Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K. Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol. 2011;11:163.
Yadav SK. Cold stress tolerance mechanisms in plants. A review Agronomy for Sustainable Development 2010;30:515–527.
Guo X, Liu D, Chong K. Cold signaling in plants: insights into mechanisms and regulation. J Integr Plant Biol. 2018;60:745–56.
Sanghera GS, Wani SH, Hussain W, Singh NB. Engineering cold stress tolerance in crop plants. Curr Genomics. 2011;12:30–43.
Zhu J, Dong CH, Zhu JK. Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Curr Opin Plant Biol. 2007;10:290–5.
Theocharis A, Clement C, Barka EA. Physiological and molecular changes in plants grown at low temperatures. Planta. 2012;235:1091–105.
Thomashow MF. PLANT COLD ACCLIMATION: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol. 1999;50:571–99.
Hoermiller II, Naegele T, Augustin H, Stutz S, Weckwerth W, Heyer AG. Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana. Plant Cell Environ. 2017;40:602–10.
Chinnusamy V, Zhu JK, Sunkar R. Gene regulation during cold stress acclimation in plants. Methods Mol Biol. 2010;639:39–55.
Zhu JK. Abiotic stress signaling and responses in plants. Cell. 2016;167:313–24.
Knight MR, Knight H. Low-temperature perception leading to gene expression and cold tolerance in higher plants. New Phytol. 2012;195:737–51.
Ritonga FN, Chen S. Physiological and molecular mechanism involved in cold stress tolerance in plants. Plants (Basel). 2020;9:560.
Stockinger EJ, Gilmour SJ, Thomashow MF. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci U S A. 1997;94:1035–40.
Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 1998;16:433–42.
Chinnusamy V, Zhu J, Zhu JK. Cold stress regulation of gene expression in plants. Trends Plant Sci. 2007;12:444–51.
Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, et al. Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome. Plant Cell. 2018;30:1424–44.
Penfield S. Temperature perception and signal transduction in plants. New Phytol. 2008;179:615–28.
Wang DZ, Jin YN, Ding XH, Wang WJ, Zhai SS, Bai LP, et al. Gene regulation and signal transduction in the ICE-CBF-COR signaling pathway during cold stress in plants. Biochemistry (Mosc). 2017;82:1103–17.
Barah P, Jayavelu ND, Rasmussen S, Nielsen HB, Mundy J, Bones AM. Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. BMC Genomics. 2013;14:722.
Li Q, Byrns B, Badawi MA, Diallo AB, Danyluk J, Sarhan F, et al. Transcriptomic insights into Phenological development and cold tolerance of wheat grown in the field. Plant Physiol. 2018;176:2376–94.
Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ, et al. Transcriptome analysis of cold acclimation in barley Albina and xantha mutants. Plant Physiol. 2006;141:257–70.
Guan S, Xu Q, Ma D, Zhang W, Xu Z, Zhao M, et al. Transcriptomics profiling in response to cold stress in cultivated rice and weedy rice. Gene. 2019;685:96–105.
Li M, Sui N, Lin L, Yang Z, Zhang Y. Transcriptomic profiling revealed genes involved in response to cold stress in maize. Funct Plant Biol. 2019;46:830–44.
Calzadilla PI, Maiale SJ, Ruiz OA, Escaray FJ. Transcriptome response mediated by cold stress in Lotus japonicus. Front Plant Sci. 2016;7:374.
Zhang Y, Zhang Y, Lin Y, Luo Y, Wang X, Chen Q, et al. A transcriptomic analysis reveals diverse regulatory networks that respond to cold stress in strawberry (Fragariaxananassa). Int J Genomics. 2019;2019:7106092.
Kang WH, Sim YM, Koo N, Nam JY, Lee J, Kim N, et al. Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L. Sci Data. 2020;7:17.
Yang QS, Gao J, He WD, Dou TX, Ding LJ, Wu JH, et al. Comparative transcriptomics analysis reveals difference of key gene expression between banana and plantain in response to cold stress. BMC Genomics. 2015;16:446.
