Andaya VC, Mackill DJ. Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot. 2003;54:2579–85.
Pradhan SK, Nayak DK, Guru M, Pandit E, Das S, Barik SR, Mohanty SP, Anandan A. Screening and classification of genotypes for seedling stage chillingstress tolerance in rice and validation of the trait using SSR markers. Plant Genet Resour; Charact Util. 2015;15(46). https://doi.org/10.1017/S1479262115000192.
Pandit E, Tasleem S, Barik SR, Mohanty DP, Nayak DK, Mohanty SP, Das S, Pradhan SK. Genome-wide association mapping reveals multiple qtls governing tolerance response for seedling stage chilling stress in indica rice. Front Plant Sci. 2017;8:552. https://doi.org/10.3389/fpls.2017.00552.
Das S, Pandit E, Guru M, Nayak DK, Tasleem S, Barik SR, Mohanty DP, Mohanty SP, Patra BC, Pradhan SK. Genetic diversity, population structure, marker validation and kinship analysis for seedling stage cold tolerance in indica rice. Oryza. 2018;55:396–405.
Sthapit BR, Witcombe JR. Inheritance of tolerance to chilling stress in rice during germination and plumule greening. Crop Sci. 1998;38:660–5.
Jiang L, Liu SJ, Hou MY, Tang JY, Chen LM, Zhai HQ, et al. Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crop Res. 2006;98:68–75. https://doi.org/10.1016/j.fcr.2005.12.015.
Pradhan SK, Barik SR, Sahoo A, Mohapatra S, Nayak DK, Mahender A, Meher J, Anandan A, Pandit E. Population structure, genetic diversity and molecular marker-trait association analysis for high temperature stress tolerance in rice. PLoS One. 2016;11(8):e0160027. https://doi.org/10.1371/journal.pone.0160027.
Mittler R. Abiotic stress, the field environment and stress combination. Trends Plant Sci. 2006;11:15–9.
Moller IM. Plant mitochondria and oxidative stress: Electron transport, NADPH turnover, and metabolism of reactive oxygen species. Annu Rev Plant Physiol Plant Mol Biol. 2001;52:561–91.
Mittler R. Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci. 2002;7:405–10.
Miller G, Shulaev V, Mittler R. Reactive oxygen signaling and abiotic stress. Physiol Plant. 2008;133:481–9.
Miller G, Shulaev V, Mittler R. Redox regulation in photosynthetic organisms: signaling, acclimation, and practical implications. Antioxid Redox Signal. 2008b;11:861–905.
Chinnusamy V, Zhu J, Zhu JK. Cold stress regulation of gene expression in plants. Trends Plant Sci. 2007;12:444–51.
Zhou MQ, Shen C, Wu LH, Tang KX, Lin J. CBF-dependent signaling pathway: a key responder to low temperature stress in plants. Crit Rev Biotechnol. 2011;31:186–92.
Cheng C, Yun KY, Ressom HW, Mohanty B, Bajic VB, Jia Y, Yun SJ, de los Reyes BG. An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics. 2007;8:175.
Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K. Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol. 2006;9:436–42.
Nakashima K, Ito Y, Yamaguchi-Shinozaki K. Transcriptional regulatory networks in response to abiotic stresses in Arabidopsis and grasses. Plant Physiol. 2009;149:88–95.
Mittal D, Chakrabarti S, Sarkar A, Singh A, Grover A. Heat shock factor genefamily in rice: genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses. Plant Physiol Biochem. 2009;47:785–95.
Kant P, Gordon M, Kant S, Zolla G, Davydov O, Heimer YM, Chalifa-Caspi V, Shaked R, Barak S. Functional-genomics-based identification of genes that regulate Arabidopsis responses to multiple abioticstresses. Plant Cell Environ. 2008;31:697–714.
Ma TL, Wu WH, Wang Y. Transcriptome analysis of rice root responses to potassium deficiency. BMC Plant Biol. 2012;12:161.
