Abstract
Key message
By comparing series full-length cDNA libraries stressed and control, the dynamic process of salt stress response in Upland cotton was studied, and reactive oxygen species and gibberellins signaling pathways were proposed.
Abstract
The Upland cotton is the most important fiber plant with highly salt tolerance. However, the molecular mechanism underlying salt tolerance in domesticated cotton was unclear. Here, seven full-length cDNA libraries were constructed for seedling roots of Upland cotton ‘Zhong G 5’ at 0, 3, 12 and 48 h after the treatment of control or 150 mM NaCl stress. About 3300 colonies in each library were selected robotically for 5′-end pyrosequencing, resulting in 20,358 expressed sequence tags (ESTs) totally. And 8516 uniESTs were then assembled, including 2914 contigs and 5602 singletons, and explored for Gene Ontology (GO) function. GO comparison between serial stress libraries and control reflected the growth regulation, stimulus response, signal transduction and biology regulation processes were conducted dynamically in response to salt stress. MYB, MYB-related, WRKY, bHLH, GRAS and ERF families of transcription factors were significantly enriched in the early response. 65 differentially expressed genes (DEGs), mainly associated with reactive oxygen species (ROS) scavenging, gibberellins (GAs) metabolism, signal transduction, transcription regulation, stress response and transmembrane transport, were identified and confirmed by quantitative real-time PCR. Overexpression of selected DEGs increased tolerance against salt stress in transgenic yeast. Results in this study supported that a ROS–GAs interacting signaling pathway of salt stress response was activated in Upland cotton. Our results provided valuable gene resources for further investigation of the molecular mechanism of salinity tolerance.
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Abbreviations
- ABA:
-
Abscisic acid
- BP:
-
Biological process
- BR:
-
Brassinosteroids
- CC:
-
Cellular components
- CDPK:
-
Calcium-dependent protein kinase
- CK:
-
Control library
- DEGs:
-
Differentially expressed genes
- Dof:
-
DNA binding with one finger
- ESTs:
-
Expressed sequence tags
- GAs:
-
Gibberellins
- GO:
-
Gene Ontology
- GRAS:
-
GAI [(Gibberellic acid)-insensitive], RGA (Repressor of GAI) and SCR (SCARECROW)
- MAPK:
-
Mitogen-activated protein kinase
- MF:
-
Molecular functions
- NR:
-
Stress library
- qRT-PCR:
-
Quantitative reverse transcriptase polymerase chain reaction
- ROS:
-
Reactive oxygen species
- TFs:
-
Transcription factors
References
Achard P, Cheng H, De Grauwe L et al (2006) Integration of plant responses to environmentally activated phytohormonal signals. Science 311:91–94. doi:10.1126/science.1118642
Achard P, Renou JP, Berthome R, Harberd NP, Genschik P (2008) Plant DELLAs restrain growth and promote survival of adversity by reducing the levels of reactive oxygen species. Curr Biol 18:656–660. doi:10.1016/j.cub.2008.04.034
An F, Zhang X, Zhu Z et al (2012) Coordinated regulation of apical hook development by gibberellins and ethylene in etiolated Arabidopsis seedlings. Cell Res 22:915–927. doi:10.1038/cr.2012.29
Asano T, Hayashi N, Kobayashi M et al (2012) A rice calcium-dependent protein kinase OsCPK12 oppositely modulates salt-stress tolerance and blast disease resistance. Plant J 69:26–36. doi:10.1111/j.1365-313X.2011.04766.x
Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995. doi:10.1101/gr.7.10.986
