Skip to main content
SpringerLink
Log in

Molecular Responses to Cold Stress in Temperate Fruit Crops with Focus on Rosaceae Family

  • Chapter
  • First Online:
Genomics Assisted Breeding of Crops for Abiotic Stress Tolerance, Vol. II

Part of the book series: Sustainable Development and Biodiversity ((SDEB,volume 21))

Abstract

Cold stress is considered as one of the main limiting environmental factors causing a significant loss in the production of fruit crops. Although many fruit crops require chilling during winter to develop fruiting buds, late winter, and early spring frost can severely damage buds, flowers, and fruits and can lead to the reduction of productivity. Among different plant families, the Rosaceae family contains several economically pivotal fruit-producing crops, such as Fragaria (strawberries), Malus (apple), Rubus (blueberries) and Prunus (stone fruits), which suffer from cold injuries during the blooming period. This chapter provides a general overview of the role of various molecular components involved in sensing and signal transduction processes as well as the regulation of gene expression in response to cold stress in fruit crops. Besides, the impact of next-generation sequencing approaches is highlighted in the molecular studies of the Rosaceae family. Also, we have addressed the existing gaps to help researchers identify areas that need more attention.

These authors have equally contributed to this work

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Alexiou P, Vergoulis T, Gleditzsch M, Prekas G et al (2009) miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res 38(Database issue):D137–D141

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Alisoltani A, Shiran B, Fallahi H, Ebrahimie E (2015) Gene regulatory network in almond (Prunus dulcis Mill.) in response to frost stress. Tree Genet Genomes 11:1–15

    Article  Google Scholar 

  • Alisoltani A, Ebrahimi S, Azarian S, Hematyar M et al (2016) Parallel consideration of SSRs and differentially expressed genes under abiotic stress for targeted development of functional markers in almond and related Prunus species. Sci Hortic 198:462–472

    Article  CAS  Google Scholar 

  • Alkio M, Jonas U, Declercq M, Van Nocker S, Knoche M (2014) Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes. Hortic Res 1:11

    Google Scholar 

  • Allen DJ, Ratner K, Giller YE, Gussakovsky EE, Shahak Y, Ort DR (2000) An overnight chill induces a delayed inhibition of photosynthesis at midday in mango (Mangifera indica L.). J Exp Bot 51:1893–1902. https://doi.org/10.1093/jexbot/51.352.1893

    Article  CAS  PubMed  Google Scholar 

  • Artlip TS, Wisniewski ME, Bassett CL, Norelli JL (2013) CBF gene expression in peach leaf and bark tissues is gated by a circadian clock. Tree Physiol 33:866–877

    Article  CAS  PubMed  Google Scholar 

  • Artlip TS, Wisniewski ME, Norelli JL (2014) Field evaluation of apple overexpressing a peach CBF gene confirms its effect on cold hardiness, dormancy, and growth. Environ Exp Bot 106:79–86

    Article  CAS  Google Scholar 

  • Baniulis D, Stepulaitiene I, Lukoseviciute V, Blazyte A, Stanys V, Rugienius R, Sasnauskas A (2012) Accumulation of dehydrin-like proteins in pear (Pyrus communis L.) microshoots during cold acclimation. Žemdirbystė (Agriculture) 99:293–298

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Barros PM, Gonçalves N, Saibo NJ, Oliveira MM (2012) Functional characterization of two almond C-repeat-binding factors involved in cold response. Tree Physiol 32(9):1113–1128

    Article  CAS  PubMed  Google Scholar 

  • Bayat H, Noghondar MA, Neamati H, Nezami A (2013) Exogenous application of ascorbic acid alleviates chilling injury in apricot (Prunus armeniaca L. cv. Shahroudi) flowers. J Stress Physiol Biochem 9:199–206

    Google Scholar 

  • Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36:D149–D153

    Article  CAS  PubMed  Google Scholar 

  • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao S, Yang Z, Cai Y, Zheng Y (2011) Fatty acid composition and antioxidant system in relation to susceptibility of loquat fruit to chilling injury. Food Chem 127:1777–1783