Ishimaru Y, Suzuki M, Masuda H, Takahashi M, Nakanishi H, Mori S. OsZIP4, a novel zinc-regulated zinc transporter in rice. J Exp Bot. 2005;56:3207–14.
Wei G, Tao Y, Liu G, Chen C, Luo R, XiaH GQ, Zeng H, Lu Z, Han Y, Li X, Song G, Zhai H, Peng Y, Li D, Xu H, Wei X, Cao M, Deng H, Xin Y, Fu X, Yuan L, Yu J, Zhu Z, Zhu L. A transcriptomic analysis of super hybrid rice LYP9 and its parents. Proc Natl Acad Sci. 2009;106:7695–701.
Mittal D, Madhyastha DA, Grover A. Genome-wide transcriptional profiles duringtemperature and oxidative stress reveal coordinated expression patterns and overlapping regulons in rice. PLoS One. 2012;7:e40899.
Dubey S, Misra P, Dwivedi S, Chatterjee S, Bag SK, Mantri S, Mehar HA, Rai A, Kumar S, Shri M, Tripathi P, Tripathi RD, Trivedi PK, Chakrabarty D, Tuli R. Transcriptomic and metabolomic shifts in rice roots in response to Cr (VI) stress. BMC Genomics. 2010;11:648.
Zhang T, Zhao X, Wang W, Pan Y, Huang L, Liu X, Zong Y, Zhu L, Yang D, Fu B. Comparative transcriptome profiling of colding stress responsiveness in two contrasting rice genotypes. PloSone. 2012;7:e43274.
Lu T, Lu G, Fan D, Zhu C, Li W, Zhao Q, Feng Q, Zhao Y, Guo Y, Li W, Huang X, Han B. Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq. Genome Res. 2010;20:1238–49.
Zhai R, Feng Y, Wang H, Zhan X, Shen X, Wu W, Zhang Y, Chen D, Dai G, Yang Z, Cao L, Cheng S. Transcriptome analysis of rice root heterosis by RNA-Seq. BMC Genomics. 2013;14:19.
He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng XW. Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell. 2010;22:17–33.
Oono Y, Kawahara Y, Kanamori H, Mizuno H, Yamagata H, Yamamoto H, Hosokawa S, Ikawa H, Akahane I, Zhu Z, Wu J, Itoh T, Matsumoto T. mRNA-Seq reveals a comprehensive transcriptome profile of Rice under phosphate stress. Rice. 2011;4:50–65.
Hu Y, Zhang L, He S, Huang M, Tan J, Zhao L, Yan S, Li H, Zhou K, Liang Y, et al. Cold stress selectively unsilences tandem repeats in heterochromatin associated with accumulation of H3K9ac. Plant Cell Environ. 2012;35:2130–42.
Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J. DRTF: a database of rice transcription factors. Bioinformatics. 2006;22(10):1286–7.
Zhang ZH, Su L, Chen W, Li W, Zhu YG. A major QTL conferring cold tolerance at early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci. 2005;168:527–53.
Zhan F, Huang L, Wang W, Zhao X, Zhu L, Fu B, Li Z. Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background. BMC Genomics. 2012;13:461.
Socquet-Juglard D, Kamber T, Pothier JF, Christen D, Gessler C, Duffy B, Patocchi A. Comparative RNA-Seq Analysis of Early-Infected Peach Leaves by the Invasive Phytopathogen Xanthomonas arboricola pv. pruni. PLoS ONE. 2013;8(1):e54196. https://doi.org/10.1371/journal.pone 0054196.
Wang H, Wang H, Shao H, Tang X. Recent advances in utilizing transcription factors to improve plant abiotic stress tolerance by transgenic technology. Front Plant Sci. 2016;7:67. https://doi.org/10.3389/fpls.2016.00067.
Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng LH, Wanamaker SI, Mandal J, Xu J, Cui XP, Close TJ. Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol. 2005;139(2):822–35.
