Hadiarto T, Tran LS. Progress studies of drought-responsive genes in rice. Plant cell reports. 2011;30(3):297–310.
Article
CAS
PubMed
Google Scholar
Choudhary SP, Yu JQ, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS. Benefits of brassinosteroid crosstalk. Trends Plant Sci. 2012;17(10):594–605.
Article
CAS
PubMed
Google Scholar
Jogaiah S, Govind SR, Tran LS. Systems biology-based approaches toward understanding drought tolerance in food crops. Crit Rev Biotechnol. 2013;33(1):23–39.
Article
PubMed
Google Scholar
Mizuno T. Two-component phosphorelay signal transduction systems in plants: from hormone responses to circadian rhythms. Biosci Biotechnol Biochem. 2005;69(12):2263–76.
Article
CAS
PubMed
Google Scholar
Schaller GE, Shiu SH, Armitage JP. Two-component systems and their co-option for eukaryotic signal transduction. Curr Biol. 2011;21(9):R320-330.
Article
CAS
PubMed
Google Scholar
Ha S, Vankova R, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS. Cytokinins: metabolism and function in plant adaptation to environmental stresses. Trends Plant Sci. 2012;17(3):172–9.
Article
CAS
PubMed
Google Scholar
Schaller GE, Kieber JJ, Shiu SH. Two-component signaling elements and histidyl-aspartyl phosphorelays. Arabidopsis Book. 2008;6:e0112.
Article
PubMed Central
PubMed
Google Scholar
Tanaka Y, Suzuki T, Yamashino T, Mizuno T. Comparative studies of the AHP histidine-containing phosphotransmitters implicated in His-to-Asp phosphorelay in Arabidopsis thaliana. Biosci Biotechnol Biochem. 2004;68(2):462–5.
Article
CAS
PubMed
Google Scholar
Mähönen AP, Bishopp A, Higuchi M, Nieminen KM, Kinoshita K, Törmäkangas K, Ikeda Y, Oka A, Kakimoto T, Helariutta Y. Cytokinin signaling and its inhibitor AHP6 regulate cell fate during vascular development. Science. 2006;311(5757):94–8.
Article
PubMed
Google Scholar
Punwani JA, Hutchison CE, Schaller GE, Kieber JJ. The subcellular distribution of the Arabidopsis histidine phosphotransfer proteins is independent of cytokinin signaling. Plant J. 2010;62(3):473–82.
Article
CAS
PubMed
Google Scholar
Jung KW, Oh SI, Kim YY, Yoo KS, Cui MH, Shin JS. Arabidopsis histidine-containing phosphotransfer factor 4 (AHP4) negatively regulates secondary wall thickening of the anther endothecium during flowering. Mol Cells. 2008;25(2):294–300.
CAS
PubMed
Google Scholar
Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, et al. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling. Plant Cell. 2006;18(11):3073–87.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nishiyama R, Watanabe Y, Leyva-Gonzalez MA, Ha CV, Fujita Y, Tanaka M, Seki M, Yamaguchi-Shinozaki K, Shinozaki K, Herrera-Estrella L, et al. Arabidopsis AHP2, AHP3, and AHP5 histidine phosphotransfer proteins function as redundant negative regulators of drought stress response. Proc Natl Acad Sci U S A. 2013;110(12):4840–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Deng Y, Dong H, Mu J, Ren B, Zheng B, Ji Z, Yang WC, Liang Y, Zuo J. Arabidopsis histidine kinase CKI1 acts upstream of histidine phosphotransfer proteins to regulate female gametophyte development and vegetative growth. Plant Cell. 2010;22(4):1232–48.
Article
PubMed Central
CAS
PubMed
Google Scholar
Feng J, Wang C, Chen Q, Chen H, Ren B, Li X, Zuo J. S-nitrosylation of phosphotransfer proteins represses cytokinin signaling. Nat Commun. 2013;4:1529.