    Article  CAS  Google Scholar 

  • 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 15:1

    Google Scholar 

  • Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Catala R, Ouyang J, Abreu IA, Hu Y, Seo H, Zhang X, Chua N-H (2007) The Arabidopsis E3 SUMO ligase SIZ1 regulates plant growth and drought responses. Plant Cell 19:2952–2966

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Mao Y, Liu H, Yu F, Li S, Yin T (2014) Transcriptome analysis of differentially expressed genes relevant to variegation in peach flowers. PloS ONE 9:e90842

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chengguo D, Xianli L, Dongsheng G, Huanfang L, Meng L (2004) Studies on regulations of endogenous ABA and GA~ 3 in sweet cherry flower buds on dormancy. Acta Hort Sinica 31:149–154

    Google Scholar 

  • Chinnusamy V, Ohta M, Kanrar S, Lee B-H, Hong X, Agarwal M, Zhu J-K (2003) ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev 17:1043–1054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chinnusamy V, Zhu J, Zhu J-K (2007) Cold stress regulation of gene expression in plants. Trends Plant Sci 12:444–451

    Article  CAS  PubMed  Google Scholar 

  • Chinnusamy V, Zhu J-K, Sunkar R (2010) Gene regulation during cold stress acclimation in plants. Methods Mol Biol 639:39–55

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Crisosto C, Mitchell F, Ju Z (1999) Susceptibility to chilling injury of peach, nectarine, and plum cultivars grown in California. Hort Sci 34(6):1116–1118

    Google Scholar 

  • Cushman JC, Bohnert HJ (2000) Genomic approaches to plant stress tolerance. Curr Opin Plant Biol 3:117–124

    Article  CAS  PubMed  Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dai J, Wang H, Ge Q (2013) The decreasing spring frost risks during the flowering period for woody plants in temperate area of eastern China over past 50 years. J Geogr Sci 23:641–652

    Article  Google Scholar 

  • Destefano-Beltrán L, Knauber D, Huckle L, Suttle J (2006) Chemically forced dormancy termination mimics natural dormancy progression in potato tuber meristems by reducing ABA content and modifying expression of genes involved in regulating ABA synthesis and metabolism. J Exp Bot 57:2879–2886

    Article  PubMed  CAS  Google Scholar 

  • Dhanapal AP, Crisosto CH (2013) Association genetics of chilling injury susceptibility in peach (Prunus persica (L.) Batsch) across multiple years. 3 Biotech 3:481–490

    Article  PubMed  PubMed Central  Google Scholar 

  • Die JV, Rowland LJ (2013) Advent of genomics in blueberry. Mol Breed 32:493–504

    Article  Google Scholar 

  • Ding C-K, Wang CY, Gross KC, Smith DL (2001) Reduction of chilling injury and transcript accumulation of heat shock proteins in tomato fruit by methyl jasmonate and methyl salicylate. Plant Sci 161:1153–1159

    Article  CAS  Google Scholar 

  • Ding C-K, Wang C, Gross KC, Smith DL (2002) Jasmonate and salicylate induce the expression of pathogenesis-related-protein genes and increase resistance to chilling injury in tomato fruit. Planta 214:895–901

    Article  CAS  PubMed  Google Scholar 

  • Ding Z, Tian S, Meng X, Xu Y (2009) Hydrogen peroxide is correlated with browning in peach fruit stored at low temperature. Front Chem Eng China 3:363–374

    Article  CAS  Google Scholar 

  • Dong C-H, Agarwal M, Zhang Y, Xie Q, Zhu J-K (2006) The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proc Natl Acad Sci USA 103:8281–8286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du D, Zhang Q, Cheng T, Pan H, Yang W, Sun L (2013) Genome-wide identification and analysis of late embryogenesis abundant (LEA) genes in Prunus mume. Mol Biol Rep 40:1937–1946

    Article  CAS  PubMed  Google Scholar 

  • Eldem V, Akçay UÇ, Ozhuner E, Bakır Y, Uranbey S, Unver T (2012) Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS ONE 7:e50298

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ensminger I, Busch F, Huner N (2006) Photostasis and cold acclimation: sensing low temperature through photosynthesis. Physiol Plant 126:28–44

    Article  CAS  Google Scholar 

  • Fang X, Zhao Y, Ma Q, Huang Y et al (2013) Identification and comparative analysis of cadmium tolerance-associated miRNAs and their targets in two soybean genotypes. PLoS ONE 8:e81471