Taji T, Seki M, Satou M, Sakurai T, Kobayashi M, Ishiyama K, Narusaka Y, Narusaka M, Zhu JK, Shinozaki K. Comparative genomics in salt tolerance between Arabidopsis and Arabidopsis-related halophyte salt cress using Arabidopsis microarray. Plant Physiol. 2004;135:1697–709.
Frank G, Pressman E, Ophir R, Althan L, Shaked R, FreedmanM SS, Firon N. Transcriptional profiling of maturing tomato (Solanum lycopersicum L.) microspores reveals the involvement of heat shock proteins, ROS scavengers, hormones, and sugars in the heat stress response. J Exp Bot. 2009;60:3891–908.
Kumar K, Kumar KM, HSR R, Cho YG. Insights into genomics of salt stress response in rice. Rice. 2013;6:27. https://doi.org/10.1186/1939-8433-6-27.
Bita CE, Zenoni S, Vriezen WH, Mariani C, Pezzotti M, Gerats T. Temperature stress differentially modulates transcription in meiotic anthers of heat-tolerant and heat-sensitive tomato plants. BMC Genomics. 2011;12:384.
Binh LT, Oono K. Molecular cloning and characterization of genes related to chilling tolerance in rice. Plant Physiol. 1992;99:1146–50.
Fowler S, Thomashow MF. Arabidopsis transcriptome profiling indicatesthat multiple regulatory pathways are activated during cold acclimation inaddition to the CBF cold response pathway. Plant Cell. 2002;14:1675–90.
Soranzo N, SariGorla M, Mizzi L, De-Toma G, Frova C. Organizationand structural evolution of the rice glutathione S-transferase gene family. Mol Gen Genomics. 2004;271:511–21.
Kavanagh KL, Jörnvall H, Persson B, Oppermann U. Medium- andshort-chaindehydrogenase/reductase gene and protein families: the SDRsuperfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell Mol Life Sci. 2008;65:3895–906.
Mahapatra SS, Wolfraim L, Poole RJ, Dhindsa RS. Molecular cloning and relationship to freezing tolerance of cold acclimation- specific genes of alfalfa. Plant Physiol. 1989;89:375–80.
Guy CL. Cold acclimation and freezing stress tolerance: role of protein metabolism. Annu Rev Plant Physiol Plant Mol Biol. 1990;41:187–223.
Pramanik MH, Imai R. Functional identification of a trehalose 6-phosphate phosphatasegene that is involved in transient induction of trehalose biosynthesis during chilling stress inrice. Plant Mol Biol. 2005;58:751–62.
Garg AK, Kim JK, Owens TG, Ranwala AP, Choi YD, Kochian LV, Wu RJ. Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses. Proc Natl Acad Sci. 2002;99:15898–903.
Jang IC, Oh SJ, Seo JS, Choi WB, Song SI, Kim CH, Kim YS, Seo HS, Choi YD, Nahm BH. Expression of a bifunctional fusion of the Escherichia coli genes fortrehalose-6- phosphate synthase and trehalose- 6-phosphate phosphatase in transgenicriceplants increases trehalose accumulation and abiotic stress tolerance without stunting growth. Plant Physiol. 2003;131:516–24.
Ge LF, Chao DY, Shi M, Zhu MZ, Gao JP, Lin HX. Overexpression of the trehalose-6 phosphate phosphatase gene OsTPP1 confers stress tolerance in rice and results in the activation of stress responsive genes. Planta. 2008;228:191–201.
Iordachescu M, Imai R. Trehalose biosynthesis in response to abiotic stresses. J Integr Plant Biol. 2008;50:1223–9.
Pennycooke JC, Jones ML, Stushnoff C. Down-regulating α-galactosidase enhances freezing tolerance in transgenic Petunia. Plant Physiol. 2003;133:901–9.
Routaboul JM, Fischer SF, Browse J. Trienoic fatty acids are required to maintain chloroplast function at low temperatures. Plant Physiol. 2000;124(4):1697–705.