Babitha KC, Ramu SV, Pruthvi V, Mahesh P, Nataraja KN, Udayakumar M (2013) Co-expression of AtbHLH17 and AtWRKY28 confers resistance to abiotic stress in Arabidopsis. Transgenic Res 22:327–341. doi:10.1007/s11248-012-9645-8
Bahin E, Bailly C, Sotta B, Kranner I, Corbineau F, Leymarie J (2011) Crosstalk between reactive oxygen species and hormonal signalling pathways regulates grain dormancy in barley. Plant Cell Environ 34:980–993. doi:10.1111/j.1365-3040.2011.02298.x
Baxter A, Mittler R, Suzuki N (2014) ROS as key players in plant stress signalling. J Exp Bot 65:1229–1240. doi:10.1093/jxb/ert375
Beebo A, Thomas D, Der C et al (2009) Life with and without AtTIP1;1, an Arabidopsis aquaporin preferentially localized in the apposing tonoplasts of adjacent vacuoles. Plant Mol Biol 70:193–209. doi:10.1007/s11103-009-9465-2
Bienert GP, Moller AL, Kristiansen KA, Schulz A, Moller IM, Schjoerring JK, Jahn TP (2007) Specific aquaporins facilitate the diffusion of hydrogen peroxide across membranes. J Biol Chem 282:1183–1192. doi:10.1074/jbc.M603761200
Boudsocq M, Sheen J (2013) CDPKs in immune and stress signaling. Trends Plant Sci 18:30–40. doi:10.1016/j.tplants.2012.08.008
Boursiac Y, Boudet J, Postaire O, Luu DT, Tournaire-Roux C, Maurel C (2008) Stimulus-induced downregulation of root water transport involves reactive oxygen species-activated cell signalling and plasma membrane intrinsic protein internalization. Plant J 56:207–218. doi:10.1111/j.1365-313X.2008.03594.x
Cabello JV, Lodeyro AF, Zurbriggen MD (2014) Novel perspectives for the engineering of abiotic stress tolerance in plants. Curr Opin Biotechnol 26C:62–70. doi:10.1016/j.copbio.2013.09.011
Chaudhary B, Hovav R, Rapp R, Verma N, Udall JA, Wendel JF (2008) Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evol Dev 10:567–582. doi:10.1111/j.1525-142X.2008.00272.x
Chaudhary B, Hovav R, Flagel L, Mittler R, Wendel JF (2009) Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genom 10:378. doi:10.1186/1471-2164-10-378
Chinnusamy V, Zhu J, Zhu JK (2006) Salt stress signaling and mechanisms of plant salt tolerance. Genet Eng (N Y) 27:141–177. doi:10.1007/0-387-25856-6_9
Colebrook EH, Thomas SG, Phillips AL, Hedden P (2014) The role of gibberellin signalling in plant responses to abiotic stress. J Exp Biol 217:67–75. doi:10.1242/jeb.089938
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676. doi:10.1093/bioinformatics/bti610
Deinlein U, Stephan AB, Horie T, Luo W, Xu G, Schroeder JI (2014) Plant salt-tolerance mechanisms. Trends Plant Sci 19:371–376. doi:10.1016/j.tplants.2014.02.001
Divi UK, Rahman T, Krishna P (2010) Brassinosteroid-mediated stress tolerance in Arabidopsis shows interactions with abscisic acid, ethylene and salicylic acid pathways. BMC Plant Biol 10:151. doi:10.1186/1471-2229-10-151
Dynowski M, Schaaf G, Loque D, Moran O, Ludewig U (2008) Plant plasma membrane water channels conduct the signalling molecule H2O2. Biochem J 414:53–61. doi:10.1042/BJ20080287
Gallego-Bartolome J, Minguet EG, Grau-Enguix F et al (2012) Molecular mechanism for the interaction between gibberellin and brassinosteroid signaling pathways in Arabidopsis. Proc Natl Acad Sci USA 109:13446–13451. doi:10.1073/pnas.1119992109
Golldack D, Luking I, Yang O (2011) Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Rep 30:1383–1391. doi:10.1007/s00299-011-1068-0
Golldack D, Li C, Mohan H, Probst N (2013) Gibberellins and abscisic acid signal crosstalk: living and developing under unfavorable conditions. Plant Cell Rep 32:1007–1016. doi:10.1007/s00299-013-1409-2
Hou X, Lee LY, Xia K, Yan Y, Yu H (2010) DELLAs modulate jasmonate signaling via competitive binding to JAZs. Dev Cell 19:884–894. doi:10.1016/j.devcel.2010.10.024