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Feng X-M, Zhao Q, Zhao L-L, Qiao Y et al (2012) The cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1 encodes an ICE-like protein in apple. BMC Plant Biol 12:22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Folta KM, Gardiner SE (eds) (2009) Genetics and genomics of Rosaceae. Springer, New York

    Google Scholar 

  • Friedländer MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407–415

    Article  PubMed  CAS  Google Scholar 

  • Furuya T, Matsuoka D, Nanmori T (2013) Phosphorylation of Arabidopsis thaliana MEKK1 via Ca2+ signaling as a part of the cold stress response. J Plant Res 126:833–840

    Article  CAS  PubMed  Google Scholar 

  • Gao Z, Shi T, Luo X, Zhang Z, Zhuang W, Wang L (2012) High-throughput sequencing of small RNAs and analysis of differentially expressed microRNAs associated with pistil development in Japanese apricot. BMC Genom 13:1

    Article  CAS  Google Scholar 

  • Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF (1998) Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J 16:433–442

    Article  CAS  PubMed  Google Scholar 

  • Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158

    Article  CAS  PubMed  Google Scholar 

  • Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E (2015) Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms. Front Plant Sci 6

    Google Scholar 

  • Gülen H, Çetinkaya C, Kadıoğlu M, Kesici M, Cansev A, Eriş A (2008) Peroxidase activity and lipid peroxidation in strawberry (Fragaria X ananassa) plants under low temperature. J Biol Environ Sci 2

    Google Scholar 

  • Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429–3431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly 125:167–188

    Article  CAS  Google Scholar 

  • Hsu S-D, Chu C-H, Tsou A-P, Chen S-J et al (2008) miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res 36:D165–D169

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Li K, Jin C, Zhang S (2015) ICE1 of Pyrus ussuriensis functions in cold tolerance by enhancing PuDREBa transcriptional levels through interacting with PuHHP1. Sci Rep 5

    Google Scholar 

  • Iezzoni A, Hancock J, Owens C (2002) Enhancement of freezing tolerance of strawberry by heterologous expression of CBF1. In: XXVI International Horticultural Congress: Berry Crop Breeding, Production and Utilization for a New Century. 626:93–100

    Google Scholar 

  • Ismail M, Grierson W (1977) Seasonal susceptibility of grapefruit to chilling injury as modified by certain growth regulators. Hort Sci 12(2):18–120

    Google Scholar 

  • Janská A, Maršík P, Zelenková S, Ovesna J (2010) Cold stress and acclimation–what is important for metabolic adjustment? Plant Biol 12:395–405

    Article  PubMed  CAS  Google Scholar 

  • Jiang H, Wong WH (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24:2395–2396

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jonak C, Kiegerl S, Ligterink W, Barker PJ, Huskisson NS, Hirt H (1996) Stress signaling in plants: a mitogen-activated protein kinase pathway is activated by cold and drought. Proc Natl Acad Sci USA 93:11274–11279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  PubMed  Google Scholar 

  • Kaja E, Szcześniak MW, Jensen PJ, Axtell MJ, McNellis T, Makałowska I (2015) Identification of apple miRNAs and their potential role in fire blight resistance. Tree Genet Genomes 11:1–11

    Article  Google Scholar 

  • Karimi S, Yadollahi A, Arzani K (2013) Responses of almond genotypes to osmotic stress induced in vitro. J Nuts 4:1–7

    CAS  Google Scholar 

  • Karimi M, Ghazanfari F, Fadaei A, Ahmadi L, Shiran B, Rabei M, Fallahi H (2016) The small-RNA profiles of almond (Prunus dulcis Mill.) reproductive tissues in response to cold stress. PloS ONE 11(6):e0156519

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Katiyar A, Smita S, Muthusamy SK, Chinnusamy V, Pandey DM, Bansal KC (2015) Identification of novel drought-responsive microRNAs and trans-acting siRNAs from Sorghum bicolor (L.) Moench by high-throughput sequencing analysis. Front Plant Sci 6:506. https://doi.org/10.3389/fpls.2015.00506

  • Ke X, Yin Z, Song N, Dai Q et al (2014) Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree. Fungal Genet Biol 68:31–38