Chen H, Chen X, Chen D, Li J, Zhang Y, Wang A. A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites. BMC Plant Biol. 2015;15:132.
Li Y, Wang X, Ban Q, Zhu X, Jiang C, Wei C, et al. Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis. BMC Genomics. 2019;20:624.
Zhang X, Teixeira da Silva JA, Niu M, Li M, He C, Zhao J, et al. Physiological and transcriptomic analyses reveal a response mechanism to cold stress in Santalum album L. leaves. Sci Rep. 2017;7:42165.
Sun LL, Wang YB, Wang RL, Wang RT, Zhang P, Ju Q, et al. Physiological, transcriptomic, and metabolomic analyses reveal zinc oxide nanoparticles modulate plant growth in tomato. Environmental Science-Nano. 2020;7:3587–604.
Jin J, Zhang H, Zhang J, Liu P, Chen X, Li Z, et al. Integrated transcriptomics and metabolomics analysis to characterize cold stress responses in Nicotiana tabacum. BMC Genomics. 2017;18:496.
Goossens A, Hakkinen ST, Laakso I, Seppanen-Laakso T, Biondi S, De Sutter V, et al. A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc Natl Acad Sci U S A. 2003;100:8595–600.
Schweiger R, Schwenkert S. Protein-protein interactions visualized by bimolecular fluorescence complementation in tobacco protoplasts and leaves. J Vis Exp. 2014;9:51327.
Zhao L, Liu F, Xu W, Di C, Zhou S, Xue Y, et al. Increased expression of OsSPX1 enhances cold/subfreezing tolerance in tobacco and Arabidopsis thaliana. Plant Biotechnol J. 2009;7:550–61.
Khodakovskaya M, McAvoy R, Peters J, Wu H, Li Y. Enhanced cold tolerance in transgenic tobacco expressing a chloroplast omega-3 fatty acid desaturase gene under the control of a cold-inducible promoter. Planta. 2006;223:1090–100.
Kodama H, Hamada T, Horiguchi G, Nishimura M, Iba K. Genetic enhancement of cold tolerance by expression of a gene for chloroplast [omega]-3 fatty acid desaturase in transgenic tobacco. Plant Physiol. 1994;105:601–5.
Zhuo C, Wang T, Guo Z, Lu S. Overexpression of MfPIP2-7 from Medicago falcata promotes cold tolerance and growth under NO3 (−) deficiency in transgenic tobacco plants. BMC Plant Biol. 2016;16:138.
Wei Y, Chen H, Wang L, Zhao Q, Wang D, Zhang T. Cold acclimation alleviates cold stress-induced PSII inhibition and oxidative damage in tobacco leaves. Plant Signal Behav. 2022;17:2013638.
Ya J, Zhang C, Yang H, Yang Y, Huang C, Tian Y. Lu X. proteomic analysis of cold stress responses in tobacco seedlings. Afr J Biotechnol. 2011;10:18991–9004.
Zhao Q, Xiang X, Liu D, Yang A, Wang Y. Tobacco transcription factor NtbHLH123 confers tolerance to cold stress by regulating the NtCBF pathway and reactive oxygen species homeostasis. Front Plant Sci. 2018;9:381.
Wang C, Deng P, Chen L, Wang X, Ma H, Hu W, et al. A wheat WRKY transcription factor TaWRKY10 confers tolerance to multiple abiotic stresses in transgenic tobacco. PLoS One. 2013;8:e65120.
Lin P, Shen C, Chen H, Yao XH, Lin J. Improving tobacco freezing tolerance by co-transfer of stress-inducible CbCBF and CbICE53 genes. Biol Plant. 2017;61:520–8.
Khan SA, Li MZ, Wang SM, Yin HJ. Revisiting the role of plant transcription factors in the Battle against abiotic stress. Int J Mol Sci. 2018;19:1634.
Singh K, Foley RC, Onate-Sanchez L. Transcription factors in plant defense and stress responses. Curr Opin Plant Biol. 2002;5:430–6.