Hovav R, Udall JA, Chaudhary B, Hovav E, Flagel L, Hu G, Wendel JF (2008) The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet 4:e25. doi:10.1371/journal.pgen.0040025
Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877. doi:10.1101/gr.9.9.868
Ishibashi Y, Tawaratsumida T, Kondo K et al (2012) Reactive oxygen species are involved in gibberellin/abscisic acid signaling in barley aleurone cells. Plant Physiol 158:1705–1714. doi:10.1104/pp.111.192740
Jiang C, Belfield EJ, Mithani A et al (2012) ROS-mediated vascular homeostatic control of root-to-shoot soil Na delivery in Arabidopsis. EMBO J 31:4359–4370. doi:10.1038/emboj.2012.273
Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30. doi:10.1093/nar/28.1.27
Khokon AR, Okuma E, Hossain MA et al (2011) Involvement of extracellular oxidative burst in salicylic acid-induced stomatal closure in Arabidopsis. Plant Cell Environ 34:434–443. doi:10.1111/j.1365-3040.2010.02253.x
Kumar R (2014) Role of microRNAs in biotic and abiotic stress responses in crop plants. Appl Biochem Biotechnol 174:93–115. doi:10.1007/s12010-014-0914-2
Leshem Y, Melamed-Book N, Cagnac O et al (2006) Suppression of Arabidopsis vesicle-SNARE expression inhibited fusion of H2O2-containing vesicles with tonoplast and increased salt tolerance. Proc Natl Acad Sci USA 103:18008–18013. doi:10.1073/pnas.0604421103
Li Y, Zhang L, Wang X, Zhang W, Hao L, Chu X, Guo X (2013) Cotton GhMPK6a negatively regulates osmotic tolerance and bacterial infection in transgenic Nicotiana benthamiana, and plays a pivotal role in development. FEBS J 280:5128–5144. doi:10.1111/febs.12488
Li J, Jia H, Wang J (2014a) cGMP and ethylene are involved in maintaining ion homeostasis under salt stress in Arabidopsis roots. Plant Cell Rep 33:447–459. doi:10.1007/s00299-013-1545-8
Li Y, Zhang L, Lu W, Wang X, Wu CA, Guo X (2014b) Overexpression of cotton GhMKK4 enhances disease susceptibility and affects abscisic acid, gibberellin and hydrogen peroxide signalling in transgenic Nicotiana benthamiana. Mol Plant Pathol 15:94–108. doi:10.1111/mpp.12067
Lin M, Lai D, Pang C, Fan S, Song M, Yu S (2013) Generation and analysis of a large-scale expressed sequence Tag database from a full-length enriched cDNA library of developing leaves of Gossypium hirsutum L. PLoS One 8:e76443. doi:10.1371/journal.pone.0076443
Liu M, Shi J, Lu C (2013) Identification of stress-responsive genes in Ammopiptanthus mongolicus using ESTs generated from cold- and drought-stressed seedlings. BMC Plant Biol 13:88. doi:10.1186/1471-2229-13-88
Luo X, Wu J, Li Y et al (2013) Synergistic effects of GhSOD1 and GhCAT1 overexpression in cotton chloroplasts on enhancing tolerance to methyl viologen and salt stresses. PLoS One 8:e54002. doi:10.1371/journal.pone.0054002
Ma HS, Liang D, Shuai P, Xia XL, Yin WL (2010) The salt- and drought-inducible poplar GRAS protein SCL7 confers salt and drought tolerance in Arabidopsis thaliana. J Exp Bot 61:4011–4019. doi:10.1093/jxb/erq217
Ma J, Wei H, Song M et al (2012) Transcriptome profiling analysis reveals that flavonoid and ascorbate-glutathione cycle are important during anther development in Upland cotton. PLoS One 7:e49244. doi:10.1371/journal.pone.0049244
Marty F (1999) Plant vacuoles. Plant Cell 11:587–600. doi:10.1105/tpc.11.4.587
Maurel C, Verdoucq L, Luu DT, Santoni V (2008) Plant aquaporins: membrane channels with multiple integrated functions. Annu Rev Plant Biol 59:595–624. doi:10.1146/annurev.arplant.59.032607.092734