    Article  CAS  PubMed  Google Scholar 

  • Kim S-K, Nam J-W, Rhee J-K, Lee W-J, Zhang B-T (2006) miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinf 7:411

    Article  CAS  Google Scholar 

  • Kitashiba H, Ishizaka T, Isuzugawa K, Nishimura K, Suzuki T (2004) Expression of a sweet cherry DREB1/CBF ortholog in Arabidopsis confers salt and freezing tolerance. J Plant Physiol 161:1171–1176

    Article  CAS  PubMed  Google Scholar 

  • Kramer GF, Wang CY (1989) Correlation of reduced chilling injury with increased spermine and spermidine levels in zucchini squash. Physiol Plant 76:479–484

    Article  CAS  Google Scholar 

  • Ku Y-S, Wong JW-H, Mui Z, Liu X, Hui JH-L, Chan T-F, Lam H-M (2015) Small RNAs in plant responses to abiotic stresses: regulatory roles and study methods. Int J Mol Sci 16:24532–24554

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langmead B (2010) Aligning short sequencing reads with Bowtie. Curr Prot Bioinform 11:7. https://doi.org/10.1002/0471250953.bi1107s32

    Article  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee C-Y, Chiu Y-C, Wang L-B, Kuo Y-L, Chuang EY, Lai L-C, Tsai M-H (2013) Common applications of next-generation sequencing technologies in genomic research. Transl Cancer Res 2:33–45

    CAS  Google Scholar 

  • Leng X, Han J, Wang X, Zhao M, Sun X, Wang C, Fang J (2015) Characterization of a calmodulin-binding transcription factor from strawberry. Plant Genome 8

    Google Scholar 

  • Levitt J (1980a) Freezing resistance-types, measurement and changes. Responses of plants to environmental stress. Academic Press, New York, pp 116–162

    Google Scholar 

  • Levitt J (1980b) Responses of plants to environmental stresses, vol II. Water, radiation, salt, and other stresses. Academic Press, New York, p 365

    Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Ruan J, Durbin R (2008a) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li R, Li Y, Kristiansen K, Wang J (2008b) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714

    Article  CAS  PubMed  Google Scholar 

  • Li B, Zhang C, Cao B, Qin G, Wang W, Tian S (2012) Brassinolide enhances cold stress tolerance of fruit by regulating plasma membrane proteins and lipids. Amino Acids 43:2469–2480

    Article  CAS  PubMed  Google Scholar 

  • Li B, Duan H, Li J, Deng XW, Yin W, Xia X (2013) Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol 81:525–539

    Article  CAS  PubMed  Google Scholar 

  • Liang D, Xia H, Wu S, Ma F (2012a) Genome-wide identification and expression profiling of dehydrin gene family in Malus domestica. Mol Bio Rep 39:10759–10768

    Article  CAS  Google Scholar 

  • Liang G, He H, Yu D (2012b) Identification of nitrogen starvation-responsive microRNAs in Arabidopsis thaliana. PLoS ONE 7:e48951

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liang L, Zhang B, Yin X-R, Xu C-J, Sun C-D, Chen K-S (2013) Differential expression of the CBF gene family during postharvest cold storage and subsequent shelf-life of peach fruit. Plant Mol Biol Rep 31:1358–1367

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H-H, Tian X, Li Y-J, Wu C-A, Zheng C-C (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14:836–843

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu J, Jennings SF, Tong W, Hong H (2011) Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development. J Biomed Sci Eng 4:666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H, Ouyang B, Zhang J, Wang T, Li H, Zhang Y, Yu C, Ye Z (2012) Differential modulation of photosynthesis, signaling, and transcriptional regulation between tolerant and sensitive tomato genotypes under cold stress PloS ONE 7:e50785

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luo X, Gao Z, Shi T, Cheng Z, Zhang Z, Ni Z (2013) Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis. PloS ONE 8:e79090

    Article  PubMed  PubMed Central  Google Scholar 

  • Lurie S, Crisosto C (2005) Chilling injury in peach and nectarine. Postharvest Biol Technol 37:195–208

    Article  Google Scholar 

  • Lv D-K, Bai X, Li Y, Ding X-D et al (2010) Profiling of cold-stress-responsive miRNAs in rice by microarrays. Gene 459:39–47

