Abstract
Key message
Improved knowledge about plant cold stress tolerance offered by modern omics technologies will greatly inform future crop improvement strategies that aim to breed cultivars yielding substantially high under low-temperature conditions.
Abstract
Alarmingly rising temperature extremities present a substantial impediment to the projected target of 70% more food production by 2050. Low-temperature (LT) stress severely constrains crop production worldwide, thereby demanding an urgent yet sustainable solution. Considerable research progress has been achieved on this front. Here, we review the crucial cellular and metabolic alterations in plants that follow LT stress along with the signal transduction and the regulatory network describing the plant cold tolerance. The significance of plant genetic resources to expand the genetic base of breeding programmes with regard to cold tolerance is highlighted. Also, the genetic architecture of cold tolerance trait as elucidated by conventional QTL mapping and genome-wide association mapping is described. Further, global expression profiling techniques including RNA-Seq along with diverse omics platforms are briefly discussed to better understand the underlying mechanism and prioritize the candidate gene (s) for downstream applications. These latest additions to breeders’ toolbox hold immense potential to support plant breeding schemes that seek development of LT-tolerant cultivars. High-yielding cultivars endowed with greater cold tolerance are urgently required to sustain the crop yield under conditions severely challenged by low-temperature.
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References
Abe N, Kotaka S, Toriyama K, Kobayashi M (1989) Development of the “Rice Norin PL 8” with high tolerance to cool temperature at the booting stage. Res Bull Hokkaido Natl Agric Exp Stn 152:9–17
Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, Zheng X, Zhu JK (2006) A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem 281:37636–37645
Allen DJ, Ort DR (2001) Impacts of chilling temperatures on photosynthesis in warm-climate plants. Trends Plant Sci 6:36–42
Alm V, Busso CS, Ergon A, Rudi H, Larsen A, Humphreys MW, Rognli OA (2011) QTL analyses and comparative genetic mapping of frost tolerance, winter survival and drought tolerance in meadow fescue (Festuca pratensis Huds.). Theor Appl Genet 123:369–382
Alonso-Blanco C, Gomez-Mena C, Llorente F, Koornneef M, Salinas J, Martínez-Zapater JM (2005) Genetic and molecular analyses of natural variation indicate CBF2 as a candidate gene for underlying a freezing tolerance quantitative trait locus in Arabidopsis. Plant Physiol 139:1304–1312
Andaya VC, Mackill DJ (2003a) QTLs conferring cold tolerance at the booting stage of rice using recombinant inbred lines from a japonica/indica cross. Theor Appl Genet 106:1084–1090
Andaya VC, Mackill DJ (2003b) Mapping of QTLs associated with cold tolerance during the vegetative stage in rice. J Exp Bot 54:2579–2585
Andaya VC, Tai TH (2006) Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theor Appl Genet 113:467–475
Andaya VC, Tai TH (2007) Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Breed 20:349–358
Arbaoui M, Link W, Satovic Z, Torres AM (2008) Quantitative trait loci of frost tolerance and physiologically related trait in faba bean (Vicia faba L.). Euphytica 164:93–104
Ariel F, Romero-Barrios N, Jégu T, Benhamed M, Crespi M (2015) Battles and hijacks: noncoding transcription in plants. Trends Plant Sci 20:362–371
Arms EM, Bloom AJ, St Clair DA (2015) High-resolution mapping of a major effect QTL from wild tomato Solanum habrochaites that influences water relations under root chilling. Theor Appl Genet 128:1713–1724
Artus NN, Uemura M, Steponkus PL, Gilmour SJ, Lin CT, Thomashow MF (1996) Constitutive expression of the cold regulated Arabidopsis thaliana COR 15a gene affects both chloroplast and protoplast freezing tolerance. Proc Natl Acad Sci USA 93:13404–13409
Asghari A, Mohammadi SA, Moghaddam M, Mohammaddust H (2007) Identification of QTLs controlling cold resistance-related traits in Brassica napus L. using RAPD markers. J Food Agric Environ 3&4:188–192
Avia K, Pilet-Nayel ML, Bahrman N, Baranger A, Delbreil B, Fontaine V, Hamon C, Hanocq E, Niarquin M, Sellier H, Vuylsteker C, Prosperi JM, Lejeune-Hénaut I (2013) Genetic variability and QTL mapping of freezing tolerance and related traits in Medicago truncatula. Theor Appl Genet 126:2353–2366
Badawi M, Reddy YV, Agharbaoui Z, Tominaga Y, Danyluk J, Sarhan F, Houde M (2008) Structure and functional analysis of wheat ICE (Inducer of CBF Expression) genes. Plant Cell Physiol 49:1237–1249
Båga M, Chodaparambil SV, Limin AE, Pecar M, Fowler DB, Chibbar RN (2007) Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat. Funct Integr Genom 7:53–68
Bai B, Wu J, Sheng WT, Zhou B, Zhou LJ, Zhuang W, Yao DP, Deng QY (2015) Comparative analysis of anther transcriptome profiles of two different rice male sterile lines genotypes under cold stress. Int J Mol Sci 16:11398–11416
Barah P, Jayavelu ND, Rasmussen S, Nielsen HB, Mundy J, Bones AM (2013) Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes. BMC Genom 14:722
Barakat A, Sriram A, Park J, Zhebentyayeva T, Main D, Abbott A (2012) Genome wide identification of chilling responsive microRNAs in Prunus persica. BMC Genom 13:481
Bevilacqua CB, Basu S, Pereira A, Tseng TM, Zimmer PD, Burgos NR (2015) Analysis of stress-responsive gene expression in cultivated and weedy rice differing in cold stress tolerance. PLoS One 10:e0132100
Boer R, Campbell LC, Fletcher DJ (1993) Characteristics of frost in a major wheat-growing region of Australia. Aust J Agric Res 44:1731–1743
Bonnecarrère V, Quero G, Monteverde E, Rosas J, de Vida FP, Cruz M, Corredor E, Garaycochea S, Monza J (2014) Candidate gene markers associated with cold tolerance in vegetative stage of rice (Oryza sativa L.). Euphytica 203:385–398
Burow G, Burke JJ, Xin Z, Franks CD (2010) Genetic dissection of early-season cold tolerance in sorghum (Sorghum bicolor (L.) Moench). Mol Breed 28:391–402
Calzadilla PI, Maiale SJ, Ruiz OA, Escaray FJ (2016) Transcriptome response mediated by cold stress in Lotus japonicas. Front Plant Sci 7:374
Campoli C, Matus-Cádiz MA, Pozniak CJ, Cattivelli L, Fowler DB (2009) Comparative expression of Cbf genes in the Triticeae under different acclimation induction temperatures. Mol Genet Genom 282:141–152
Cao X, Wu Z, Jiang F, Zhou R, Yang Z (2014) Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis. BMC Genom 15:1130
Carvallo MA, Pino MT, Jeknic Z, Zou C, Doherty CJ, Shiu SH, Chen TH, Thomashow MF (2011) A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana. J Exp Bot 62:3807–3819
Casao MC, Igartua E, Karsai I, Bhat PR, Cuadrado N, Gracia MP, Lasa JM, Casas AM (2011) Introgression of an intermediate VRNH1 allele in barley (Hordeum vulgare L.) leads to reduced vernalization requirement without affecting freezing tolerance. Mol Breed 28:475–484
Case AJ, Skinner DZ, Garland-Campbell KA, Carter AH (2013) freezing tolerance-associated quantitative trait loci in the Brundage × Coda wheat recombinant inbred line population. Crop Sci 54:982–992
Cattivelli L, Baldi P, Crosatti C, Di Fonzo N, Faccioli P, Grossi M, Mastrangelo AM, Pecchioni N, Stanca AM (2002) Chromosome regions and stress-related sequences involved in resistance to abiotic stress in Triticeae. Plant Mol Biol 48:649–665
Chan Z, Wang Y, Cao M, Gong Y, Mu Z, Wang H, Hu Y, Deng X, He XJ, Zhu JK (2016) RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway. New Phytol 209:1527–1539
Chawade A, Lindlof A, Olsson B, Olsson O (2013) Global expression profiling of Low Temperature Induced Genes in the Chilling Tolerant Japonica Rice Jumli Marshi. PLoS One 8:e81729
Chen A, Reinheimer J, Brûlé-Babel A, Baumann U, Pallotta M, Fincher GB, Collins NC (2009) Genes and traits associated with chromosome 2H and 5H regions controlling sensitivity of reproductive tissues to frost in barley. Theor Appl Genet 118:1465–1476
Chen L, Zhang Y, Ren Y, Xu J, Zhang Z, Wang Y (2012) Genome-wide identification of cold-responsive and new microRNAs in Populus tomentosa by high-throughput sequencing. Biochem Biophys Res Commun 417:892–896
Chen J, Han G, Shang C, Li J, Zhang H, Liu F, Wang J, Liu H, Zhang Y (2015a) Proteomic analyses reveal differences in cold acclimation mechanisms in freezing-tolerant and freezing-sensitive cultivars of alfalfa. Front Plant Sci 6:105
Chen H, Chen X, Chen D, Li J, Zhang Y, Wang A (2015b) A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites. BMC Plant Biol 15:132
Cheng KS (1993) Rice genetic resources in Yunnan. Wu Zhengyi Symposium on Biodiversity in Yunnan. Yunnan Presshouse of Science and Technology, Kunming, pp 90–94
Chinnusamy V, Ohta M, Kanrar S, Lee B-h, Hong X, Agarwal M, Zhu JK (2003) ICE1, a regulator of cold induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev 17:1043–1054
Chinnusamy V, Zhu J, Zhu JK (2007) Cold stress regulation of gene expression plants. Trends Plant Sci 12:444–451