Wenying L, Kenming Y, Tengfei H, Feifei L, Dongxu Z, Jianxia L. The temperature induced physiological responses of Avene nuda L. A cold tolerant plant species. Sci World J. 2013; Article ID 658793. https://doi.org/10.1155/2013/658793.
Gong Z, Dong CH, Lee H, Zhu J, Xiong L, Gong D, Stevenson B, Zhu JK. ADEAD box RNA helicase is essential formRNA export and important for development and stress responses in Arabidopsis. Plant Cell. 2005;17:256–67.
Sharoni AM, Nuruzzaman M, Satoh K, Shimizu T, Kondoh H, Sasaya T, Choi R, Omura T, Kikuchi S. Gene structures, classification and expression models of the AP2/EREBP transcription factor family in rice. Plant Cell Physiol. 2011;52:344–60.
Yun KY, Park MR, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic VB, Bruskiewich R, de Los Reyes BG. Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biol. 2010;10:16.
Dubouzet JG, Sakuma Y, Ito Y, Kasuga M, Dubouzet EG, Miura S, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. OsDREB genes in rice, Oryzasativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. Plant J. 2003;33:751–63.
Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K. AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta. 1819;2012:86–96.
Ramamoorthy R, Jiang SY, Kumar N, Venkatesh PN, Ramachandran S. A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments. Plant Cell Physiol. 2008;49:865–79.
Berri S, Abbruscato P, Faivre-Rampant O, Brasileiro AC, Fumasoni I, Satoh K, Kikuchi S, Mizzi L, Morandini P, Pè ME, Piffanelli P. Characterization of WRKY co-regulatory networks in rice and Arabidopsis. BMC Plant Biol. 2009;9:120.
Vannini C, Locatelli F, Bracale M, Magnani E, Marsoni M, Osnato M, Mattana M, Baldoni E, Coraggio I. Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants. Plant J. 2004;37:115–27.
Dai X, Xu Y, Ma Q, Xu W, Wang T, Xue Y, Chong K. Overexpression of an R1R2R3 MYB gene, OsMYB3R-2, increases tolerance to freezing, drought, and salt stress in transgenic Arabidopsis. Plant Physiol. 2007;143:1739–51.
Su CF, Wang YC, Hsieh TH, Lu CA, Tseng TH, Yu SM. A novel MYBS3-dependent pathway confers cold tolerance in rice. Plant Physiol. 2010;153:145–58.
Mahantesha NK, Shameer OK, Mathew RG, Ramanathan S. STIFDB2: an updated version of plant stress-responsive transcription factor Data Base with additional stress signals, Stress-Responsive Transcription Factor Binding Sites and Stress-Responsive Genes in Arabidopsis and Rice. Plant and Cell Physiol. 2013;54:e8. https://doi.org/10.1093/pcp/pcs185.
Shameer K, Ambika S, Varghese SM, Karaba N, Udayakumar M, Sowdhamini R. STIFDB-Arabidopsis stress responsive transcription factor Data Base. Int J Plant Genomics. 2009;2009:583429. https://www.ncbi.nlm.nih.gov/pubmed/19841686.
Ambika S, Varghese SM, Shameer K, Udayakumar M, Sowdhamini R. STIF: hidden Markov model-based search algorithm for the recognition of binding sites of stress upregulated transcription factors and genes in Arabidopsis thaliana. Bioinformation. 2008;2(10):431–7.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–78.
Thumma BR, Sharma N, Southerton SG. Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection. BMC Genomics. 2012;1(13):364.
Kyndt T, Denil S, Haegeman A, Trooskens G, De-Meyer T, Criekinge VW, Gheysen G. Transcriptome analysis of rice mature root tissue and root tips in early development by massive parallel sequencing. J Exp Bot. 2012;63:2141–57.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-∆∆CT method. Methods. 2001;25:402–8.