    Article  CAS  PubMed  Google Scholar 

  • Maghuly F, Borroto-Fernandez EG, Khan MA, Herndl A, Marzban G, Laimer M (2009) Expression of calmodulin and lipid transfer protein genes in Prunus incisa × serrula under different stress conditions. Tree Physiol 29:437–444

    Article  CAS  PubMed  Google Scholar 

  • Mahajan S, Tuteja N (2005) Cold, salinity and drought stresses: an overview. Arch Biochem Biophys 444:139–158

    Article  CAS  PubMed  Google Scholar 

  • Maragkakis M, Reczko M, Simossis VA, Alexiou P et al (2009) DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res 37(Web Server issue):W273–W276

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Matzneller P, Götz K-P, Chmielewski F-M (2016) Spring frost vulnerability of sweet cherries under controlled conditions. Int J Biometeorol 60:123–130

    Article  PubMed  Google Scholar 

  • Medina J, Bargues M, Terol J, Pérez-Alonso M, 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meng D, Li Y, Bai Y, Li M, Cheng L (2016) Genome-wide identification and characterization of WRKY transcriptional factor family in apple and analysis of their responses to waterlogging and drought stress. Plant Physiol Biochem 103:71–83

    Article  CAS  PubMed  Google Scholar 

  • Mikami K, Kanesaki Y, Suzuki I, Murata N (2002) The histidine kinase Hik33 perceives osmotic stress and cold stress in Synechocystis sp. PCC 6803. Mol Microbiol 46:905–915

    Article  CAS  PubMed  Google Scholar 

  • Miranda C, Santesteban LG, Royo JB (2005) Variability in the relationship between frost temperature and injury level for some cultivated Prunus species. Hort Sci 40:357–361

    Google Scholar 

  • Mittler R (2002) Oxidative stress, antioxidants and stress tolerance. Trends Plant Sci 7:405–410

    Article  CAS  PubMed  Google Scholar 

  • Miura K, Tada Y (2014) Regulation of water, salinity, and cold stress responses by salicylic acid. Front Plant Sci 23(5):4

    Google Scholar 

  • Miura K, Jin JB, Lee J, Yoo CY et al (2007) SIZ1-mediated sumoylation of ICE1 controls CBF3/DREB1A expression and freezing tolerance in Arabidopsis. Plant Cell 19:1403–1414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moellering ER, Muthan B, Benning C (2010) Freezing tolerance in plants requires lipid remodeling at the outer chloroplast membrane. Science 330:226–228

    Article  CAS  PubMed  Google Scholar 

  • Mondal TK, Sutoh K (2013) OMICS: applications in biomedical, agricultural, and environmental sciences In: Barh D, Zambare V, Azevedo V (eds) Application of next—generation sequencing for abiotic stress tolerance. CRC Press, pp 347–365

    Google Scholar 

  • Montgomery TA, Howell MD, Cuperus JT, Li D et al (2008a) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133:128–141

    Article  CAS  PubMed  Google Scholar 

  • Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD et al (2008b) AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci USA 105:20055–20062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264

    Article  CAS  PubMed  Google Scholar 

  • Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10:135–151

    Article  CAS  PubMed  Google Scholar 

  • Mousavi S, Alisoltani A, Shiran B, Fallahi H, Ebrahimie E, Imani A, Houshmand S (2014) De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS ONE 9:e104541

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Murata N, Sato N, Takahashi N, Hamazaki Y (1982) Compositions and positional distributions of fatty acids in phospholipids from leaves of chilling-sensitive and chilling-resistant plants. Plant Cell Physiol 23:1071–1079

    CAS  Google Scholar 

  • Nilo-Poyanco R, Vizoso P, Sanhueza D, Balic I, Meneses C, Orellana A, Campos-Vargas R (2018) A Prunus persica genome‐wide RNA-seq approach uncovers major differences in the transcriptome among chilling injury sensitive and non-sensitive varieties. Physiol Plant https://doi.org/10.1111/ppl.12831

    Article  PubMed  CAS  Google Scholar 

  • Niu Q, Qian M, Liu G, Yang F, Teng Y (2013) A genome-wide identification and characterization of mircoRNAs and their targets in ‘Suli’pear (Pyrus pyrifolia white pear group). Planta 238:1095–1112