Chinnusamy V, Zhu JK, Sunkar R (2010) Gene regulation during cold stress acclimation in plants. Methods Mol Biol 639:39–55
Cho HY, Hwang SG, Kim DS, Jang CS (2012) Genome-wide transcriptome analysis of rice genes responsive to chilling stress. Can J Plant Sci 92:447–460
Choi DW, Rodriguez EM, Close TJ (2002) Barley Cbf3 gene identification, expression pattern, and map location. Plant Physiol 129:1781–1787
Clarke HJ, Siddique KHM (2004) Response of chickpea genotypes to low temperature stress during reproductive development. Field Crops Res 90:323–334
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 363:557–572
Crimp SJ, Zheng B, Khimashia N, Gobbett DL, Chapman S, Howden M, Nicholls Neville (2016) Recent changes in southern Australian frost occurrence: implications for wheat production risk. Crop Pasture Sci 67:801–811
Croser JS, Clarke HJ, Siddique KHM, Khan TN (2003) Low-temperature stress: implications for chickpea (Cicer arietinum L.) improvement. Crit Rev Plant Sci 22:185–219
Cui S, Huang F, Wang J, Ma X, Cheng Y, Liu J (2005) A proteomic analysis of cold stress responses in rice seedlings. Proteomics 5:3162–3172
Cui D, Xu C, Tang C, Yang C, Yu T, Xin-xiang A, Cao G, Xu F, Zhang J, Hang L (2013) Genetic structure and association mapping of cold tolerance in improved japonica rice germplasm at booting stage. Euphytica 193:369–382
da Cruz RP, Milach SCK (2004) Cold tolerance at the germination stage of rice: methods of evaluation and characterization of genotypes. Sci Agric 61:1–8
da Cruz RP, Sperotto RA, Di Cargnelutt, Adamski JM, de FreitasTerra T, Fett JP (2013) Avoiding damage and achieving cold tolerance in rice plants. Food Energy Secur 2:96–119
Dai LY, Lin XH, Ye CR, Kato A, Saito K, Yu TQ, Xu FR, Zhang DP (2003) Studies on cold tolerance of rice, Oryza sativa L. III. Molecular basis for special fertility percentage as evaluation criterion of cold tolerance. Acta Agron Sin 29:708–714
Dai L, Lin X, Ye C, Ise K, Saito K, Kato A, Xu F, Yu T, Zhang D (2004) Identification of quantitative trait loci controlling cold tolerance at the reproductive stage in Yunnan landrace of rice, Kunmingxiaobaigu. Breed Sci 54:253–258
Dametto A, Sperotto RA, Adamski JM, Blasi ÉA, Cargnelutti D, de Oliveira LF, Ricachenevsky FK, Fregonezi JN, Mariath JE, da Cruz RP, Margis R, Fett JP (2015) Cold tolerance in rice germinating seeds revealed by deep RNAseq analysis of contrasting indica genotypes. Plant Sci 238:1–12
De Storme N, Geelen D (2014) The impact of environmental stress on 569 male reproductive development in plants: biological processes 570 and molecular mechanisms. Plant Cell Environ 37:1–18
Deng HB, Che FL, Xiao YH, Tang WB, Pan Y, Liu ZX, Chen LY (2011) Effects of low temperature stress during flowering period on pollen characters and flag leaf physiological and biochemical characteristics of rice. Ying Yong Sheng Tai Xue Bao 22:66–72
Dhillon T, Stockinger EJ (2013) Cbf14 copy number variation in the A, B, and D genomes of diploid and polyploid wheat. Theor Appl Genet 126:2777–2789
Dhillon T, Pearce SP, Stockinger EJ, Distelfeld A, Li C, Knox AK, Vashegyi I, Vágújfalvi A, Galiba G, Dubcovsky J (2010) Regulation of freezing tolerance and flowering in temperate cereals: the VRN-1 connection. Plant Physiol 153:1846–1858
Ding Y, Li H, Zhang X, Xie Q, Gong Z, Yang S (2015) OST1 kinase modulates freezing tolerance by enhancing ICE1 stability in Arabidopsis. Dev Cell 32:278–289
Doherty CJ, Van Buskirk HA, Myers SJ, Thomashow MF (2009) Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. Plant Cell 21:972–984
Dong CH, Hu X, Tang W, Zheng X, Kim YS, Lee BH, Zhu JK (2006) A putative Arabidopsis nucleoporin AtNUP160 is critical for RNA export and required for plant tolerance to cold stress. Mol Cell Biol 26:9533–9543
Dong MA, Farre EM, Thomashow MF (2011) Circadian clock associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci USA 108:7241–7246
Drozdov SN, Titov AF, Balagurova NI, Kritenko SP (1984) The effect of temperature on cold and heat resistance of growing plants. II. Cold resistant species. J Exp Bot 35:1603–1608
Du F, Xu JN, Li D, Wang XY (2015) The identification of novel and differentially expressed apple-tree genes under low-temperature stress using high-throughput Illumina sequencing. Mol Biol Rep 42:569–580
Dumont E, Fontaine V, Vuylsteker C, Sellier H, Bodèle S, Voedts N, Devaux R, Frise M, Avia K, Hilbert JL, Bahrman N, Hanocq E, Lejeune-Hénaut I, Delbreil B (2009) Association of sugar content QTL and PQL with physiological traits relevant to frost damage resistance in pea under field and controlled conditions. Theor Appl Genet 118:1561–1571
Dumont E, Bahrman N, Goulas E, Valot B, Sellier H, Hilbert JL, Vuylsteker C, Lejeune-Hénaut I, Delbreil B (2011) A proteomic approach to decipher chilling response from cold acclimation in pea (Pisum sativum L.). Plant Sci 180:86–98
Eagles HA, Wilson J, Cane K, Vallance N, Eastwood RF, Kuchel H, Martin PJ, Trevaskis B (2016) Frost-tolerance genes Fr-A2 and Fr-B2 in Australian wheat and their effects on days to heading and grain yield in lower rainfall environments in southern Australia. Crop Pasture Sci 67:119–127
Eizenga GC, Shakiba E, Jodari F, Duke S, Korniviel P, Jackson A, Mezey J, McCouch S (2015) The secrets of cold tolerance at seedling stage and heading in rice as revealed by association mapping. PAG, 2015, San Diego, CA
Ellis RH, Summerfield RJ, Edmeades GO, Roberts EH (1992) Photoperiod, temperature and the interval from sowing to tassel initiation in diverse cultivars of maize. Crop Sci 32:1225–1232
Endo T, Chiba B, Wagatsuma K, Saeki K, Ando T, Shomura A, Mizubayashi T, Ueda T, Yamamato T, Nishio T (2016) Detection of QTLs for cold tolerance of rice cultivar ‘Kuchum’ and effect of QTL pyramiding. Theor Appl Genet 129:631–640
Falk DE, Reinbergs E, Meatherall G (1997) OAC Elmira winter barley. Can J Plant Sci 77:639–640
Farrell TC, Fox KM, William RL, Fukai S, Lewin LG (2006) Minimising cold damage during reproductive development among temperate rice genotypes. II. Genotypic variation and flowering traits related to cold tolerance screening. Aust J Agric Res 57:89–100
Farrell TC, Williams RL, Fukai S (2001) The cost of low temperature to the NSW rice industry. Proc 10th Aust Agron Conf 1:1300–1430
Fiedler K, Bekele WA, Matschegewski C, Snowdon R, Wieckhorst S, Zacharias A, Uptmoor R (2016) Cold tolerance during juvenile development in sorghum: a comparative analysis by genome wide association and linkage mapping. Plant Breed. doi:10.1111/pbr.12394
Fiedler K, Bekele WA, Friedt W, Snowdon R, Stützel H, Zacharias A, Uptmoor R (2012) Genetic dissection of the temperature dependent emergence processes in sorghum using a cumulative emergence model and stability parameters. Theor Appl Genet 125(8):1647–1661
Fisk SP, Cuesta-Marcos A, Cistue L, Rusell J, Smith KP, Baenziger S, Bedo Z, Corey A, Filichkin T (2013) FR-H3: a new QTL to assist in the development of fall-sown barley with superior low temperature tolerance. Theor Appl Genet 126:335–347
Foolad MR, Chen FQ, Lin GY (1998) RFLP mapping of QTLs conferring cold tolerance during seed germination in an interspecific cross of tomato. Mol Breed 4:519–529
Fowler S, Thomashow MF (2002) Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold-acclimation in addition to the CBF cold response pathway. Plant Cell 14:1675–1690
Fowler SG, Cook D, Thomashow MF (2005) Low temperature induction of Arabidopsis CBF1, 2, and 3 is gated by the circadian clock. Plant Physiol 137:961–968
Fracheboud Y, Ribaut JM, Vargas M, Messmer R, Stamp P (2002) Identification of quantitative trait loci for cold-tolerance of photosynthesis in maize (Zea mays L.). J Exp Bot 53:1967–1977
Fracheboud Y, Jompuk C, Ribaut J-M, Stamp P, Leipner J (2004) Genetic analysis of cold-tolerance of photosynthesis in maize. Plant Mol Biol 56:241–253
Francia E, Rizza F, Cattivelli L, Stanca AM, Galiba G, Toth B, Hayes PM, Skinner JS, Pecchioni N (2004) Two loci on chromosome 5H determine low-temperature tolerance in a ‘Nure’ (winter)_‘Tre- ‘Tremois’ (spring) barley map. Theor Appl Genet 108:670–680
Francia E, Barabaschi D, Tondelli A, Laidò G, Rizza F, Stanca AM, Busconi M, Fogher C, Stockinger EJ, Pecchioni N (2007) Fine mapping of a HvCBF gene cluster at the frost resistance locus Fr-H2 in barley. Theor Appl Genet 115:1083–1091
Francia E, Morcia C, Pasquariello M, Mazzamurro V, Milc JA, Rizza F, Terzi V, Pecchioni N (2016) Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley. Plant Mol Biol 92:161–175
Franklin KA, Whitelam GC (2007) Light-quality regulation of freezing tolerance in Arabidopsis thaliana. Nat Genet 39:1410–1413
Frederiks TM, Christopher JT, Fletcher SHE, Borrell AK (2011) Post head-emergence frost resistance of barley genotypes in the northern grain region of Australia. Crop Pasture Sci 62:736–745
Fujino K, Iwata N (2011) Selection for low-temperature germinability on the short arm of chromosome 3 in rice cultivars adapted to Hokkaido, Japan. Theor Appl Genet 123:1089–1097
Fujino K, Matsuda Y ( 2010) Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice. Plant Mol Biol 72:137–152
Fujino K, Sekiguchi H (2011) Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Plant Mol Biol 75:1–10
Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799
Fujino K, Sekigushi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proc Natl Acad Sci USA 105:12623–12628
Fuller MP, Fuller AM, Kaniouras S, Christophers J, Fredericks T (2007) The freezing characteristics of wheat at ear emergence. Eur J Agron 26:435–441
Funatsuki H, Kawaguchi K, Matsuba S, Sato Y, Ishimoto M (2005) Mapping of QTL associated with chilling tolerance during reproductive growth in soybean. Theor Appl Genet 111:851–861
Galiba G, Quarrie SA, Sutka J, Morgounov A, Snape JW (1995) RFLP mapping of the vernalization (Vrn1) and frost resistance (Fr1) genes on chromosome 5A of wheat. Theor Appl Genet 90:1174–1179
Galiba G, Vágújfalvi A, Li C, Soltész A, Dubcovsky J (2009) Regulatory genes involved in the determination of frost tolerance in temperate cereals. Plant Sci 176:12–19
Gault CM, Budka JS, Lepak NK, Cotich D, Rodger-Melnick E, Buckler ES (2016) Cellular processes and regulatory networks searching for the genetic basis of cold tolerance in Maize’s Sister Genus Tripsacum. PAG, San Diego
Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48:909–930
Gilmour SJ, Artus NN, Thomashow MF (1992) cDNA sequence analysis and expression of two cold-regulated genes of Arabidopsis thaliana. Plant Mol Biol 18:13–21
Gilmour SJ, Sebolt AM, Salazar MP, Everard JD, Thomashow MF (2000) Over expression of the Arabidopsis CBF3 transcriptional activator mimics multiple biochemical changes associated with cold acclimation. Plant Physiol 124:1854–1865
Gilmour SJ, Fowler SG, Thomashow MF (2004) Arabidopsis transcriptional activators CBF1, CBF2, and CBF3 have matching functional activities. Plant Mol Biol 54:767–781
Glaszmann JC, Kaw RN, Khush GS (1990) Genetic divergence among cold tolerant rices (Oryza sativa L.). Euphytica 45:95–104
Godfray HC, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, Pretty J, Robinson S, Thomas SM, Toulmin C (2010) Food security: the challenge of feeding 9 billion people. Science 327:812–818
Gomez LD, Vanacker H, Buchner P, Noctor G, Foyer CH (2004) Intercellular distribution of glutathione synthesis in maize leaves and its response to short-term chilling. Plant Physiol 134:1662–1671
Goodstal FJ, Kohler GR, Randall LB, Bloom AJ, Clair DAS (2005) A major QTL introgressed from wild Lycopersicon hirsutum confers chilling tolerance to cultivated tomato (Lycopersicon esculentum). Theor Appl Genet 111:898–905
Greenup AG, Sasani S, Oliver SN, Walford SA, Millar AA, Trevaskis B (2011) Transcriptome analysis of the vernalization response in Barley (Hordeum vulgare) seedlings. PLoS One 6:e17900
Grimaud F, Renaut J, Dumont E, Sergeant K, Lucau-Danila A, Blervacq AS, Sellier H, Bahrman N, Lejeune-Hénaut I, Delbreil B, Goulas E (2013) Exploring chloroplastic changes related to chilling and freezing tolerance during cold acclimation of pea (Pisum sativum L.). J Proteom 80:145–159
Guan Q, Wu J, Zhang Y, Jiang C, Chai C, Zhu J (2013a) A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. Plant Cell 25:342–356
Guan YN, Huang ZL, Zhang WJ, Shi XD, Zhang PP (2013b) Effects of low temperature stress on photosynthetic performance of different genotypes wheat cultivars. Ying Yong Sheng Tai Xue Bao 24:1895–1899
Gulik PJ, Drouin S, Yu Z, Danyluk J, Poisson G, Monroy AF, Sarhan F (2005) Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48:913–923
Guy CL, Li QB (1998) The organization and evolution of the spinach stress 70 molecular chaperone gene family. Plant Cell 10:539–556
Han LZ, Zhang YY, Qiao YL, Cao GL, Zhang SY, Kim JH, Koh HJ (2006) Genetic and QTL analysis for low-temperature vigor of germination in rice. Yi Chuan Xue Bao 33:998–1006
Han L, Qiao Y, Zhang S, Zhang Y, Cao G, Kim J, Lee K, Koh H (2007) Identification of quantitative trait loci for cold response of seedling vigor traits in rice. J Genet Genome 34:239–246
Hanin M, Brini F, Ebel C, Toda Y, Takeda S, Masmoudi K (2011) Plant dehydrins and stress tolerance Versatile proteins for complex mechanisms. Plant Signal Behav 6:1503–1509
Hashimoto M, Komatsu S (2007) Proteomic analysis of rice seedlings during cold stress. Proteomics 7:1293–1302
Herman EM, Rotter K, Premakumar R, Elwinger G, Bae H, Ehler-King L, Chen S, Livingston DP 3rd (2006) Additional freeze hardiness in wheat acquired by exposure to 23 8C is associated with extensive physiological, morphological, and molecular changes. J Exp Bot 57:3601–3618
Hou MY, Wang CM, Jiang L, Wan JM, Yasui H, Yoshimura A (2004) Inheritance and QTL mapping of low temperature germinability in rice (Oryza sativa L.). Yi Chuan Xue Bao 31:701–706
Houde M, Dhindsa RS, Sarhan F (1992) A molecular marker to select for freezing tolerance in Gramineae. Mol Gen Genet 234:43–48
Hsieh TH, Lee JT, Charng YY, Chan MT (2002a) Tomato plants ectopically expressing Arabidopsis CBF1show enhanced resistance to water deficit stress. Plant Physiol 130:618–626
Hsieh TH, Lee JT, Yang PT, Chiu LH, Charng YY, Wang YC, Chan MT (2002b) Heterology expression of the Arabidopsis C-repeat/dehydration response element binding factor 1 gene confers elevated tolerance to chilling and oxidative stresses in transgenic tomato. Plant Physiol 129:1086–1094
Hu Y, Zhang L, Zhao L, Li J, He S, Zhou K, Yang F, Huang M, Jiang L, Li L (2011) Trichostatin A selectively suppresses the cold-induced transcription of the ZmDREB1 gene in maize. PLoS One 6:e22132
Hu Y, Zhang L, He S, Huang M, Tan J, Zhao L, Yan S, Li H, Zhou K, Liang Y, Li L (2012) Cold stress selectively unsilences tandem repeats in heterochromatin associated with accumulation of H3K9ac. Plant Cell Environ 35:2130–2142
Hu S, Lübberstedt T, Zhao G, Lee M (2016) QTL mapping of low-temperature germination ability in the maize IBM Syn4 RIL population. PLoS One 11:e0152795
Huang X, Han B (2014) Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol 65:531–551
Huang J, Zhang J, Li W, Hu W, Duan L, Feng Y, Qiu F, Yue B (2013) Genome-wide association analysis of ten chilling tolerance indices at the germination and seedling stages in maize. J Integr Plant Biol 55:735–744
Huang CK, Shen YL, Huang LF, Wu SJ, Yeh CH, Lu CA (2015) The DEAD-Box RNA helicase AtRH7/PRH75 participates in pre-rRNA processing, plant development and cold tolerance in Arabidopsis. Plant Cell Physiol 57:174–191
Hughes MA, Dunn MA (1996) The molecular biology of plant acclimation to low temperature. J Exp Bot 47:291–305
Hund A, Fracheboud Y, Soldati A, Frascaroli E, Salvi S, Stamp P (2004) QTL controlling root and shoot traits of maize seedlings under cold stress. Theor Appl Genet 109:618–629
Hur YJ, Cho JH, Park HS, Noh TH, Park DS, Lee JY, Sohn YB, Shin D, Song YC, Kwon YU, Lee JH (2016) Pyramiding of two rice bacterial blight resistance genes, Xa3 and Xa4, and a closely linked cold-tolerance QTL on chromosome 11. Theor Appl Genet 129:1861–1871
Ikeda T, Ohnishi S, Senda M, Miyoshi T, Ishimoto M, Kitamura K, Funatsuki H (2009) A novel major quantitative trait locus controlling seed development at low temperature in soybean (Glycine max). Theor Appl Genet 118:1477–1488
IRRI (1979) Report of a rice cold tolerance workshop. In: IRRI Proceedings of rice cold tolerance workshop, Office of Rural Development, Suweon, Korea, p 139
Ito Y, Katsura K, Maruyama K, Taji T, Kobayashi M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2006) Functional analysis of rice DREB1/CBF-type transcription factors involved in cold-responsive gene expression in transgenic rice. Plant Cell Physiol 47:141–153
Iwata N, Fujino K (2010) Genetic effects of major QTLs controlling low-temperature germinability in different genetic backgrounds in rice (Oryza sativa L.). Genome 53:763–768
Iwata N, Shinada H, Kiuchi H, Sato T, Fujino K (2010) Mapping QTLs controlling seedling establishment using a direct seeding method in rice. Breed Sci 60:353–360
Jaglo-Ottosen KR, Gilmour SJ, Zarka DG, Schabenberger O, Thomashow MF (1998) Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280:104–106
Jaglo-Ottosen KR, Kleff S, Amundsen KL, Zhang X, Haake V, Zhang JZ, Deits T, Thomashow MF (2001) Components of the Arabidopsis C-repeat/dehydration-responsive element binding factor cold-response pathway are conserved in Brassica napus and other plant species. Plant Physiol 127:910–917
Janmohammadi M, Zolla L, Rinalducci S (2015) Low temperature tolerance in plants: changes at the protein level. Phytochemistry 117:76–89
Jeong EG, Yea JD, Baek MK, Moon HP, Choi HC, Yoon KM, Ahn SN (2000) Estimation of critical temperature for traits related to cold tolerance in rice. Korean J Breed 32:363–368
Ji SL, Jiang L, Wang YH, Zhang WW, Liu X, Liu SJ, Chen LM, Zhai HQ, Wan JM (2009) Quantitative trait loci mapping and stability for low temperature germination ability of rice. Plant Breed 128:387–392
Ji Z, Zeng Y, Zeng D, Ma L, Li X, Liu B, Yang C (2010) Identification of QTLs for rice cold tolerance at plumule and 3-leaf-seedling stages by using QTLNetwork software. Rice Sci 17 (4)
Ji H, Wang Y, Cloix C, Li K, Jenkins GI, Wang S, Shang Z, Shi Y, Yang S, Li X (2015) The Arabidopsis RCC1 family protein TCF1 regulates freezing tolerance and cold acclimation through modulating lignin biosynthesis. PLoS Genet 11:e1005471