Kitsios G, Doonan JH. Cyclin dependent protein kinases and stress responses in plants. Plant Signal Behav. 2011;6:204–9.
Jonak C, Kiegerl S, Ligterink W, Barker PJ, Huskisson NS, Hirt H. Stress signaling in plants: a mitogen-activated protein kinase pathway is activated by cold and drought. Proc Natl Acad Sci U S A. 1996;93:11274–9.
Mizoguchi T, Ichimura K, Shinozaki K. Environmental stress response in plants: the role of mitogen-activated protein kinases. Trends Biotechnol. 1997;15:15–9.
Yang L, Wu K, Gao P, Liu X, Li G, Wu Z. GsLRPK, a novel cold-activated leucine-rich repeat receptor-like protein kinase from Glycine soja, is a positive regulator to cold stress tolerance. Plant Sci. 2014;215-216:19–28.
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
Purty RS, Sachar M, Chatterjee S. Structural and expression analysis of salinity stress responsive phosphoserine phosphatase from Brassica juncea (L.). J Proteomics Bioinformatics. 2017;10:119–27.
Zhao KX, Chu SS, Zhang XD, Wang L, Rono JK, Yang ZM. AtWRKY21 negatively regulates tolerance to osmotic stress in Arabidopsis. Environ Exp Bot. 2020;169:103920.
Mathe C, Garda T, Freytag C, M MH. The role of serine-threonine protein phosphatase PP2A in plant oxidative stress signaling-facts and hypotheses. Int J Mol Sci 2019;20:3028.
Javed T, Shabbir R, Ali A, Afzal I, Zaheer U, Gao SJ. Transcription factors in plant stress responses: challenges and potential for sugarcane improvement. Plants (Basel). 2020;9:491.
Xie Z, Nolan TM, Jiang H, Yin Y. AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Front Plant Sci. 2019;10:228.
Dong NQ, Sun Y, Guo T, Shi CL, Zhang YM, Kan Y, et al. UDP-glucosyltransferase regulates grain size and abiotic stress tolerance associated with metabolic flux redirection in rice. Nat Commun. 2020;11:2629.
Bang W, Kim S, Ueda A, Vikram M, Yun D, Bressan RA, et al. Arabidopsis carboxyl-terminal domain phosphatase-like isoforms share common catalytic and interaction domains but have distinct in planta functions. Plant Physiol. 2006;142:586–94.
Huynh-Thu VA, Irrthum A, Wehenkel L, Geurts P. Inferring regulatory networks from expression data using tree-based methods. PLoS One. 2010;5:e12776.
Kim CY, Vo KTX, Nguyen CD, Jeong DH, Lee SK, Kumar M, et al. Functional analysis of a cold-responsive rice WRKY gene, OsWRKY71. Plant Biotechnol Rep. 2016;10:13–23.
Zou C, Jiang W, Yu D. Male gametophyte-specific WRKY34 transcription factor mediates cold sensitivity of mature pollen in Arabidopsis. J Exp Bot. 2010;61:3901–14.
Yang Y, Liu J, Zhou X, Liu S, Zhuang Y. Identification of WRKY gene family and characterization of cold stress-responsive WRKY genes in eggplant. Peer J. 2020;8:e8777.
Yuan Y, Fang L, Karungo SK, Zhang L, Gao Y, Li S, et al. Overexpression of VaPAT1, a GRAS transcription factor from Vitis amurensis, confers abiotic stress tolerance in Arabidopsis. Plant Cell Rep. 2016;35:655–66.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods. 2001;25:402–8.
Lamalakshmi Devi E, Kumar S, Singh B, Sharma S, Beemrote A, Devi C, Chongtham S, Chongtham H, Yumlembam R, Athokpam H, et al. Adaptation Strategies and Defence Mechanisms of Plants During Environmental Stress. In: Medicinal Plants and Environmental Challenges. Edited by Ghorbanpour M, Varma A. Cham: Springer International Publishing; 2017:359–413.
Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG. Epigenetic regulation in plant abiotic stress responses. J Integr Plant Biol. 2020;62:563–80.