    Article  CAS  PubMed  Google Scholar 

  • Nogueira FT, De Rosa VE, Menossi M, Ulian EC, Arruda P (2003) RNA expression profiles and data mining of sugarcane response to low temperature. Plant Physiol 132:1811–1824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Owens CL, Thomashow MF, Hancock JF, Iezzoni AF (2002) CBF1 orthologs in sour cherry and strawberry and the heterologous expression of CBF1 in strawberry. J Am Soc Hortic Sci 127:489–494

    Article  CAS  Google Scholar 

  • Paredes M, Quiles MJ (2015) The effects of cold stress on photosynthesis in hibiscus plants. PLoS ONE 10:e0137472

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Parsons CS, Day RH (1970) Freezing injury of root crops: beets, carrots, parsnips, radishes, and turnips. Marketing Research Report United States Department of Agriculture 866

    Google Scholar 

  • Pastore A, Martin SR, Politou A, Kondapalli KC, Stemmler T, Temussi PA (2007) Unbiased cold denaturation: low-and high-temperature unfolding of yeast frataxin under physiological conditions. J Am Chem Soc 129:5374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pei H, Ma N, Chen J, Zheng Y et al (2013) Integrative analysis of miRNA and mRNA profiles in response to ethylene in rose petals during flower opening. PLoS ONE 8:e64290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Proebsting E Jr, Mills H (1978) Low temperature resistance [frost hardiness] of developing flower buds of six deciduous fruit species. J Am Soc Hortic Sci 103:191–198

    Google Scholar 

  • Rehmsmeier M, Steffen P, Höchsmann M, Giegerich R (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10:1507–1517

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rikin A, Atsmon D, Gitler C (1979) Chilling injury in cotton (Gossypium hirsutum L.) Prevention by abscisic acid. Plant Cell Physiol 20:1537–1546

    Article  CAS  Google Scholar 

  • Rodrigo J (2000) Spring frosts in deciduous fruit trees—morphological damage and flower hardiness. Sci Hortic 85:155–173

    Article  Google Scholar 

  • Rowland LJ, Alkharouf N, Darwish O, Ogden EL, Polashock JJ, Bassil NV, Main D (2012) Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biol 12:46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (1999) Molecular responses to cold drought, heat, and salt stress in higher plants, vol 1. RG Landes Company, Austin

    Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K, Seki M (2003) Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol 6:410–417

    Article  CAS  PubMed  Google Scholar 

  • Song JB, Gao S, Wang Y, Li BW, Zhang YL, Yang ZM (2016) miR394 and its target Gene LCR are involved in cold stress response in Arabidopsis. Plant Gene 5:56–64

    Article  CAS  Google Scholar 

  • Stepulaitiene I, Zebrauskiene A, Stanys V (2013) Frost resistance is associated with development of sour cherry (Prunus cerasus L.) generative buds. Žemdirbystė (Agriculture) 100:175–178

    Article  Google Scholar 

  • Sun S-K, Yang N-N, Chen L-J, Irfan M, Zhao X-H, Li T-L (2015) Characterization of LpGPAT Gene in Lilium pensylvanicum and response to cold stress. Biomed Res Int Article ID 792819 https://doi.org/10.1155/2015/792819

    Google Scholar 

  • Sunkar R, Zhu J-K (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16:2001–2019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sunkar R, Chinnusamy V, Zhu J, Zhu J-K (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12:301–309

    Article  CAS  PubMed  Google Scholar 

  • Szymajda M, Pruski K, Żurawicz E, Sitarek M (2013) Freezing injuries to flower buds and their influence on yield of apricot (Prunus armeniaca L.) and peach (Prunus persica L.). Can J Plant Sci 93:191–198

    Article  Google Scholar 

  • Tang Z, Zhang L, Xu C, Yuan S, Zhang F, Zheng Y, Zhao C (2012) Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male-sterile line by deep sequencing. Plant Physiol 159:721–738

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thiebaut F, Rojas CA, Almeida KL, Grativol C et al (2012) Regulation of miR319 during cold stress in sugarcane. Plant Cell Environ 35:502–512

    Article  CAS  Google Scholar 

  • Thomashow MF (1999) Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Plant Biol 50:571–599