Article
PubMed
Google Scholar
Liu B, De Storme N, Geelen D. Cold interferes with male meiotic cytokinesis in Arabidopsis thaliana independently of the AHK2/3-AHP2/3/5 cytokinin signaling module. Cell Biol Int. 2017;41(8):879–89.
Article
CAS
PubMed
Google Scholar
Hu Y, Chen J, Fang L, Zhang Z, Ma W, Niu Y, Ju L, Deng J, Zhao T, Lian J, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet. 2019;51(4):739–48.
Article
CAS
PubMed
Google Scholar
Wohlbach DJ, Quirino BF, Sussman MR. Analysis of the Arabidopsis histidine kinase ATHK1 reveals a connection between vegetative osmotic stress sensing and seed maturation. Plant Cell. 2008;20(4):1101–17.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tran LS, Urao T, Qin F, Maruyama K, Kakimoto T, Shinozaki K, Yamaguchi-Shinozaki K. Functional analysis of AHK1/ATHK1 and cytokinin receptor histidine kinases in response to abscisic acid, drought, and salt stress in Arabidopsis. Proc Natl Acad Sci U S A. 2007;104(51):20623–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tran LS, Shinozaki K, Yamaguchi-Shinozaki K. Role of cytokinin responsive two-component system in ABA and osmotic stress signalings. Plant Signal Behav. 2010;5(2):148–50.
Article
PubMed Central
CAS
PubMed
Google Scholar
Urao T, Yakubov B, Yamaguchi-Shinozaki K, Shinozaki K. Stress-responsive expression of genes for two-component response regulator-like proteins in Arabidopsis thaliana. FEBS Lett. 1998;427(2):175–8.
Article
CAS
PubMed
Google Scholar
Nguyen KH, Ha CV, Nishiyama R, Watanabe Y, Leyva-González MA, Fujita Y, Tran UT, Li W, Tanaka M, Seki M, et al. Arabidopsis type B cytokinin response regulators ARR1, ARR10, and ARR12 negatively regulate plant responses to drought. Proc Natl Acad Sci U S A. 2016;113(11):3090–5.
Article
PubMed Central
CAS
PubMed
Google Scholar
Liu Z, Zhang M, Kong L, Lv Y, Zou M, Lu G, Cao J, Yu X. Genome-wide identification, phylogeny, duplication, and expression analyses of two-component system genes in Chinese cabbage. DNA Res (Brassica rapa ssp pekinensis). 2014;21(4):379–96.
Google Scholar
Hwang I, Chen H-C, Sheen J. Two-Component Signal Transduction Pathways in Arabidopsis. Plant Physiol. 2002;129(2):500–15.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mochida K, Yoshida T, Sakurai T, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS. Genome-wide analysis of two-component systems and prediction of stress-responsive two-component system members in soybean. DNA Res. 2010;17(5):303–24.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chu ZX, Ma Q, Lin YX, Tang XL, Zhou YQ, Zhu SW, Fan J, Cheng BJ. Genome-wide identification, classification, and analysis of two-component signal system genes in maize. Gen Mol Res. 2011;10(4):3316–30.
Article
CAS
Google Scholar
Aury JM, Jaillon O, Duret L, Noel B, Jubin C, Porcel BM, Ségurens B, Daubin V, Anthouard V, Aiach N, et al. Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature. 2006;444(7116):171–8.
Article
CAS
PubMed
Google Scholar
Bowers JE, Chapman BA, Rong J, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature. 2003;422(6930):433–8.
Article
CAS
PubMed
Google Scholar
Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature. 2004;431(7011):946–57.
Article
PubMed
Google Scholar
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 2007;449(7161):463–7.
Article
CAS
PubMed
Google Scholar
Kellis M, Birren BW, Lander ES. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature. 2004;428(6983):617–24.
Article
CAS
PubMed
Google Scholar
Paterson AH, Bowers JE, Chapman BA. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A. 2004;101(26):9903–8.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, et al. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 2012;13(1):R3.