Jia Y, Ding Y, ShiY Zhang X, Gong Z, Yang S (2016) The cbfs triple mutants reveal the essential functions of CBFs in cold acclimation and allow the definition of CBF regulons in Arabidopsis. New Phytol 212:345–353
Jiang W, Jin YM, Lee J, Lee KL, Piao R, Han L, Shin JC, Jin RD, Cao T, Pan HY, Du X, Ko HJ (2011) Quantitative trait loci for cold tolerance of rice recombinant inbred lines in low temperature environments. Mol Cell 32:579–587
Jompuk C, Fracheboud Y, Stamp P, Leipner J (2005) Mapping of quantitative trait loci associated with chilling tolerance in maize (Zea mays L.) seedlings grown under field conditions. J Exp Bot 56:1153–1163
Kabaki N, Yoneyama T, Tajima K (1982) Physiological mechanism of growth retardation in rice seedlings as affected by low temperature. Jpn J Crop Sci 51:82–88
Kahraman A, Kusmenoglu I, Aydin N, Aydogan A, Erskine W, Muehlbauer FJ (2004) QTL mapping of winter hardiness genes in lentil. Crop Sci 44:13–22
Kaneda C, Beachell HM (1974) Response of indica-japonica rice hybrids to low temperatures. SABRAO J 6:17–32
Kang G, Li G, Yang W, Han Q, Ma H, Wang Y, Ren J, Zhu Y, Guo T (2013) Transcriptional profile of the spring freeze response in the leaves of bread wheat (Triticum aestivum L.). Acta Physiol Plant 35:575–587
Khraiwesh B, Zhu JK, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819:137–148
Kim Y et al (2013) Roles of CAMTA transcription factors and salicylic acid in configuring the low-temperature transcriptome and freezing tolerance of Arabidopsis. Plant J 75:364–376
Kim SM, Suh JP, Lee CK, Lee JH, Kim YG, Jena KK (2014) QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice (Oryza sativa L.). Mol Genet Genom 289:333–343
Kim YS, Lee M, Lee JH, Lee HJ, Park CM (2015) The unified ICE-CBF pathway provides a transcriptional feedback control of freezing tolerance during cold acclimation in Arabidopsis. Plant Mol Biol 89:187–201
Kisha TJ, Taylor GA, Bowman HF, Wiesner LE, Jackson GD, Carlson GR, Bergman JW, Kushnak JD, Stallknecht GF, Stewart VR (1992) Registration of Tiber hard red winter wheat. Crop Sci 32:1292–1293
Kizis D, Lumbreras V, Pages M (2001) Role of AP2/EREBP transcription factors in gene regulation during abiotic stress. FEBS Lett 498:187–189
Klein A, Houtin H, Rond C, Marget P, Jacquin f, Boucherot K, Huart m, Riviere n, Boutet G, Lejeune-Henaut I (2014) QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance. Theor Appl Genet:1319–1330
Kole C, Thormann CE, Karlsson BH, Palta JP, Gaffney P, Yandell B, Osborn TC (2002) Comparative mapping of loci controlling winter survival and related traits in oilseed Brassica rapa and B. napus. Mol Breeding 9:201–210
Knight H (2000) Calcium signaling during abiotic stress in plants. Int Rev Cytol 195:269–325
Knight MR, Knight H (2012) Low-temperature perception leading to gene expression and cold tolerance in higher plants. New Phytol 195:737–751
Knight H, Trewavas AJ, Knight MR (1996) Cold calcium signaling in Arabidopsis involves two cellular pools and a change in calcium signature after acclimation. Plant Cell 8:489–503
Knoll J, Gunaratna N, Ejeta G (2008) QTL analysis of early season cold tolerance in Sorghum. Theor Appl Genet 116:577–587
Knox AK, Li C, Vágújfalvi A, Galiba G, Stockinger EJ, Dubcovsky J (2008) Identification of candidate CBF genes for the frost tolerance locus Fr-Am 2 in Triticum monococcum. Plant Mol Biol 67:257–270
Knox AK, Dhillon T, Cheng H, Tondelli A, Pecchioni N, Stockinger EJ (2010) CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals. Theor Appl Genet 121:21–35
Kobayashi F, Takumi S, Kume S, Ishibashi M, Ohno R, Murai K, Nakamura C (2005) Regulation by Vrn-1/Fr-1 chromosomal intervals of CBF-mediated Cor/Lea gene expression and freezing tolerance in common wheat. J Exp Bot 56:887–895
Kobayashi F, Maeta E, Terashima A, Kawaura K, Ogihara Y, Takumi S (2008) Development of abiotic stress tolerance via bZIP-type transcription factor LIP19 in common wheat. J Exp Bot 59:891–905
Koc I, Filiz E, Tombuloglu H (2015) Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars. Biotech Biotechnol Equip 29:851–860
Kolar SC, Hayes PM, Chen THH, Lindernan RG (1991) Genotypic variation for cold tolerance in winter and facultative barley. Crop Sci 31:1149–1152
Korte A, Farlow A (2013) The advantages and limitations of trait analysis with GWAS: a review. Plant Methods 9:29
Koseki M, Kitazawa N, Yonebayashi S, Maehara Y, Wang ZX, Minobe Y (2010) Identification and fine mapping of a major quantitative trait locus originating from wild rice, controlling cold tolerance at the seedling stage. Mol Genet Genom 284:45–54
Kosová K, Tom Prásil I, Prásilová P, Vítámvás P, Chrpová J (2010) The development of frost tolerance and DHN5 protein accumulation in barley (Hordeum vulgare) doubled haploid lines derived from Atlas 68 × Igri cross during cold acclimation. J Plant Physiol 167:343–350
Kosová K, Vítámvás P, Prášil IT (2011) Expression of dehydrins in wheat and barley under different temperatures. Plant Sci 180:46–52
Kosová K, Vítámvás P, Planchon S, Renaut J, Vanková R, Prášil IT (2013) Proteome analysis of cold response in spring and winter wheat (Triticum aestivum) crowns reveals similarities in stress adaptation and differences in regulatory processes between the growth habits. J Proteome Res 12:4830–4845
Kumar S, Malik J, Thakur P, Kaistha S, Sharma KD, Upadhyaya HD, Berger JD, Nayyar H (2011) Growth and metabolic responses of contrasting chickpea (Cicer arietinum L.) genotypes to chilling stress at reproductive phase. Acta Physiol Plant 33:779–787
Kurkela S, Franck M (1990) Cloning and characterization of a cold- and ABA-inducible Arabidopsis gene. Plant Mol Biol 15:137–144
Kuroki M, Saito K, Matsuba S, Yokogami N, Shimizu H, Ando I, Sato Y (2007) A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8. Theor Appl Genet 115:593–600
Kwon CS, Lee D, Choi G, Chung WI (2009) Histone occupancy- dependent and-independent removal of H3K27 trimethylation at cold- responsive genes in Arabidopsis. Plant J 60:112–121
Lang Z, Zhu J (2015) OST1 phosphorylates ICE1 to enhance plant cold tolerance. Sci China Life Sci 58:317–318
Laudencia-Chingcuano D, Fowler DB (2015) Deep sequencing of cold acclimated wheat crown transcriptome. PAG San Diego, CA 10–14 January
Lee MH (2001) Low temperature tolerance in rice: the Korean experience. Pp. 109–117 in S. Fukai and J. Basnayake, eds. Increased lowland rice production in the Mekong Region. In: Proceedings of an international workshop, Vientiane, Laos, 30 October to 2 November 2000. Australian Center for International Agricultural Research, Canberra, Australia
Lee CM, Thomashow MF (2012) Photoperiodic regulation of the C repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc Natl Acad Sci USA 109:15054–15059
Lee BH, Henderson DA, Zhu JK (2005) The Arabidopsis cold-responsive transcriptome and its regulation by ICE1. Plant Cell 17:3155–3175
Lee BH, Kapoor A, Zhu J, Zhu JK (2006) STABILIZED1, a stress-upregulated nuclear protein, is required for pre-mRNA splicing, mRNA turnover, and stress tolerance in Arabidopsis. Plant Cell 18:1736–1749
Lee J, Lee W, Kwon S-W (2015) A quantitative shotgun proteomics analysis of germinated rice embryos and coleoptiles under low-temperature conditions. Proteome Sci 13:27
Legrand S, Marque G, Blassiau C, Bluteau A, Canoy AS, Fontaine V, Jaminon O, Bahrman N, Mautord J, Morin J, Petit A, Baranger A, Rivière N, Wilmer J, Delbreil B, Lejeune-Hénaut I (2013) Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea. J Plant Physiol 170:1148–1157
Lejeune-Henaut I, Hanocq E, Bethenourt L, Fontaine V, Delbreil B, Morin J, Petit A, Devaux R, Boilleau M, Stempniak JJ (2008) The flowering locus Hr colocalizes with a major QTL affecting winter frost tolerance in Pisum sativum L. Theor Appl Genet 116:1105–1116
Li TG, Guo WM (1993) Identification and study on tolerance in main stresses of China cultivated rice germplasm resource. In: Ying CS (ed) Rice germplasm resources in China. China Agricultural Science and Technology Press, Beijing, pp 71–75
Li L, Liu X, Xie K, Wang Y, Liu F, Lin Q, Wang W, Yang C, Lu B, Liu S, Chen L, Jiang L, Wan J (2013) qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.). Theor Appl Genet 126:2313–2322
Limin AE, Fowler DB (2002) Developmental traits affecting low-temperature tolerance response in near-isogenic lines for the Vernalization locus Vrn-A1 in wheat (Triticum aestivum L. em Thell). Ann Bot 89:579–585
Lin C, Thomashow MF (1992) A cold-regulated Arabidopsis gene encodes a polypeptide having potent cryoprotective activity. Biochem Biophys Res Commun 183:1103–1108
Lindlöf A, Chawade A, Sikora P, Olsson O (2015) Comparative transcriptomics of Sijung and Jumli Marshi rice during early chilling stress imply multiple protective mechanisms. PLoS One 10:e0125385
Lissarre M, Ohta M, Sato A, Miura K (2010) Cold-responsive gene regulation during cold acclimation in plants. Plant Signal Behav 5:948–952
Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain, separate two cellular signal transduction pathways in drought- and low temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10:1391–1406
Liu F, Sun C, Tan L, Fu Y, Li D, Wang X (2003) Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages. Chinese Sci Bull 48:2068–2071
Liu F, Xu W, Qa Song, Tan L, Liu J, Zhu Z, Fu Y, Su Z, Sun C (2013) Microarray-assisted fine-mapping of quantitative trait loci for cold tolerance in rice. Mol Plant 6:757–767
Liu W, Maurer HP, Li G, Tucker MR, Gowda M et al (2014) Genetic architecture of winter hardiness and frost tolerance in triticale. PLoS One 9:e99848
Liu W, Lu T, Li Y, Pan X, Duan Y, Min J, Fu X, Sheng X, Xiao J, Liu S, Tan J, Yao Y, Li X (2015a) Mapping of quantitative trait loci for cold tolerance at the early seedling stage in landrace rice Xiang 743. Euphytica 201:401–409
Liu X, Hao L, Li D, Zhu L, Hu S (2015b) Long non-coding RNAs and their biological roles in plants. Genom Proteom Bioinf 13:137–147
Liu L, Venkatesh J, Jo YD, Koeda S, Hosokawa M, Kang JH, Goritschnig S, Kang BC (2016) Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense). Theor Appl Genet 129:1541–1556
Long-Zhai H, Yuan-Yuan Z, Yong-Li Q, Gui-Lan C, San-Yuan Z, Jong-Hwan K, Hee-Jong K (2006) Genetic and QTL analysis for low-temperature vigor of germination in rice. Acta Genet Sinica 33:998–1006
Long-zhi H, Yong-li Q, Gui-lan C, Yuan-yuan Z, Yong-ping A, Jong-doo Y, Hee-jong K (2004) QTLs analysis of cold tolerance during early growth period for rice. Rice Sci 11:245–250
Lou Q, Chen L, Sun Z, Xing Y, Li J, Xu X, Mei H, Luo L (2007) A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica 158:87–94
Lucau-Danila A, Toitot C, Goulas E, Blervacq AS, Hot D, Bahrman N, Sellier H, Lejeune-Henaut Delbreil B (2012) Transcriptome analysis in pea allows to distinguish chilling and acclimation mechanisms. Plant Physiol Biochem 58:236–244
Lv DK, Bai X, Li Y, Ding XD, Ge Y, Cai H, Ji W, Wu N, Zhu YM (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–47
Lv Y, Guo Z, Li X, Ye H, Li X, Xiong L (2016) New insights into the genetic basis of natural chilling and cold shock tolerance in rice by genome-wide association analysis. Plant Cell Environ 39:556–570
Ma Y, Dai X, Xu Y, Luo W, Zheng X, Zeng D, Pan Y, Lin X, Liu H, Zhang D, Xiao J, Guo X, Xu S, Niu Y, Jin J, Zhang H, Xu X, Li L, Wang W, Qian Q, Ge S, Chong K (2015) COLD1 confers chilling tolerance in rice. Cell 160:1209–1221
Mackill DJ, Lei XM (1997) Genetic variation for traits related to temperate adaptation of rice cultivars. Crop Sci 37:1340–1346
Mao D, Yu L, Chen D, Li L, Zhu Y, Xiao Y, Zhang D, Chen C (2015) Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theor Appl Genet 128:1359–1371
Mastrangelo AM, Belloni S, Barilli S, Ruperti B, Fonzo ND, Stanca AM, Cattivelli L (2005) Low temperature promotes intron retention in two e-cor genes of durum wheat. Planta 221:705–715
Matsui A, Nguyen AH, Nakaminami K, Seki M (2013) Arabidopsis non-coding RNA regulation in abiotic stress responses. Int J Mol Sci 14:22642–22654
Medina J, Bargues M, Terol J, Perez-Alonso Salinas J (1999) The Arabidopsis CBF gene family is composed of three genes encoding AP2 domain-containing proteins whose expression is regulated by low temperature but not by abscisic acid or dehydration. Plant Physiol 119:463–470
Medina J, Catalá R, Salinas J (2011) The CBFs: three arabidopsis transcription factors to cold acclimate. Plant Sci 180:3–11
Meissner M, Orsini E, Ruschhaupt M, Melchinger AE, Hincha DK, Heyer AG (2013) Mapping quantitative trait loci for freezing tolerance in a recombinant inbred line population of Arabidopsis thaliana accessions Tenela and C24 reveals REVEILLE1 as negative regulator of cold acclimation. Plant Cell Environ 36:1256–1267
Meng PH, Macquet A, Loudet O, Marion-Poll A, North HM (2008) Analysis of natural allelic variation controlling Arabidopsis thaliana seed germinability in response to cold and dark: identification of three major quantitative trait loci. Mol Plant 1:145–154
Mickelbart MV, Hasegawa PM, Bailey-Serres J (2015) Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 4:237–251
Miedema P, Sinnaeve J (1980) Photosynthesis and respiration of maize seedlings at suboptimal temperatures. J Exp Bot 31:813–819
Miller AK, Galiba G, Dubcovsky J (2006) A cluster of 11 CBF transcription factors is located at the frost tolerance locus Fr-Am 2 in Triticum monococcum. Mol Genet Genom 275:193–203
Misawa S, Mori N, Takumi S, Yoshida S, Nakamura C (2000) Mapping of QTLs for low temperature response in seedlings of rice (Oryza sativa L.). Cereal Res Commun 28:33–40
Mitchell-Olds T (2010) Complex-trait analysis in plants. Genome Biol 11:113
Miura K, Furumoto T (2013) Cold signaling and cold response in plants. Int J Mol Sci 14:5312–5337
Miura K, Lin SY, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Breed Sci 51:293–299
Miura K, Jin JB, Lee J, Yoo CY, Stirm V, Miura T, Ashworth EN, Bressan RA, Yun DJ, Hasegawa PM (2007) SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell 19:1403–1414
Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) AP2/ERF family transcription factors in plant abiotic stress responses. Biochim Biophys Acta (BBA) Gene Regul Mech 1819:86–96
Mohammadi R, Amri A, Ahmadi H, Jafarzadeh (2015) Characterization of tetraploid wheat landraces for cold tolerance and agronomic traits under rainfed conditions of Iran. J Agric Sci 153:631–645
Monroy AF, Dryanova A, Malette B, Oren DH, Ridha Farajalla M, Liu W, Danyluk J, Ubayasena LW, Kane K, Scoles GJ, Sarhan F, Gulick PJ (2007) Regulatory gene candidates and gene expression analysis of cold acclimation in winter and spring wheat. Plant Mol Biol 64:409–423
Moraes de Freitas GP, Basu S, Ramegowda V, Braga EB, Pereira A (2016) Comparative analysis of gene expression in response to cold stress in diverse rice genotypes. Biochem Biophys Res Commun 471:253–259
Mori M, Onishi K, Tokizono Y, Shinada H, Yoshimura T, Numao Y, Miura H, Sato T (2011) Detection of novel quantitative trait locus for cold tolerance at the booting stage derived from a tropical japonica rice variety Silewah. Breed Sci 61:61–68
Motomura Y, Kobayashi F, Iehisa JCM, Takumi S (2013) A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat. Breed Sci 63:58–67
Nah G, Lee M, Kim DS, Rayburn AL, Voigt T, Lee DK (2016) Transcriptome analysis of spartina pectinata in response to freezing stress. PLoS One 11:e0152294
Nakagahra M, Okuno K, Vaughan D (1997) Rice genetic resources: history, conservation, investigative characterization and use in Japan. Plant Mol Biol 35:69–77
Nakamichi N, Kusano M, Fukushima A, Kita M, Ito S, Yamashino T, Saito K, Sakakibara H, Mizuno T (2009) Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol 50:447–462
Nayyar H, Bains T, Kumar S (2005) Low temperature induced floral abortion in chickpea: relationship to abscisic acid and cryoprotectants in reproductive organs. Environ Exp Bot 53:39–47
Neilson KA, Mariani M, Haynes PA (2011) Quantitative proteomic analysis of cold-responsive proteins in rice. Proteomics 11:1696–1706
Nishiyama Ito IN, Hayase H, Satake T (1969) Protecting effect of temperature and depth of irrigation water from sterile injury caused by cooling treatment at the meiotic stage of rice plants (in Japanese quoted by Satake, T., l9i6). Proc Crop Sci Soc Jpn 3g:554–555
Niu J, Wang J, Hu H, Chen Y, An J, Cai J, Sun R, Sheng Z, Liu X, Lin S (2016) Crosstalk between freezing response and signaling for regulatory transcriptions of MIR475b and its targets bymiR475b promoter in Populus suaveolens. Sci Rep 6:20648
Novák A, Boldizsár Á, Ádám É, Kozma-Bognár L, Majláth I, Båga M, Tóth B, Chibbar R, Galiba G (2016) Light-quality and temperature-dependent CBF14 gene expression modulates freezing tolerance in cereals. J Exp Bot 67:1285–1295
Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proc Natl Acad Sci USA 101:3985–3990
Novillo F, Medina J, Salinas J (2007) Arabidopsis CBF1 and CBF3 have a different function than CBF2 in cold acclimation and define different gene classes in the CBF regulon. Proc Natl Acad Sci USA 104:21002–21007
Ogura T, Busch W (2015) From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development. Curr Opin Plant Biol 23:98–108
Oh CS, Choi YH, Lee SJ, Yoon DB, Moon HP, Ahn SN (2004) Mapping of quantitative trait loci for cold tolerance in weedy rice. Breed Sci 54:373–380
Orvar BL, Sangwan V, Omann F, Dhindsa R (2000) Early steps in cold sensing by plant cells: the role of actin cytoskeleton and membrane fluidity. Plant J 23:785–794
Ou Y, Liu X, Xie C, Zhang H, Lin Y, Li M, Song B, Liu J (2015) Genome-wide identification of microRNAs and their targets in cold-stored potato tubers by deep sequencing and degradome analysis. Plant Mol Biol Rep 33:584–597
Pan Y, Zhang H, Zhang D, Li J, Xiong H, Yu J, Li J, Rashid MAR, Li G, Ma X, Cao G, Han L, Zichao Li Z (2015) Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping. PLoS One 10:e0120590
Park S, Lee CM, Doherty CJ, Gilmour SJ, Kim Y, Thomashow MF (2015) Regulation of the Arabidopsis CBF regulon by a complex low temperature regulatory network. Plant J 82:193–207