    Article  CAS  Google Scholar 

  • Verde I, Abbott AG, Scalabrin S, Jung S et al (2013) The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 45:487–494

    Article  CAS  PubMed  Google Scholar 

  • Vigh L, Los DA, Horvath I, Murata N (1993) The primary signal in the biological perception of temperature: Pd-catalyzed hydrogenation of membrane lipids stimulated the expression of the desA gene in Synechocystis PCC6803. Proc Natl Acad Sci USA 90:9090–9094

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang L, Chen S, Kong W, Li S, Archbold DD (2006) Salicylic acid pretreatment alleviates chilling injury and affects the antioxidant system and heat shock proteins of peaches during cold storage. Postharvest Biol Technol 41:244–251

    Article  CAS  Google Scholar 

  • Wang T, Pan H, Wang J, Yang W, Cheng T, Zhang Q (2014) Identification and profiling of novel and conserved microRNAs during the flower opening process in Prunus mume via deep sequencing. Mol Genet Genomics 289:169–183

    Article  CAS  PubMed  Google Scholar 

  • Wang D, Gao Z, Du P, Xiao W et al (2015) Expression of ABA metabolism-related genes suggests similarities and differences between seed dormancy and bud dormancy of peach (Prunus persica). Front Plant Sci 11(6):1248

    Google Scholar 

  • Wang F, Guo Z, Li H, Wang M et al (2016a) Phytochrome A and B function antagonistically to regulate cold tolerance via abscisic acid-dependent jasmonate signaling. Plant Physiol 170:459–471

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Cao J, Jiang W (2016b) Changes in sugar metabolism caused by exogenous oxalic acid related to chilling tolerance of apricot fruit. Postharvest Biol Technol 114:10–16

    Article  CAS  Google Scholar 

  • Whiteman TM (1957) Freezing points of fruits, vegetables and florist stocks. Marketing research report no. 196, US Department of Agriculture

    Google Scholar 

  • Wisniewski ME, Bassett CL, Renaut J, Farrell R, Tworkoski T, Artlip TS (2006) Differential regulation of two dehydrin genes from peach (Prunus persica) by photoperiod, low temperature and water deficit. Tree Physiol 26:575–584

    Article  CAS  PubMed  Google Scholar 

  • Wisniewski M, Norelli J, Artlip T (2015) Overexpression of a peach CBF gene in apple: a model for understanding the integration of growth, dormancy, and cold hardiness in woody plants. Front Plant Sci 6

    Google Scholar 

  • Wu J, Wang D, Liu Y, Wang L, Qiao X, Zhang S (2014) Identification of miRNAs involved in pear fruit development and quality. BMC Genom 15:1

    CAS  Google Scholar 

  • Xia R, Zhu H, Y-q An, Beers EP, Liu Z (2012) Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol 13:R47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu J, Xing S, Cui H, Chen X, Wang X (2015) Genome-wide identification and characterization of the apple (Malus domestica) HECT ubiquitin-protein ligase family and expression analysis of their responsiveness to abiotic stresses. Mol Genet Genomics 1–12

    Google Scholar 

  • Yadav SK (2010) Cold stress tolerance mechanisms in plants: a review. Agron Sustain Dev 30:515–527

    Article  CAS  Google Scholar 

  • Yamaguchi-Shinozaki K, Shinozaki K (1994) A novel cis-acting element in an Arabidopsis gene is involved in responsiveness to drought, low-temperature, or high-salt stress. Plant Cell 6:251–264

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yang J-H, Qu L-H (2012) DeepBase: annotation and discovery of microRNAs and other noncoding RNAs from deep-sequencing data. Next-generation MicroRNA expression profiling technology: Methods Protocols, pp 233–248

    Google Scholar 

  • Yang W, Liu X-D, Chi X-J, Wu C-A et al (2011) Dwarf apple MbDREB1 enhances plant tolerance to low temperature, drought, and salt stress via both ABA-dependent and ABA-independent pathways. Planta 233:219–229

    Article  CAS  PubMed  Google Scholar 

  • Yang C, Li D, Mao D, Liu X et al (2013) Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.). Plant Cell Environ 36:2207–2218