Middleton AM, Ubeda-Tomas S, Griffiths J et al (2012) Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Proc Natl Acad Sci USA 109:7571–7576. doi:10.1073/pnas.1113666109
Mittler R, Vanderauwera S, Suzuki N et al (2011) ROS signaling: the new wave? Trends Plant Sci 16:300–309. doi:10.1016/j.tplants.2011.03.007
Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681. doi:10.1146/annurev.arplant.59.032607.092911
Navarro L, Bari R, Achard P, Lison P, Nemri A, Harberd NP, Jones JD (2008) DELLAs control plant immune responses by modulating the balance of jasmonic acid and salicylic acid signaling. Curr Biol 18:650–655. doi:10.1016/j.cub.2008.03.060
Page JT, Gingle AR, Udall JA (2013) PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms. G3 (Bethesda) 3:517–525. doi:10.1534/g3.112.005298
Park W, Scheffler BE, Bauer PJ, Campbell BT (2012) Genome-wide identification of differentially expressed genes under water deficit stress in upland cotton (Gossypium hirsutum L.). BMC Plant Biol 12:90. doi:10.1186/1471-2229-12-90
Peng Z, He S, Gong W et al (2014) Comprehensive analysis of differentially expressed genes and transcriptional regulation induced by salt stress in two contrasting cotton genotypes. BMC Genom 15:760. doi:10.1186/1471-2164-15-760
Petrov VD, Van Breusegem F (2012) Hydrogen peroxide-a central hub for information flow in plant cells. AoB Plants 2012:pls014. doi:10.1093/aobpla/pls014
Ranjan A, Pandey N, Lakhwani D, Dubey NK, Pathre UV, Sawant SV (2012) Comparative transcriptomic analysis of roots of contrasting Gossypium herbaceum genotypes revealing adaptation to drought. BMC Genom 13:680. doi:10.1186/1471-2164-13-680
Rymen B, Sugimoto K (2012) Tuning growth to the environmental demands. Curr Opin Plant Biol 15:683–690. doi:10.1016/j.pbi.2012.07.005
Schmidt R, Mieulet D, Hubberten HM et al (2013) Salt-responsive ERF1 regulates reactive oxygen species-dependent signaling during the initial response to salt stress in rice. Plant Cell 25:2115–2131. doi:10.1105/tpc.113.113068
Shi YH, Zhu SW, Mao XZ et al (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18:651–664. doi:10.1105/tpc.105.040303
Shi J, Zhang L, An H, Wu C, Guo X (2011) GhMPK16, a novel stress-responsive group D MAPK gene from cotton, is involved in disease resistance and drought sensitivity. BMC Mol Biol 12:22. doi:10.1186/1471-2199-12-22
Sun X, Jones WT, Rikkerink EH (2012) GRAS proteins: the versatile roles of intrinsically disordered proteins in plant signalling. Biochem J 442:1–12. doi:10.1042/BJ20111766
Suzuki N, Koussevitzky S, Mittler R, Miller G (2012) ROS and redox signalling in the response of plants to abiotic stress. Plant Cell Environ 35:259–270. doi:10.1111/j.1365-3040.2011.02336.x
Udall JA, Swanson JM, Haller K et al (2006) A global assembly of cotton ESTs. Genome Res 16:441–450. doi:10.1101/gr.4602906
Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3:2–20. doi:10.1093/mp/ssp106
Wendel J, Brubaker C, Seelanan T (2010) The origin and evolution of Gossypium. In: Stewart J, Oosterhuis D, Heitholt J, Mauney J (eds) Physiology of Cotton. Springer, Netherlands, pp 1–18. doi:10.1007/978-90-481-3195-2_1
Willige BC, Isono E, Richter R, Zourelidou M, Schwechheimer C (2011) Gibberellin regulates PIN-FORMED abundance and is required for auxin transport-dependent growth and development in Arabidopsis thaliana. Plant Cell 23:2184–2195. doi:10.1105/tpc.111.086355
Xu P, Liu Z, Fan X, Gao J, Zhang X, Shen X (2013) De novo transcriptome sequencing and comparative analysis of differentially expressed genes in Gossypium aridum under salt stress. Gene 525:26–34. doi:10.1016/j.gene.2013.04.066