Peacock JM (1982) Response and tolerance of sorghum to temperature stress. In: House LR, et al. (Eds.), Sorghum in the Eighties. In: Proceedings of the international symposium on Sorghum, Patancheru, India, November 2–7, 1981. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India, pp 143–159
Pearce S, Zhu J, Boldizsár Á, Vágújfalvi A, Burke A, Garland-Campbell K, Galiba G, Dubcovsky J (2013) Large deletions in the CBF gene cluster at the Fr-B2 locus are associated with reduced frost tolerance in wheat. Theor Appl Genet 126:2683–2697
Peter R, Eschholz TW, Stamp P, Liedgens M (2006) Swiss maize landraces—early vigour adaptation to cool conditions. Acta Agron Hung 54:329–336
Peter R, Eschholz TW, Stamp P, Liedgens M (2009) Swiss Flint maize landraces—a rich pool of variability for early vigour in cool environments. Field Crops Res 110:157–166
Pimental C, Davey PA, Juvik JA, Long SP (2005) Gene loci in maize influencing susceptibility to chilling dependent photoinhibition of photosynthesis. Photosyn Res 85:319–326
Pino MT, Skinner JS, Park EJ, Jeknic Z, Hayes PM, Thomashow MF, Chen THH (2007) Use of a stress inducible promoter to drive ectopic AtCBF expression improves potato freezing tolerance while minimizing negative effects on tuber yield. Plant Biotech J 5:591–604
Pomeroy MK, Andrews CJ, Stanley KP, Gao JY (1985) Physiological and metabolic responses of winter wheat to prolonged freezing stress. Plant Physiol 78(207–2):10
Porter JR, Gawith M (1999) Temperatures and the growth and development of wheat: a review. Eur J Agron 10:23–36
Presterl T, Ouzunova M, Schmidt W, Moller EM, Rober FK, Knaak C, Emst K, Westhoff P, Geiger HH (2007) Quantitative trait loci for early plant vigour of maize grown in chilly environments. Theor Appl Genet 114:1059–1070
Qingcai Z, Keyong Z, Zuwu C, Shuzhen Z (2004) Mapping QTLs controlling seedling cold tolerance in riceusing F2 population. J Hum Agric Univ 30:303–306
Ranawake AL, Manangkil OE, Yoshida S, Ishii T, Mori N, Nakamura C (2014) Mapping QTLs for cold tolerance at germination and the early seedling stage in rice (Oryza sativa L.). Biotechnol Biotechnol Equip 28:989–998
Reinheimer JL, Barr AR, Eglinton JK (2004) QTL mapping of chromosomal regions conferring reproductive frost tolerance in barley (Hordeum vulgare L.). Theor Appl Genet 109:1267–1274
Revilla P, Rodríguez VM, Ordás A, Rincent R, Charcosset A, Giauffret C, Melchinger AE, Schön CC, Bauer Eva, Altmann T, Brunel D, Moreno-González J, Campo L, Ouzunova M, Álvarez A, de Galarreta JIR, Laborde J, Malvar RA (2016) Association mapping for cold tolerance in two large maize inbred panels. BMC Plant Biol 16:127
Rodriguez VM, Malvar RA, Butron A, Ordas A, Revilla P (2007) Maize populations as sources of favorable alleles to improve cold-tolerant hybrids. Crop Sci 47:1779–1786
Rodriguez VM, Burton A, Rady MOA, Soengas P, Revilla P (2014) Identification of quantitative trait loci involved in the response to cold stress in maize (Zea mays L). Mol Breed:363–371
Roy D, Paul A, Roy A, Ghosh R, Ganguly P, Chaudhuri S (2014) Differential acetylation of histone H3 at the regulatory region of OsDREB1b facilitates chromatin remodeling and transcription activation during cold stress. PLoS One 9:e100343
Rudi H, Sandve SR, Opseth LM, Larsen A, Rognli OA (2011) Identification of candidate genes important for frost tolerance in Festuca pratensis Huds. by transcriptional profiling. Plant Sci 180:78–85
Rymen B, Fiorani F, Kartal F, Vandepoele K, Inzé D, Beemster GTS (2007) Cold nights impair leaf growth and cell cycle progression in maize through transcriptional changes of cell cycle genes. Plant Physiol 143:1429–1438
Saito K, Miura K, Nagano K, Hayano-Saito Y, Saito A, Araki H, Kato K (1995) Chromosomal location of quantitative trait loci for cool tolerance at the booting stage in rice variety ‘Norin-PL8’. Breed Sci 45:337–340
Saito K, Miura K, Nagano K, Hayano-saito Y, Araki H, Kato A (2001) Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length. Theor Appl Genet 103:862–868
Saito K, Hayano-Saito Y, Maruyama-Funatsuki W, Sato Y, Kato A (2004) Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice. Theor Appl Genet 109:512–522
Saito K, Hayano-Saito Y, Kuroki M, Sato Y (2010) Map-based cloning of the rice cold tolerance gene Ctb1. Plant Sci 179:97–102
Sakata T, Oda S, Tsunaga Y, Shomura H, Kawagishi-Kobayashi M, Aya K, Saeki K, Endo T, Nagano K, Kojima M, Sakakibara H, Watanabe M, Matsuoka M, Higashitani A (2014) Reduction of gibberellin by low temperature disrupts pollen development in rice. Plant Physiol 164:2011–2019
Sallam A, Arbaoui M, El-Esawi M, Abshire N, Martsch R (2016a) Identification and verification of QTL associated with frost tolerance using linkage mapping and GWAS in winter faba bean. Front Plant Sci 7:1098
Sallam A, Dhanapal AP, Liu S (2016b) Association mapping of winter hardiness and yield traits in faba bean (Vicia faba L.). Crop Pasture Sci 67:55–68
Sandve SR, Kosmala A, Rudi H, Fjellheim S, Rapacz M, Yamada T, Rognli OA (2011) Molecular mechanisms underlying frost tolerance in perennial grasses adapted to cold climates. Plant Sci 180:69–77
Sasaki T (1981) Experimental studies on the parental potentiality for breeding cold tolerant rice varieties in Hokkaido, with special reference to tolerance at the booting stage. Bull Hokkaido Perfect Agric Exp Stn 46:51–60
Satake T (1969) Research on cold injury of paddy rice plants in Japan. Jpn Agric Res Q 4:5–10
Satake T (1976) Sterility-type cold injury in paddy rice plants. Proceedings of the symposium on climate and rice. IRRI, Los Baños, pp 281–300
Satake T, Toriyama K (1979) Two extremely cool tolerant varieties. Intl Rice Res Newsl 4:9–10
Satoh T, Tezuka K, Kawamoto T, Matsumoto S, Satoh-Nagasawa N, Ueda K, Sakurai K, Watanabe A, Takahashi H, Akagi H (2016) Identification of QTLs controlling low-temperature germination of the East European rice (Oryza sativa L.) variety Maratteli. Euphytica 207:245–254
Shen C, Li D, He R, Fang Z, Xia Y, Gao J, Shen H, Cao M (2014) Comparative transcriptome analysis of RNA-seq data for cold-tolerant and cold-sensitive rice genotypes under cold stress. J Plant Biol 57:337–348
Shi H, Chan ZL (2014) AtHAP5A modulates freezing stress resistance in Arabidopsis independent of the CBF pathway. Plant Signal Behav 9:e29109
Shi H, Ye T, Zhong B, Liu X, Jin R, Chan Z (2014) AtHAP5A modulates freezing stress resistance in Arabidopsis through binding to CCAAT motif of AtXTH21. New Phytol 203:554–567
Shi Y, Ding Y, Yang S (2015) Cold signal transduction and its interplay with phytohormones during cold acclimation. Plant Cell Physiol 56:7–15
Shimono H, Okada M, Kanada E, Arakawa I (2007) Low temperature-induced sterility in rice: evidence for the effects of temperature before panicle initiation. Field Crops Res 101:221–231
Shinada H, Iwata N, Sato T, Fujino K (2013) Genetical and morphological characterization of cold tolerance at fertilization stage in rice. Breed Sci 63:197–204
Shinada H, Iwata N, Sato T, Fujino K (2014) QTL pyramiding for improving of cold tolerance at fertilization stage in rice. Breed Sci 63:483–488
Shirasawa S, Endo T, Nakagomi K, Yamaguchi M, Nishio T (2012) Delimitation of a QTL region controlling cold tolerance at booting stage of a cultivar, ‘Lijiangxintuanheigu’, in rice, Oryza sativa L. Theor Appl Genet 124:937–946
Shu Y, Liu Y, Li W, Song L, Zhang J, Guo C (2016) Genome-wide investigation of microRNAs and their targets in response to freezing stress in Medicago sativa L. based on high-throughput sequencing. GGG 6:755–765
Sieber AN, Longin CFH, Leiser WL, Wurschum T (2016) Copy number variation of CBF-A14 at theFr-A2 locus determines frost tolerance in winter durum wheat. Theor Appl Genet 129:1087–1097
Sihathep V, Sipaseuth, Phothisane C, Thammavong A, Sengkeo, Phamixay S, Senthonghae M, Chanphengsay M, Linquist B, Fukai S (2001) Response of dry-season irrigated rice to sowing time at four sites in Laos. ACIAR Proc 101:138–146
Singh RP, Brennan JP, Farrell T, Williams R, Reinke R, Lewin L et al (2005) Economic analysis of breeding for improved cold tolerance in rice in Australia. Aust Agribus Rev 13:1–9
Single WV (1985) Frost injury and the physiology of the wheat plant. J Aust Inst Agric Sci 51:128–134
Sinha S, Raxwal VK, Joshi B, Jagannath A, Katiyar-Agarwal S, Goel S, Kumar A, Agarwal M (2015) De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.) Front. Plant Sci 6:932
Skinner DZ (2015) Genes upregulated in winter wheat (Triticum aestivum L.) during mild freezing and subsequent thawing suggest sequential activation of multiple response mechanisms. PLoS One 10:e0133166
Skinner JS, von Zitzewitz J, Szucs P, Marquez-Cedillo L, Filichkin T, Amundsen K, Stockinger EJ, Thomashow MF, Chen TH, Hayes PM (2005) Structural, functional, and phylogenetic characterization of a large CBF gene family in barley. Plant Mol Biol 59:533–551
Skinner JS, Szucs P, von Zitzewitz J, Marquez-Cedillo L, Filichkin T, Stockinger EJ, Thomashow MF, Chen TH, Hayes PM (2006) Mapping of barley homologs to genes that regulate low temperature tolerance in Arabidopsis. Theor Appl Genet 112:832–842
