maunsbach. 2001. Genes encoding chitinase-antifreeze proteins are regulated by cold and expressed by all cell types in winter rye shoots. Physiol. Plant. 112:359-371.  

37. Rapala-Kozik, M., N. Wolak, M. Kujda, and A.K. Banas. 2012. The upregulation of thiamine (vitamin B1) biosynthesis in Arabidopsis thaliana seedlings under salt and osmotic stress conditions is mediated by abscisic acid at the early stages of this stress response. BMC Plant Biol. 12:2.  

38. Rural Development Administration (RDA). 2008. BrEMD: The Brassica rapa EST and microarray database. http://www.brassica- rapa.org/BrEMD.  

39. Renaut, J., J.F. Hausman, and M.E. Wisniewski. 2006. Proteomics and low temperature studies: Bridging the gap between gene expression and metabolism. Physiol. Plant. 126:97-109.  

40. Rossini, S., A.P. Casazza, E.C. Engelmann, M. Havaux, R.C. Jennings, and C. Soave. 2006. Suppression of both ELIP1 and ELIP2 in Arabidopsis does not affect tolerance to photoinhibition and photooxidative stress. Plant Physiol. 141:1264-1273.  

41. Sanghera, G.S., S.H. Wani, W. Hussain, and N.B. Singh. 2011. Engineering cold stress tolerance in crop plants. Curr. Genomics 12:30-43.  

42. Scott, I.M., S.M. Clarke, J.E. Wood, and L. Mur. 2004. Salicylate accumulation inhibits growth at chilling temperature in Arabidopsis. Plant Physiol. 135:1040-1049.  

43. Smoot, M.E., K. Ono, J. Ruscheinski, P.L. Wang, and T. Ideker. 2011. Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27:431-432.  

44. Tasgin, E., O. Atici, and B. Nalbantoglu. 2003. Effects of salicylic acid and cold on freezing tolerance in winter wheat leaves. Plant Growth Regul. 41:231-236.  

45. Valledor, L., T. Furuhashi, A.M. Hanak, and W. Weckwerth. 2013. Systemic cold stress adaptation of Chlamydomonas reinhardtii. Mol. Cell Proteomics 12:2032-2047.  

46. Yano, R., M. Nakamura, T. Yoneyama, and I. Nishida. 2005. Starch-related alpha-glucan/water dikinase is involved in the cold-induced development of freezing tolerance in Arabidopsis. Plant Physiol. 138:837-846.  

47. Yeh, S., B.A. Moffatt, M. Griffith, F. Xiong, D.S. Yang, S.B. Wiseman, F. Sarhan, J. Danyluk, Y.Q. Xue, C.L. Hew, A. Doherty-Kirby, and G. Lajoie. 2000. Chitinase genes responsive to cold encode antifreeze proteins in winter cereals. Plant Physiol. 124:1251-1264.  

48. Yu, J.G., G.H. Lee, J.S. Kim, E.J. Shim, and Y.D. Park. 2010. An insertional mutagenesis system for analyzing the Chinese cabbage genome using Agrobacterium T-DNA. Mol. Cells 29:267-275.  

49. Yu, X.M., M. Griffith, and S.B. Wiseman. 2001. Ethylene induces antifreeze activity in winter rye leaves. Plant Physiol. 126: 1232-1240.  

50. Zhao, J.J., X.W. Wang, B. Deng, P. Lou, J. Wu, R.F. Sun, Z.Y. Xu, J. Vromans, M. Koornneef, and G. Bonnema. 2005. Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor. Appl. Genet. 110:1301–1314.  

51. Zhao, Z. and S.M. Assmann. 2011. The glycolytic enzyme, phosphoglycerate mutase, has critical roles in stomatal move-ment, vegetative growth, and pollen production in Arabidopsis thaliana. J. Exp. Bot. 62:5179-5189.  

52. Zhao, Z., L. Tan, C. Dang, H. Zhang, Q. Wu, and L. An. 2012. Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana. BMC Plant Biol. 12:222.  

53. Zhou, D., J. Zhou, L. Meng, Q. Wang, H. Xie, Y. Guan, Z. Ma, Y. Zhong, F. Chen, and J. Liu. 2009. Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae). Gene 441:36-44.