    Article  CAS  Google Scholar 

  • Yao Y, Ni Z, Peng H, Sun F et al (2010) Non-coding small RNAs responsive to abiotic stress in wheat (Triticum aestivum L.). Funct Integr Genomics 10:187–190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeller G, Henz SR, Widmer CK, Sachsenberg T, Rätsch G, Weigel D, Laubinger S (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J 58:1068–1082

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33:W701–W704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 10:1

    Article  CAS  Google Scholar 

  • Zhang C, Ding Z, Xu X, Wang Q, Qin G, Tian S (2010a) Crucial roles of membrane stability and its related proteins in the tolerance of peach fruit to chilling injury. Amino Acids 39:181–194

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Yu J, Li D, Zhang Z et al (2010b) PMRD: plant microRNA database. Nucleic Acids Res 38:D806–D813

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Yang W, Cheng T, Pan H, Zhang Q (2013) Functional and evolutionary analysis of two CBF genes in Prunus mume. Can J Plant Sci 93:455–464

    Article  CAS  Google Scholar 

  • Zhang S, Wang Y, Li K, Zou Y, Chen L, Li X (2014a) Identification of cold-responsive miRNAs and their target genes in nitrogen-fixing nodules of soybean. Int J Mol Sci 15:13596–13614

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang X-N, Li X, Liu J-H (2014b) Identification of conserved and novel cold-responsive microRNAs in trifoliate orange (Poncirus trifoliata (L.) Raf.) using high-throughput sequencing. Plant Mol Biol Rep 32:328–341

    Article  CAS  Google Scholar 

  • Zhang Y, Zhu X, Chen X, Song C et al (2014c) 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y-H, Rong J-D, Chen L-G, Chen L-Y, He T-Y, Zheng Y-S (2015) Construction of cDNA library from Prunus campanulata leaves and preliminary expressed sequence tag (EST) analysis during cold stress. Biologia 70:1070–1077

    CAS  Google Scholar 

  • Zhao T, Liang D, Wang P, Liu J, Ma F (2012) Genome-wide analysis and expression profiling of the DREB transcription factor gene family in Malus under abiotic stress. Mol Genet Genomics 287:423–436

    Article  CAS  PubMed  Google Scholar 

  • Zhong W, Gao Z, Zhuang W, Shi T, Zhang Z, Ni Z (2013) Genome-wide expression profiles of seasonal bud dormancy at four critical stages in Japanese apricot. Plant Mol Biol 83:247–264

    Article  CAS  PubMed  Google Scholar 

  • Zhu H, Xia R, Zhao B, An Y-Q, Dardick CD, Callahan AM, Liu Z (2012) Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biol 12:1

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We would like to highlight our gratitude to Ms. Parisa Shiran for her invaluable comments and corrections.

Author information

Authors and Affiliations

  1. Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa

    Arghavan Alisoltani

  2. Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, P.O. Box 115, Shahrekord, Iran

    Marziyeh Karimi, Rudabeh Ravash & Behrouz Shiran

  3. Department of Biology, School of Sciences, Razi University, Bagh-e-Abrisham, Kermanshah, Iran

    Hossein Fallahi

Authors
  1. Arghavan Alisoltani
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marziyeh Karimi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rudabeh Ravash
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hossein Fallahi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Behrouz Shiran
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Arghavan Alisoltani or Behrouz Shiran .

Editor information

Editors and Affiliations

  1. Department of Botany, Delhi University, Delhi, India

    Vijay Rani Rajpal

  2. CIMMYT Headquarters, El Batán, Veracruz, Mexico

    Deepmala Sehgal

  3. Department of Botany, Vinoba Bhave University, Hazaribag, Jharkhand, India

    Avinash Kumar

  4. Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India

    S.N. Raina

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Alisoltani, A., Karimi, M., Ravash, R., Fallahi, H., Shiran, B. (2019). Molecular Responses to Cold Stress in Temperate Fruit Crops with Focus on Rosaceae Family. In: Rajpal, V., Sehgal, D., Kumar, A., Raina, S. (eds) Genomics Assisted Breeding of Crops for Abiotic Stress Tolerance, Vol. II. Sustainable Development and Biodiversity, vol 21. Springer, Cham. https://doi.org/10.1007/978-3-319-99573-1_7

Download citation

Publish with us

Policies and ethics

Search

Navigation