Snape JW, Semikhodskii A, Fish L, Sarma RN, Quarrie SA, Galiba G, Sutka J (1997) Mapping frost resistance loci in wheat and comparative mapping with other cereals. Acta Agron Hung 45:265–270
Sofalian O, Mohammadi SA, Aharizad S, Moghaddam M, Shakiba MR (2008) Mapping of QTLs for frost tolerance and heading time using SSR markers in bread wheat. Afr J Biotechnol 920:5260–5264
Song L, Jiang L, Chen Y, Shu Y, Bai Y, Guo C (2016) Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress. Funct Integr Genom 16:495–511
Spink JH, Kirby EJM, Frost DL, Sylvester-Bradley R, Scott RK, Foulkes MJ, Clare RW, Evans EJ (2000) Agronomic implications of variation in wheat development due to variety, sowing date, site and season. Plant Var Seeds 13:91–108
Srinivasan A, Johansen C, Saxena NP (1998) Cold tolerance during early reproductive growth of chickpea (Cicer arietinum L.): characterization of stress and genetic variation in pod set. Field Crops Res 57:181–193
Sthapit BR (1987) Chhomrong a promising cold tolerant traditional rice variety for rainfed wetlands in western hills of Nepal. IRRN 12:4
Sthapit BR, Witcombe JR (1998) Inheritance of tolerance to chilling stress in rice during germination and plumule greening. Crop Sci 38:660–665
Stockinger EJ, Gilmour SJ, Thomashow MF (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcription 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 USA 94:1035–1040
Stockinger EJ, Skinner JS, Gardner KG, Francia E, Pecchioni N (2007) Expression levels of barley Cbf genes at the Frost resistance-H2 locus are dependent upon alleles at Fr-H1 and Fr-H2. Plant J 51:308–321
Strigens A, Freitag NM, Gilbert X, Grieder C, Riedelsheimer C, Schrag TA, Messmer R (2013) Association mapping for chilling tolerance in elite flint and dent maize inbred lines evaluated in growth chamber and field experiments. Plant Cell Environ 36:1871–1887
Suh JP, Jeung JU, Lee JI, Choi YH, Yea JD, Virk PS, Mackill DJ, Jena KK (2010) Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerance genotypes of rice (Oryza sativa L.). Theor Appl Genet 120:985–995
Suh JP, Lee CK, Lee JH, Kim JJ, Kim SM, Cho YC, Park SH, Shin JC, Kim YG, Jena KK (2012) Identification of quantitative trait loci for seedling cold tolerance using RILs derived from a cross between japonica and tropical japonica rice cultivars. Euphytica 184:101–108
Sutka J (1994) Genetic control of frost tolerance in wheat (Triticum aestivum L.). Euphytica 77:277–282
Sutka J (2001) Genes for frost resistance in wheat. Euphytica 119:167–172
Sutka J, Snape JW (1989) Location of a gene for frost resistance on chromosome 5A of wheat. Euphytica 42:41–44
Sutton F, Chen DG, Ge X, Kenefick D (2009) Cbf genes of the Fr-A2 allele are differentially regulated between long-term cold acclimated crown tissue of freeze-resistant and—susceptible, winter wheat mutant lines. BMC Plant Biol 9:34
Takanashi J, Maruyama S, Kabaki N, Tajima K (1987) Temperature dependence of protein synthesis by cell-free system constructed with polysomes from rice radicle. Jpn J Crop Sci 56:44–50
Takeuchi Y, Hayasaka H, Chiba B, Tanaka I, Shimono T, Yamagishi M, Nagano K, Sasaki T, Yano M (2001) Mapping quantitative trait loci controlling cool-temperature tolerance at booting stage in temperate japonica rice. Breed Sci 51:191–197
Tamura K, Hara-Nishimura I (2014) Functional insights of nucleocytoplasmic transport in plants. Front Plant Sci 5:118
Tayeh N, Bahrman N, Sellier H, Bluteau A, Blassiau C, Fourment J, Bellec A, Debelle F, Lejeune- Henaut I, Delbreil B (2013) A tandem array of CBF/DREB1 genes is located in a major freezing tolerance QTL region on Medicago truncatula chromosome 6. BMC Genom 14:814
Teutonico RA, Yandell B, Satagopan JM, Ferreira ME, Palta JP (1995) Genetic analysis and mapping of genes controlling freezing tolerance in oilseed Brassica. Mol Breed 1:329–339
Thakur P, Kumar S, Malik JA, Berger JD (2010) Cold stress effects on reproductive development in grain crops: an overview. Environ Exp Bot 67:429–443
Thiebaut F, Rojas CA, Almeida KL, Grativol C, Domiciano GC, Lamb CRC, Engler JA, Hemerly AS, Ferreira PCG (2012) Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ 35:502–512
Thomashow MF (1998) Role of cold-responsive genes in plant freezing tolerance. Plant Physiol 118:1–7
Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Physiol Plant Mol Biol 50:571–599
Tian F, Zhu ZF, Fu YC, Wang XK, Sun CQ (2006) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet 112:570–580
Tian DQ, Pan XY, Yu YM, Wang WY, Zhang F, Ge YY, Shen XL, Shen FQ, Liu XJ (2013a) De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. BMC Genom 14:827
Tian S, Mao X, Zhang H, Chen S, Zhai C, Yang S, Jing R (2013b) Cloning and characterization of TaSnRK2.3, a novel SnRK2 gene in common wheat. J Exp Bot 64:2063–2080
To KT, Nakaminami K, Kim JM, Morosawa T, Ishida J, Tanaka M, Yokoyama S, Shinozaki K, Seki M (2011) Arabidopsis HDA6 is required for freezing tolerance. Biochem Biophys Res Commun 406:414–419
Tondelli A, Francia E, Barabaschi D, Aprile A, Skinner JS, Stockinger EJ, Stanca AM, Pecchioni N (2006) Mapping regulatory genes as candidates for cold and drought stress tolerance in barley. Theor Appl Genet 112:445–454
Toth B, Galiba G, Feher E, Sutka J, Snape JW (2003) Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theor Appl Genet 107:509–514
Truco MJ, Randall LB, Bloom AJ, Clair DAS (2000) Detection of QTLs associated with shoot wilting and root ammonium uptake under chilling temperatures in an interspecific backcross population from Lycopersicon esculentum × L. hirsutum. Theor Appl Genet 101:1082–1092
Tsuda K, Tsvetanov S, Takumi S, Mori N, Atanassov A, Nakamura C (2000) New members of a cold-responsive group-3 Lea/Rab-related Cor gene family from common wheat (Triticum aestivum L.). Genes Genet Syst 75:179–188
Tsvetanov S, Ohno R, Tsuda K, Takumi S, Mori N, Atanassov A, Nakamura C (2000) A cold-responsive wheat (Triticum aestivum L.) gene wcor14 identified in a winter-hardy cultivar ‘Mironovska 808’. Genes Genet Syst 75:49–57
Tumino G, Voorrips RE, Rizza F, Badeck FW, Morcia C, Ghizzoni R, Germeier CU, Paulo MJ, Terzi V, Smulders MJM (2016) Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios. Theor Appl Genet 129:1711–1724
Ulziibat B, Ohta H, Fukushima A, Shirasawa S, Kitashiba H, Nishio T (2016) Examination of candidates for the gene of cold tolerance at the booting stage in a delimited QTL region in rice cultivar ‘Lijiangxintuanheigu’. Euphytica 211:331–341
Vágújfalvi A, Crosatti C, Galiba G, Dubcovsky J, Cattivelli L (2000) Two loci on wheat chromosome 5A regulate the differential cold-dependent expression of the cor14b gene in frost-tolerant and frost-sensitive genotypes. Mol Genet Genomics 263:194–200
Vágújfalvi A, Galiba G, Cattivelli L, Dubcovsky J (2003) The coldregulated transcriptional activator Cbf3 is linked to the frost tolerance locus Fr-A2 on wheat chromosome 5A. Mol Genet Genomics 269:60–67
Vágújfalvi A, Aprile A, Miller A, Dubcovsky J, Delugu G, Galiba G, Cattivelli L (2005) The expression of several Cbf genes at the Fr- A2 locus is linked to frost resistance in wheat. Mol Genet Genomics 274:506–514
Vallejos CE, Tanksley SD (1983) Segregation of isozyme markers and cold tolerance in an interspecific backcross of tomato. Theor Appl Genet 66:241–247
Varshney RK, Ribaut JM, Buckler ES, Tuberosa R, Rafalski JA, Langridge P (2012) Can genomics boost productivity of orphan crops? Nat Biotechnol 30:1172–1176
Vítámvás P, Prásil IT (2008) WCS120 protein family and frost tolerance during cold acclimation, deacclimation and reacclimation of winter wheat. Plant Physiol Biochem 46:970–976
Wainaina CM, Inukai Y, Masinde PW, Ateka EM, Murage H, Kano-Nakata M, Nakajima Y, Terashima T, Mizukami Y, Nakamura M, Nonoyama T, Saka N, Asanuma S, Yamauchi A, Kitano H, Kimani J, Makihara D (2015) Evaluation of cold tolerance in NERICAs compared with Japanese standard rice varieties at the reproductive stage. J Agron Crop Sci 201:461–472
Wang Z, Wang F, Zhou R, Wang J, Zhang H (2011) Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice (Oryza sativa L.). Euphytica 181:405–413
Wang ST, Sun XL, Hoshino Y, Yu Y, Jia B, Sun ZW, Duan XB, Zhu YM (2014) MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in rice (Oryza sativa L.). PLoS One 9:e91357
Washburn JD, Murray SC, Burson BL, Klein RR, Jessup RW (2013) Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor 3 S. propinquum population. Mol Breed 31:153–162
Winfield MO, Lu C, Wilson ID, Coghill JA, Edwards KJ (2010) Plant responses to cold: transcriptome analysis of wheat. Plant Biotechnol J 8:749–771
Wooten DR, Livingston DP III, Holland JB, Marshall DS, Murphy JP (2008) Quantitative trait loci and epistasis for crown freezing tolerance in the ‘Kanota’ × ‘Ogle’ hexaploid oat mapping population. Crop Sci 48:149
Xiao N, Huang WN, Zhang XX, Gao Y, Li AH, Dai Y, Yu L, Liu GQ, Pan CH, Li YH, Dai ZY, Chen JM (2014) Fine mapping of qRC10-2, a quantitative trait locus for cold tolerance of rice roots at seedling and mature stages. PLoS One 9:e96046