Krasensky J, Jonak C. Drought, salt, and temperature stress-induced metabolic rearrangements and regulatory networks. J Exp Bot. 2012;63:1593–608.
Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, et al. Multilevel regulation of abiotic stress responses in plants. Front Plant Sci. 2017;8:1564.
Bashir K, Matsui A, Rasheed S, Seki M. Recent advances in the characterization of plant transcriptomes in response to drought, salinity, heat, and cold stress. F1000Res. 2019;8:F1000.
Winfield MO, Lu C, Wilson ID, Coghill JA, Edwards KJ. Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol J. 2010;8:749–71.
Li ZB, Zeng XY, Xu JW, Zhao RH, Wei YN. Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress. Sci Data. 2019;6:197.
Hu R, Zhu X, Xiang S, Zhan Y, Zhu M, Yin H, et al. Comparative transcriptome analysis revealed the genotype specific cold response mechanism in tobacco. Biochem Biophys Res Commun. 2016;469:535–41.
Bonora M, Patergnani S, Rimessi A, De Marchi E, Suski JM, Bononi A, et al. ATP synthesis and storage. Purinergic Signal. 2012;8:343–57.
Linka N, Theodoulou FL, Haslam RP, Linka M, Napier JA, Neuhaus HE, et al. Peroxisomal ATP import is essential for seedling development in Arabidopsis thaliana. Plant Cell. 2008;20:3241–57.
Rapacz M, Wolanin B, Hura K, Tyrka M. The effects of cold acclimation on photosynthetic apparatus and the expression of COR14b in four genotypes of barley (Hordeum vulgare) contrasting in their tolerance to freezing and high-light treatment in cold conditions. Ann Bot. 2008;101:689–99.
Savitch LV, Barker-Astrom J, Ivanov AG, Hurry V, Oquist G, Huner NP, et al. Cold acclimation of Arabidopsis thaliana results in incomplete recovery of photosynthetic capacity, associated with an increased reduction of the chloroplast stroma. Planta. 2001;214:295–303.
Huner NP, Oquist G, Hurry VM, Krol M, Falk S, Griffith M. Photosynthesis, photoinhibition and low temperature acclimation in cold tolerant plants. Photosynth Res. 1993;37:19–39.
Stitt M, Hurry V. A plant for all seasons: alterations in photosynthetic carbon metabolism during cold acclimation in Arabidopsis. Curr Opin Plant Biol. 2002;5:199–206.
Savitch L, Leonardos E, Król M, Jansson S, Grodzinski B, Huner N, et al. Two different strategies for light utilization in photosynthesis in relation to growth and cold acclimation. Plant Cell Environment. 2002;25:761–71.
Takahashi D, Li B, Nakayama T, Kawamura Y, Uemura M. Plant plasma membrane proteomics for improving cold tolerance. Front Plant Sci. 2013;4:90.
Zheng G, Tian B, Zhang F, Tao F, Li W. Plant adaptation to frequent alterations between high and low temperatures: remodelling of membrane lipids and maintenance of unsaturation levels. Plant Cell Environ. 2011;34:1431–42.
Zhang H, Dong J, Zhao X, Zhang Y, Ren J, Xing L, et al. Research Progress in membrane lipid metabolism and molecular mechanism in Peanut cold tolerance. Front Plant Sci. 2019;10:838.
Mittler R, Kim Y, Song L, Coutu J, Coutu A, Ciftci-Yilmaz S, et al. Gain- and loss-of-function mutations in Zat10 enhance the tolerance of plants to abiotic stress. FEBS Lett. 2006;580:6537–42.
Davletova S, Schlauch K, Coutu J, Mittler R. The zinc-finger protein Zat12 plays a central role in reactive oxygen and abiotic stress signaling in Arabidopsis. Plant Physiol. 2005;139:847–56.
Torres-Galea P, Hirtreiter B, Bolle C. Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME a SIGNAL TRANSDUCTION1, function cooperatively in phytochrome a signal TRANSDUCTION. Plant Physiol. 2013;161:291–304.
