Horticultural Science & Technology (원예과학기술지)

Korean Society of Horticultural Science (한국원예학회)
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A Co-expression Network of Drought Stress-related Genes in Chinese Cabbage

  • Lee, Gi-Ho (Department of Horticultural Biotechnology, Kyung Hee University) ;
  • Park, Young-Doo (Department of Horticultural Biotechnology, Kyung Hee University)
  • Received : 2016.11.14
  • Accepted : 2017.03.02
  • Published : 2017.04.28
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Abstract

Plants have evolved to adapt to abiotic stresses, such as salt, cold, and drought stress. In this study, we conducted an in-depth analysis of drought resistance mechanisms by constructing a gene co-expression network in Chinese cabbage (Brassica rapa ssp. pekinensis L.). This drought stress co-expression network has 1,560 nodes, 4,731 edges, and 79 connected components. Based on genes that showed significant co-expression in the network, drought tolerance was associated with the induction of reactive oxygen species removal by raffinose family oligosaccharides and inositol metabolism. This network could be a useful tool for predicting the functions of genes involved in drought stress resistance in Chinese cabbage.

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References

  1. Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25:1263-1274. doi:10.1007/s00299-006-0204-8
  2. Asada K (1999) The water-water cycle in chloroplasts: scavenging of active oxygens and dissipation of excess photons. Annu Rev Plant Physiol Plant Mol Biol 50:601-639. doi:10.1146/annurev.arplant.50.1.601
  3. Barnabas B, Jager K, Feher A (2008) The effect of drought and heat stress on reproductive processes in cereals. Plant Cell Environ 31:11-38. doi:10.1111/j.1365-3040.2007.01727.x
  4. Barnes J, Hut P (1986) A hierarchical O(N log N) force-calculation algorithm. Nature 324:446-449. doi:10.1038/324446a0
  5. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z, et al (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25:1091-1093. doi:10.1093/bioinformatics/btp101
  6. Chan KX, Wirtz M, Phua SY, Estavillo GM, Pogson BJ (2013) Balancing metabolites in drought: The sulfur assimilation conundrum. Trends Plant Sci 18:18-29. doi:10.1016/j.tplants.2012.07.005
  7. Chaves MM, Flexas J, Pinheiro C (2009) Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot 103:551-560. doi:10.1093/aob/mcn125
  8. Chen W, Provart NJ, Glazebrook J, Katagiri F, Chang HS, Eulgem T, Mauch F, Luan S, Zou G, et al (2002) Expression profile matrix of Arabidopsis transcription factor genes implies their putative functions in response to environmental stresses. Plant Cell 14:559-574. doi:10.1105/tpc.010410.
  9. Earl HJ, Davis RF (2003) Effect of drought stress on leaf and whole canopy radiation use efficiency and yield of maize. Agro J 95:688-696. doi:10.2134/agronj2003.0688
  10. Hale BK, Herms DA, Hansen RC, Clausen TP, Arnold D (2005) Effects of drought stress and nutrient availability on dry matter allocation, phenolic glycosides, and rapid induced resistance of poplar to two lymantriid defoliators. J Chem Ecol 31:2601-2620. doi:10.1007/s10886-005-7616-8
  11. Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Annu Rev Plant Phys 51:463-499. doi:10.1146/annurev.arplant.51.1.463
  12. Hincha DK, Zuther E, Heyer AG (2003) The preservation of liposomes by raffinose family oligosaccharides during drying is mediated by effects on fusion and lipid phase transitions. Biochim Biophys Acta 1612:172-177. doi:10.1016/S0005-2736(03)00116-0
  13. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57. doi:10.1038/nprot.2008.211
  14. Jaleel CA, Riadh K, Gopi R, Manivannan P, Ines J, Al-Juburi HJ, Zhao CX, Shao HB, Panneerselvam R (2009) Antioxidant defense response: physiological plasticity in higher plants under abiotic constraints. Acta Physiol Plant 31:427-436. doi:10.1007/s11738-009-0275-6
  15. Jamsheer KM, Laxmi A (2015) Expression of Arabidopsis FCS-Like Zinc finger genes is differentially regulated by sugars, cellular energy level, and abiotic stress. Front Plant Sci 6:746. doi:10.3389/fpls.2015.00746
  16. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res 40:D109-114. doi:10.1093/nar/gkr988
  17. Kasuga M, Liu Q, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1999) Improving plant drought, salt, and freezing tolerance by gene transfer of a single stress-inducible transcription factor. Nat Biotechnol 17:287-291. doi:10.1038/7036