Article
PubMed Central
PubMed
Google Scholar
Vekemans D, Proost S, Vanneste K, Coenen H, Viaene T, Ruelens P, Maere S, Van de Peer Y, Geuten K. Gamma paleohexaploidy in the stem lineage of core eudicots: significance for MADS-box gene and species diversification. Mol Biol Evol. 2012;29(12):3793–806.
Article
CAS
PubMed
Google Scholar
Salse J. Ancestors of modern plant crops. Curr Opin Plant Biol. 2016;30:134–42.
Article
PubMed
Google Scholar
Higuchi M, Pischke MS, Mähönen AP, Miyawaki K, Hashimoto Y, Seki M, Kobayashi M, Shinozaki K, Kato T, Tabata S, et al. In planta functions of the Arabidopsis cytokinin receptor family. Proc Natl Acad Sci U S A. 2004;101(23):8821–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nishimura C, Ohashi Y, Sato S, Kato T, Tabata S, Ueguchi C. Histidine kinase homologs that act as cytokinin receptors possess overlapping functions in the regulation of shoot and root growth in Arabidopsis. Plant Cell. 2004;16(6):1365–77.
Article
PubMed Central
CAS
PubMed
Google Scholar
Riefler M, Novak O, Strnad M, Schmülling T. Arabidopsis cytokinin receptor mutants reveal functions in shoot growth, leaf senescence, seed size, germination, root development, and cytokinin metabolism. Plant Cell. 2006;18(1):40–54.
Article
PubMed Central
CAS
PubMed
Google Scholar
Jeon J, Kim NY, Kim S, Kang NY, Novák O, Ku SJ, Cho C, Lee DJ, Lee EJ, Strnad M, et al. A subset of cytokinin two-component signaling system plays a role in cold temperature stress response in Arabidopsis. J Biol Chem. 2010;285(30):23371–86.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kang NY, Cho C, Kim NY, Kim J. Cytokinin receptor-dependent and receptor-independent pathways in the dehydration response of Arabidopsis thaliana. J Plant Physiol. 2012;169(14):1382–91.
Article
CAS
PubMed
Google Scholar
Le DT, Nishiyama R, Watanabe Y, Vankova R, Tanaka M, Seki M, le Ham H, Yamaguchi-Shinozaki K, Shinozaki K, Tran LS. Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels. PloS One. 2012;7(8):e42411.
Article
PubMed Central
CAS
PubMed
Google Scholar
Colcombet J, Hirt H. Arabidopsis MAPKs: a complex signalling network involved in multiple biological processes. Biochem J. 2008;413(2):217–26.
Article
CAS
PubMed
Google Scholar
Zhang S, Klessig DF. MAPK cascades in plant defense signaling. Trends Plant Sci. 2001;6(11):520–7.
Article
CAS
PubMed
Google Scholar
Zhang JB, Wang XP, Wang YC, Chen YH, Luo JW, Li DD, Li XB. Genome-wide identification and functional characterization of cotton (Gossypium hirsutum) MAPKKK gene family in response to drought stress. BMC Plant Biol. 2020;20(1):217.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang J, Zou D, Li Y, Sun X, Wang NN, Gong SY, Zheng Y, Li XB. GhMPK17, a cotton mitogen-activated protein kinase, is involved in plant response to high salinity and osmotic stresses and ABA signaling. PloS one. 2014;9(4):e95642.
Article
PubMed Central
PubMed
Google Scholar
Na YJ, Choi HK, Park MY, Choi SW, Xuan Vo KT, Jeon JS, Kim SY. OsMAPKKK63 is involved in salt stress response and seed dormancy control. Plant Signal Behav. 2019;14(3):e1578633.
Article
PubMed Central
PubMed
Google Scholar
Ma H, Chen J, Zhang Z, Ma L, Yang Z, Zhang Q, Li X, Xiao J, Wang S. MAPK kinase 10.2 promotes disease resistance and drought tolerance by activating different MAPKs in rice. Plant J. 2017;92(4):557–70.