Torres-Galea P, Huang LF, Chua NH, Bolle C. The GRAS protein SCL13 is a positive regulator of phytochrome-dependent red light signaling, but can also modulate phytochrome a responses. Mol Gen Genomics. 2006;276:13–30.
Jung JH, Domijan M, Klose C, Biswas S, Ezer D, Gao M, et al. Phytochromes function as thermosensors in Arabidopsis. Science. 2016;354:886–9.
Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 2000;12:393–404.
Sorek N, Sorek H, Kijac A, Szemenyei HJ, Bauer S, Hematy K, et al. The Arabidopsis COBRA protein facilitates cellulose crystallization at the plasma membrane. J Biol Chem. 2014;289:34911–20.
Li Y, Qian Q, Zhou Y, Yan M, Sun L, Zhang M, et al. BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants. Plant Cell. 2003;15:2020–31.
Song CP, Agarwal M, Ohta M, Guo Y, Halfter U, Wang P, et al. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses. Plant Cell. 2005;17:2384–96.
Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, et al. Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol. 2011;52:344–60.
Kizis D, Pages M. Maize DRE-binding proteins DBF1 and DBF2 are involved in rab17 regulation through the drought-responsive element in an ABA-dependent pathway. Plant J. 2002;30:679–89.
Liu C, Zhang T. Expansion and stress responses of the AP2/EREBP superfamily in cotton. BMC Genomics. 2017;18:118.
Chen L, Han J, Deng X, Tan S, Li L, Li L, et al. Expansion and stress responses of AP2/EREBP superfamily in Brachypodium distachyon. Sci Rep. 2016;6:21623.
Cao S, Wang Y, Li X, Gao F, Feng J, Zhou Y. Characterization of the AP2/ERF transcription factor family and expression profiling of DREB subfamily under cold and osmotic stresses in Ammopiptanthus nanus. Plants (Basel). 2020;9:455.
Espinoza C, Liang Y, Stacey G. Chitin receptor CERK1 links salt stress and chitin-triggered innate immunity in Arabidopsis. Plant J. 2017;89:984–95.
Nguyen KH, Ha CV, Nishiyama R, Watanabe Y, Leyva-Gonzalez MA, Fujita Y, 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;113:3090–5.
Pais SM, Tellez-Inon MT, Capiati DA. Serine/threonine protein phosphatases type 2A and their roles in stress signaling. Plant Signal Behav. 2009;4:1013–5.
Wang S, Guo T, Wang Z, Kang J, Yang Q, Shen Y, et al. Expression of three related to ABI3/VP1 genes in Medicago truncatula caused increased stress resistance and branch increase in Arabidopsis thaliana. Front Plant Sci. 2020;11:611.
Sinha AK, Jaggi M, Raghuram B, Tuteja N. Mitogen-activated protein kinase signaling in plants under abiotic stress. Plant Signal Behav. 2011;6:196–203.
Lin L, Wu J, Jiang M, Wang Y. Plant mitogen-activated protein kinase cascades in environmental stresses. Int J Mol Sci. 2021;22:1543.
Shou H, Bordallo P, Fan JB, Yeakley JM, Bibikova M, Sheen J, et al. Expression of an active tobacco mitogen-activated protein kinase kinase kinase enhances freezing tolerance in transgenic maize. Proc Natl Acad Sci U S A. 2004;101:3298–303.
Dong H, Wu C, Luo C, Wei M, Qu S, Wang S. Overexpression of MdCPK1a gene, a calcium dependent protein kinase in apple, increase tobacco cold tolerance via scavenging ROS accumulation. PLoS One. 2020;15:e0242139.
Edwards KD, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans AD, Bombarely A, et al. A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. BMC Genomics. 2017;18:448.
Gao J, Wang G, Ma S, Xie X, Wu X, Zhang X, et al. CRISPR/Cas9-mediated targeted mutagenesis in Nicotiana tabacum. Plant Mol Biol. 2015;87:99–110.