Yang R, Yang T, Zhang H et al (2014) Hormone profiling and transcription analysis reveal a major role of ABA in tomato salt tolerance. Plant Physiol Biochem 77:23–34. doi:10.1016/j.plaphy.2014.01.015
Yao D, Zhang X, Zhao X et al (2011) Transcriptome analysis reveals salt-stress-regulated biological processes and key pathways in roots of cotton (Gossypium hirsutum L.). Genomics 98:47–55. doi:10.1016/j.ygeno.2011.04.007
Yasumura Y, Crumpton-Taylor M, Fuentes S, Harberd NP (2007) Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land-plant evolution. Curr Biol 17:1225–1230. doi:10.1016/j.cub.2007.06.037
Yin Z, Li Y, Yu J et al (2012) Difference in miRNA expression profiles between two cotton cultivars with distinct salt sensitivity. Mol Biol Rep 39:4961–4970. doi:10.1007/s11033-011-1292-2
Yoo MJ, Wendel JF (2014) Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet 10:e1004073. doi:10.1371/journal.pgen.1004073
Yu J, Jung S, Cheng CH et al (2014) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res 42:D1229–D1236. doi:10.1093/nar/gkt1064
Yuan D, Tu L, Zhang X (2011) Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One 6:e22758. doi:10.1371/journal.pone.0022758
Yun KY, Park MR, Mohanty B et al (2010) Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biol 10:16. doi:10.1186/1471-2229-10-16
Zhang L, Xi D, Li S et al (2011a) A cotton group C MAP kinase gene, GhMPK2, positively regulates salt and drought tolerance in tobacco. Plant Mol Biol 77:17–31. doi:10.1007/s11103-011-9788-7
Zhang X, Zhen J, Li Z, Kang D, Yang Y, Kong J, Hua J (2011b) Expression profile of early responsive genes under salt stress in upland cotton (Gossypium hirsutum L.). Plant Mol Biol Report 29:626–637. doi:10.1007/s11105-010-0269-y
Zhang ZL, Ogawa M, Fleet CM et al (2011c) Scarecrow-like 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis. Proc Natl Acad Sci USA 108:2160–2165. doi:10.1073/pnas.1012232108
Zhang L, Li Y, Lu W, Meng F, Wu CA, Guo X (2012a) Cotton GhMKK5 affects disease resistance, induces HR-like cell death, and reduces the tolerance to salt and drought stress in transgenic Nicotiana benthamiana. J Exp Bot 63:3935–3951. doi:10.1093/jxb/ers086
Zhang Q, Lin F, Mao T, Nie J, Yan M, Yuan M, Zhang W (2012b) Phosphatidic acid regulates microtubule organization by interacting with MAP65-1 in response to salt stress in Arabidopsis. Plant Cell 24:4555–4576. doi:10.1105/tpc.112.104182
Zhu YN, Shi DQ, Ruan MB, Zhang LL, Meng ZH, Liu J, Yang WC (2013) Transcriptome analysis reveals crosstalk of responsive genes to multiple abiotic stresses in cotton (Gossypium hirsutum L.). PLoS One 8:e80218. doi:10.1371/journal.pone.0080218
Acknowledgments
We thank Dr. Lida Zhang (Shanghai Jiaotong University), Dr. Yi Huang (Oil Crops Research Institute, Chinese Academy of Agricultural Sciences) and Dr. Xinwang Wang (Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Dallas, TX, 75252, USA) for helpful discussion. We are grateful to Dr. Kunbo Wang (Chinese Academy of Agricultural Sciences) for gifting us the seeds of Zhong G5. This research was supported in part by the National Key Project (2014ZX08005-004B), and National High Technology Research and Development Program (2006AA10A108) to J HUA.
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Shi, G., Guo, X., Guo, J. et al. Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.). Plant Cell Rep 34, 1005–1023 (2015). https://doi.org/10.1007/s00299-015-1761-5
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DOI: https://doi.org/10.1007/s00299-015-1761-5