Xiao N, Huang W, Li A, Gao Y, Li Y, Pan C, Ji H, Zhang X, Dai Y, Dai Z (2015) Fine mapping of the qLOP2 and qPSR2 -1loci associated with chilling stress tolerance of wild rice seedlings. Theor Appl Genet 128:173–185
Xin Z, Browse J (1998) Eskimo1 mutants of Arabidopsis are constitutively freezing-tolerant. Proc Natl Acad Sci USA 95:7799–7804
Xin Z, Browse J (2000) Cold comfort farm: the acclimation of plants to freezing temperatures. Plant Cell Environ 23:893–902
Xiong L, Schumaker KS, Zhu JK (2002) Cell signaling during cold, drought, and salt stress. Plant Cell 14(Suppl):s165–s183
Xiong Y, Fei S, Arora R, Brummer E, Barker R, Jung G, Warnke S (2007) Identification of quantitative trait loci controlling winter hardiness in an annual × perennial ryegrass interspecific hybrid population. Mol Breed 19:125–136
Xu LM, Zhou L, Zeng W, Wang FM, Zhang HL, Shen SQ, Li ZC (2008) Identification and mapping of quantitative trait loci for cold tolerance at the booting stage in a japonica rice near-isogenic line. Plant Sci 174:340–347
Xu J, Li Y, Sun J, Du L, Zhang Y, Yu Q, Liu X (2013) Comparative physiological and proteomic response to abrupt low temperature stress between two winter wheat cultivars differing in low temperature tolerance. Plant Biol (Stuttg) 15:292–303
Yadav SK (2010) Cold stress tolerance mechanisms in plants. A review. Agron Sustain Dev 30:515–527
Yang T, Chaudhuri S, Yang L, Du L, Poovaiah BW (2010) A calcium/calmodulin-regulated member of the receptor-like kinase family confers cold tolerance in plants. J Biol Chem 285:7119–7126
Yang Z, Huang D, Tang W, Zheng Y, Liang K, Cutler AJ, Wu W (2013a) Mapping of quantitative trait loci underlying cold tolerance in rice seedlings via high-throughput sequencing of pooled extremes. PLoS One 8:e68433
Yang C, Li D, Mao D, Liu X, Ji C, Li X, Zhao X, Cheng Z, Chen C, Zhu L (2013b) Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). Plant Cell Environ 36:2207–2218
Yang QS, Gao J, He WD, Dou TX, Ding LJ, Wu JH, Li CY, Wu JH, Li CY, Peng XX, Zhang S, Yi GJ (2015) Comparative transcriptomics analysis reveals difference of key gene expression between banana and plantain in response to cold stress. BMC Genom 16:446
Yang T, Zhang S, Zhao Z, Liu Q, Huang Z, Mao X, Dong J, Wang X, Zhang G, Liu B (2016) Identification and pyramiding of QTLs for cold tolerance at the bud bursting and the seedling stages by use of single segment substitution lines in rice (Oryza sativa L.). Mol Breed 36:96
Ye C, Fukai S, Godwin I, Reinke RB, Snell PB, Schiller J, Basnayake J (2009) Cold tolerance in rice varieties at different growth stages. Crop Pasture Sci 60:328–338
Ye C, Fukai S, Godwin DI, Koh H, Reinke R, Zhou Y, Lambrides C, Jiang W, Snell P, Redoña E (2010) A QTL controlling low temperature induced spikelet sterility at booting stage in rice. Euphytica 176:291–301
Yi SY, Kim JH, Joung YH, Lee S, Kim WT, Yu SH, Choi D (2004) The pepper transcription factor CaPF1 confers pathogen and freezing tolerance in Arabidopsis. Plant Physiol 136:2862–2874
Yokota H, Iehisa JCM, Shimosaka E, Takumi S (2015) Line differences in Cor/Lea and fructan biosynthesis-related gene transcript accumulation are related to distinct freezing tolerance levels in synthetic wheat hexaploids. J Plant Physiol 176:78–88
Yoshida S (1981) Pp. 1–63 in fundamentals of rice crop science. International Rice Research Institute, Los Baños
Yoshida R, Kanno A, Sato T, Kameya T (1996) Cool temperature- induced chlorosis in rice plants. Plant Physiol 110:997–1005
Yu X, Hui Peng Y, Hua Zhang M, Jun Shao Y, Ai SuW, Cheng Tang Z (2006) Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery. Cell Res 16:599–608
Zhan X, Zhu JK, Lang Z (2015) Increasing freezing tolerance: kinase regulation of ICE1. Dev Cell 32:257–258
Zhang GQ, Zeng RZ, Zhang ZM, Ding XH, Li WT, Liu GF, He FH, Tulukdar A, Huang CF, Xi ZY, Qin LJ, Shi JQ, Zhao FM, Feng MJ, Shan ZL, Chen L, Guo XQ, Zhu HT, Lu YG (2004) The construction of a library of single segment substitution lines in rice (Oryza sativa L.). Rice Genet Newsl 121:85–87
Zhang ZH, Su L, Li W, Chen W, Zhu YG (2005) A major QTL conferring cold tolerance at the early seedling stage using recombinant inbred lines of rice (Oryza sativa L.). Plant Sci 168:527–534
Zhang J, Xu Y, Huan Q, Chong K (2009) Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response. BMC Genom 10:449
Zhang F, Huang L, Wang W, Zhao X, Zhu L, Fu B, Li Z (2012a) Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background. BMC Genom 13:461
Zhang T, Zhao X, Wang W, Pan Y, Huang L, Liu X, Zong Y, Zhu L, Yang D, Fu B (2012b) Comparative transcriptome profiling of chilling stress responsiveness in two contrasting rice genotypes. PLoS One 7:e43274
Zhang S, Zheng J, Liu B, Peng S, Leung H, Zhao J, Wang X, Yang T, Huang Z (2014a) Identification of QTLs for cold tolerance at seedling stage in rice (Oryza sativa L.) using two distinct methods of cold treatment. Euphytica 195:95–104
Zhang Y, Zhu X, Chen X, Song C, Zou Z, Wang Y, Wang M, Fang W, Li X (2014b) Identification and characterization of cold-responsive microRNAs in tea plant (Camellia sinensis) and their targets using high-throughput sequencing and degradome analysis. BMC Plant Biol 14:271
Zhang Q, Chen Q, Wang S, Hong Y, Wang Z (2014c) Rice and cold stress: methods for its evaluation and summary of cold tolerance-related quantitative trait loci. Rice (N Y) 7(1):24
Zhang S, Wang Y, Li K, Zou Y, Chen L, Li X (2015) Identification of cold-responsive miRNAs and their target genes in nitrogen-fixing nodules of soybean. Int J Mol Sci 15:13596–13614
Zhao Y, Gowda M, Würschum T, Longin CF, Korzun V, Kollers S, Schachschneider R, Zeng J, Fernando R, Dubcovsky J, Reif JC (2013) Dissecting the genetic architecture of frost tolerance in Central European winter wheat. J Exp Bot 64:4453–4460
Zhao C, Zhaobo Lang Z, Zhu JK (2015a) Cold responsive gene transcription becomes more complex. Trends Plant Sci 20:466–468
Zhao J, Zhang S, Yang T, Zeng Z, Huang Z, Liu Q, Wang X, Leach J, Leung H, Liu B (2015b) Global transcriptional profiling of a cold-tolerant rice variety under moderate cold stress reveals different cold stress response mechanisms. Physiol Plant 154:381–394
Zhao C, Zhang Z, Xie S, Si T, Li Y, Zhu JK (2016) Mutational evidence for the critical role of CBF genes in cold acclimation in arabidopsis. Plant Physiol 171:2744–2759
Zheng B, Chapman SC, Christopher JT, Frederiks TM, Chenu K (2015a) Frost trends and their estimated impact on yield in the Australian wheatbelt. J Exp Bot 66:3611–3623
Zheng C, Zhao L, Wang Y, Shen J, Zhang Y, Jia S, Li Y, Ding Z (2015b) Integrated RNA-Seq and sRNA-Seq analysis identifies chilling and freezing responsive key molecular players and pathways in tea plant (Camellia sinensis). PLoS One 10:e0125031
Zhou QY, Tian AG, Zou HF, Xie ZM, Lei G, Huang J, Wang CM, Wang HW, Zhang JS, Chen SY (2008) Soybean WRKY-type transcription factor genes, GmWRKY13, GmWRKY21, and GmWRKY54, confer differential tolerance to abiotic stresses in transgenic Arabidopsis plants. Plant Biotechnol J 6:486–503
Zhou L, Zeng Y, Zheng W, Tang B, Yang S, Zhang H, Li J, Li Z (2010) Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using near-isogenic line. Theor Appl Genet 121:895–905
Zhou MQ, Shen C, Wu LH, Tang KX, Lin J (2011) CBF-dependent signaling pathway: a key responder to low temperature stress in plants. Crit Rev Biotechnol 31:186–192
Zhou L, Zeng Y, Hu G, Pan Y, Yang S, You A, Zhang H, Li J, Li Z (2012) Characterization and identification of cold tolerant near-isogenic lines in rice. Breed Sci 62(2):196–201
Zhu J, Shi H, Lee BH, Damsz B, Cheng S, Stirm V, Zhu JK, Hasegawa PM, Bressan RA (2004) An Arabidopsis homeodomain transcription factor gene, HOS9, mediates cold tolerance through a CBF-independent pathway. Proc Natl Acad Sci USA 101:9873–9878
Zhu J, Verslues PE, Zheng X, Lee BH, Zhan X, Manabe Y, Sokolchik I, Zhu Y, Dong CH, Zhu JK, Hasegawa PM, Bressan RA (2005) HOS10 encodes an R2R3-type MYB transcription factor essential for cold acclimation in plants. Proc Natl Acad Sci USA 102:9966–9971
Zhu J, Dong CH, Zhu JK (2007) Interplay between cold-responsive gene regulation, metabolism and RNA processing during plant cold acclimation. Curr Opin Plant Biol 10:290–295
Zhu J, Pearce S, Burke A, See DR, Skinner DZ, Dubcovsky J, Garland- Campbell K (2014) Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theor Appl Genet 127:1183–1197
Zhu Y, Chen K, Mi X, Chen T, Ali J, Ye G, Xu J, Li Z (2015) Identification and fine mapping of a stably expressed QTL for cold tolerance at the booting stage using an interconnected breeding population in rice. PLoS One 10:e0145704
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The authors acknowledge the support from the Indian Council of Agricultural Research (ICAR), New Delhi, India. We also apologize that other LT related references could not be cited due to space constraints.
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Jha, U.C., Bohra, A. & Jha, R. Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. Plant Cell Rep 36, 1–35 (2017). https://doi.org/10.1007/s00299-016-2073-0
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DOI: https://doi.org/10.1007/s00299-016-2073-0