  18. Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130:2129-2141. doi:10.1104/pp.008532
  19. Lee SC, Lim MH, Kim JA, Lee SI, Kim JS, Jin M, Kwon SJ, Mun JH, Kim YK, et al (2008) Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24K oligo microarray. Mol Cells 26:595-605
  20. Lee SG, Kim SK, Lee HJ, Choi CS, Park ST (2016) Impacts of climate change on the growth, morphological and physiological responses, and yield of Kimchi cabbage leaves. Hortic Environ Biotechnol 57:470-477. doi:10.1007/s13580-016-1163-9
  21. Lee TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, et al (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol 151:16-33. doi:10.1104/pp.109.139030
  22. Li M, Li Y, Li H, Wu G (2011) Overexpression of AtNHX5 improves tolerance to both salt and drought stress in Broussonetia papyrifera (L.) Vent. Tree Physiol 31:349-357. doi:10.1093/treephys/tpr003
  23. Liu ZW, Shao CR, Zhang CJ, Zhou JX, Zhang SW, Li L, Chen S, Huang HW, Cai T, et al (2014) The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet 10:e1003948. doi:10.1371/journal.pgen.1003948
  24. Moon JS, Hur YY, Jung SM, Choi YJ, Nam JC, Park JG, Koh SW (2007) Transcript profiling of native Korean grapevine species Vitis flexuosa exposed to dehydration and rehydration treatment. Hortic Environ Biotechnol 58:66-77. doi:10.1007/s13580-017-0064-x
  25. Park JS, Yu JG, Park YD (2007) Characterization of a drought tolerance-related gene of Chinese cabbage in a transgenic tobacco plant. Hortic Environ Biotechnol 58:48-55. doi:10.1007/s13580-017-0157-6
  26. Perozich J, Nicholas H, Lindahl R, Hempel J (1999) The big book of aldehyde dehydrogenase sequences. An overview of the extended family. Adv Exp Med Biol 463:1-7. doi:10.1007/978-1-4615-4735-8_1
  27. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, et al (2003) Monitoring expression profiles of rice genes under cold, drought, and high-salinity stresses and abscisic acid application using cDNA microarray and RNA gel-blot analyses. Plant Physiol 133:1755-1767. doi:10.1104/pp.103.025742
  28. RDA (the rural development administration) (2008) BrEMD: the Brassica rapa EST and microarray database. http://www.brassicarapa.org/BrEMD
  29. Reddy AS, Marquez Y, Kalyna M, Barta A (2013) Complexity of the alternative splicing landscape in plants. Plant Cell 25:3657-3683.doi:10.1105/tpc.113.117523
  30. Roth S, MacDonald EP, Lindroth RL (1997) Atmospheric $CO_2$ and soil water availability: consequences for tree-insect interactions. Can J For Res 27:1281-1290. doi:10.1139/cjfr-27-8-1281
  31. Saijo Y, Hata S, Kyozuka J, Shimamoto K, Izui K (2000) Over-expression of a single $Ca^{2+}$-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J 23:319-327. doi:10.1046/j.1365-313x.2000.00787.x
  32. Shi H, Ye T, Zhu JK, Chan Z (2014) Constitutive production of nitric oxide leads to enhanced drought stress resistance and extensive transcriptional reprogramming in Arabidopsis. J Exp Bot 65:4119-4131. doi:10.1093/jxb/eru184
  33. Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27:431-432. doi:10.1093/bioinformatics/btq675
  34. Somerville C, Briscoe J (2001) Genetic engineering and water. Science 292:2217. doi:10.1126/science.292.5525.2217
  35. Valluru R, Van den Ende W (2008) Plant fructans in stress environments: emerging concepts and future prospects. J Exp Bot 59:2905-2916. doi:10.1093/jxb/ern164
  36. Yang J, Zhang J, Wang Z, Zhu Q, Wang W (2001) Hormonal changes in the grains of rice subjected to water stress during grain filling. Plant Physiol 127:315-323. doi:10.1104/pp.127.1.315
  37. Yu JG, Lee GH, Park YD (2016) Characterization of a drought-tolerance gene, BrDSR, in Chinese cabbage. Kor J Hort Sci Technol 34:102-111. doi:10.12972/kjhst.20160011
  38. Yu JG, Park YD (2015) Isolation and functional identification of a new gene, BrDSR, related to drought tolerance derived from Brassica rapa. Kor J Hort Sci Technol 33:575-584. doi:10.7235/hort.2015.15056
  39. Zhang M, Li G, Huang W, Bi T, Chen G, Tang Z, Su W, Sun W (2010) Proteomic study of Carissa spinarum in response to combined heat and drought stress. Proteomics 10:3117-3129. doi:10.1002/pmic.200900637
  40. Zhou Y, Lam HM, Zhang J (2007) Inhibition of photosynthesis and energy dissipation induced by water and high light stresses in rice. J Exp Bot 58:1207-1217. doi:10.1093/jxb/erl291
  41. Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247-273. doi:10.1146/annurev.arplant.53.091401.143329