Article
CAS
PubMed
Google Scholar
Furuya T, Matsuoka D, Nanmori T. Membrane rigidification functions upstream of the MEKK1-MKK2-MPK4 cascade during cold acclimation in Arabidopsis thaliana. FEBS Lett. 2014;588(11):2025–30.
Article
CAS
PubMed
Google Scholar
Kong Q, Qu N, Gao M, Zhang Z, Ding X, Yang F, Li Y, Dong OX, Chen S, Li X, et al. The MEKK1-MKK1/MKK2-MPK4 kinase cascade negatively regulates immunity mediated by a mitogen-activated protein kinase kinase kinase in Arabidopsis. Plant Cell. 2012;24(5):2225–36.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shi J, Zhang L, An H, Wu C, Guo X. GhMPK16, a novel stress-responsive group D MAPK gene from cotton, is involved in disease resistance and drought sensitivity. BMC Mol Biol. 2011;12:22.
Article
PubMed Central
CAS
PubMed
Google Scholar
Miller G, Suzuki N, Ciftci-Yilmaz S, Mittler R. Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant Cell Environ. 2010;33(4):453–67.
Article
CAS
PubMed
Google Scholar
Kakimoto T. Perception and signal transduction of cytokinins. Annu Rev Plant Biol. 2003;54:605–27.
Article
CAS
PubMed
Google Scholar
To JPC, Kieber JJ. Cytokinin signaling: two-components and more. Trends Plant Sci. 2008;13(2):85–92.
Article
CAS
PubMed
Google Scholar
Hwang I, Sheen J. Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature. 2001;413(6854):383–9.
Article
CAS
PubMed
Google Scholar
Sun L, Zhang Q, Wu J, Zhang L, Jiao X, Zhang S, Zhang Z, Sun D, Lu T, Sun Y. Two rice authentic histidine phosphotransfer proteins, OsAHP1 and OsAHP2, mediate cytokinin signaling and stress responses in rice. Plant Physiol. 2014;165(1):335–45.
Article
PubMed Central
CAS
PubMed
Google Scholar
Du X, Huang G, He S, Yang Z, Sun G, Ma X, Li N, Zhang X, Sun J, Liu M, et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet. 2018;50(6):796–802.
Article
CAS
PubMed
Google Scholar
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 2012;492(7429):423–7.
Article
CAS
PubMed
Google Scholar
Liu X, Zhao B, Zheng HJ, Hu Y, Lu G, Yang CQ, Chen JD, Chen JJ, Chen DY, Zhang L, et al. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites. Sci Rep. 2015;5:14139.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhu T, Liang C, Meng Z, Sun G, Meng Z, Guo S, Zhang R. CottonFGD: an integrated functional genomics database for cotton. BMC Plant Biol. 2017;17(1):101.
Article
PubMed Central
PubMed
Google Scholar
Wang J, Zhang Y, Xu N, Zhang H, Fan Y, Rui C, Han M, Malik WA, Wang Q, Sun L, et al. Genome-wide identification of CK gene family suggests functional expression pattern against Cd(2+) stress in Gossypium hirsutum L. Int J Biol Macromol. 2021;188:272–82.
Article
CAS
PubMed
Google Scholar
Yu CS, Lin CJ, Hwang JK. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 2004;13(5):1402–6.
Article
PubMed Central
CAS
PubMed
Google Scholar
Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14(6):1188–90.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol. 2016;33(7):1870–4.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202-208.
Article
PubMed Central
CAS
PubMed
Google Scholar
Guo AY, Zhu QH, Chen X, Luo JC. GSDS: a gene structure display server. Yi Chuan. 2007;29(8):1023–6.
Article
CAS
PubMed
Google Scholar
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol Plant. 2020;13(8):1194–202.
Article
CAS
PubMed
Google Scholar
Yu J, Jung S, Cheng C-H, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D. CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res. 2014;42(D1):D1229–36.
Article
CAS
PubMed
Google Scholar
Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101–8.
Article
CAS
PubMed
Google Scholar