Regulatory insights underlying apple to cold stress

Abstract

Apple (Malus domestica) is one of the most widely cultivated and consumed fruits worldwide, valued for its rich nutrition and health benefits. Low temperature (LT) significantly limits apple growth, productivity, and fruit quality. Understanding the intricate regulatory networks, underlying cold tolerance is crucial for developing resilient apple cultivars. In this review, we comprehensively summarize the molecular control enabling apple to withstand cold stress, encompassing transcription cascades, phytohormonal networks, reactive oxygen species (ROS) regulation, epigenetic modifications, and post-translational modifications (PTMs), as well as the crosstalk with drought, immune, and light signaling pathways. We also discuss the management strategies for enhancing apple cold tolerance, including the exploitation of wild germplasm resources, multi-omics-based network integration, gene editing, molecular marker-assisted breeding, rootstock grafting, and emerging bioinoculants approaches. This review provides a foundational framework for molecular breeding and gene regulatory strategies to improve cold resilience in apple.

References

[1] Feng X, Zhao Q, Zhao L, et al. The cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1 encodes an ICE-like protein in apple. BMC Plant Biol. 2012; 12: 22

[2] Ding Y, Shi Y, Yang S . Regulatory networks underlying plant responses and adaptation to cold stress. Annu Rev Genet. 2024; 58: 43-65

[3] Thomashow MF . Plant cold acclimation: freezing tolerance genes and regulatory mechanisms. Annu Rev Genet. 1999; 50: 571-99

[4] Ren C, Fan P, Li S, et al. Advances in understanding cold tolerance in grapevine. Plant Physiol. 2023; 192: 1733-46

[5] Kang H, Thomas H, Xia X, et al. An integrative overview of cold response and regulatory pathways in horticultural crops. J Integr Plant Biol. 2025; 67: 1028-59

[6] Song Y, Zhang X, Li M, et al. The direct targets of CBFs: in cold stress response and beyond. J Integr Plant Biol. 2021; 63: 1874-87

[7] Li B, Qu S, Kang J, et al. The MdCBF1/2-MdTST1/2 module regulates sugar accumulation in response to low temperature in apple. Plant J. 2024; 118: 787-801

[8] Shi Y, Ding Y, Yang S . Molecular regulation of CBF signaling in cold acclimation. Trends Plant Sci. 2018; 23: 623-37

[9] Pittman J, Hirschi K . CAX-ing a wide net: Cation/H(+) transporters in metal remediation and abiotic stress signalling. Plant Biol (Stuttg). 2016; 18: 741-9

[10] Mao K, Yang J, Wang M, et al. Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters. BMC Plant Biol. 2021; 21: 81

[11] Xu H, Wang N, Wang Y, et al. Overexpression of the transcription factor MdbHLH33 increases cold tolerance of transgenic apple callus. Plant Cell Tissue Organ Cult. 2018; 134: 131-40

[12] Tan K, Song X, Xu Z, et al. The MdICE1/MdFAMA-MdTYDC transcriptional module confers cold tolerance by regulating dopamine metabolism in apple. Plant Biotechnol J. 2026; 24: 3012-31

[13] Dong H, Wu C, Luo C, et al. Overexpression of MdCPK1a gene, a calcium dependent protein kinase in apple, increase tobacco cold tolerance via scavenging ROS accumulation. PLoS One. 2020; 15: e0242139

[14] Yang J, Guo X, Mei Q, et al. MdbHLH4 negatively regulates apple cold tolerance by inhibiting MdCBF1/3 expression and promoting MdCAX3L-2 expression. Plant Physiol. 2023; 191: 789-806

[15] An J, Xu R, Liu X, et al. Abscisic acid insensitive 4 interacts with ICE1 and JAZ proteins to regulate ABA signaling-mediated cold tolerance in apple. J Exp Bot. 2022; 73: 980-97

[16] Wang Y, Jiang H, Mao Z, et al. Ethylene increases the cold tolerance of apple via the MdERF1B-MdCIbHLH1 regulatory module. Plant J. 2021; 106: 379-93

[17] An J, Liu Z, Zhang X, et al. Brassinosteroid signaling regulator BIM1 integrates brassinolide and jasmonic acid signaling during cold tolerance in apple. Plant Physiol. 2023; 193: 1652-74

[18] An J, Wang X, Zhang X, et al. An apple MYB transcription factor regulates cold tolerance and anthocyanin accumulation and undergoes MIEL1-mediated degradation. Plant Biotechnol J. 2020; 18: 337-53

[19] An J, Wang X, Zhang X, et al. Apple B-box protein BBX37 regulates jasmonic acid mediated cold tolerance through the JAZ-BBX37-ICE1-CBF pathway and undergoes MIEL1-mediated ubiquitination and degradation. New Phytol. 2021; 229: 2707-29

[20] An J, Yao J, Wang X, et al. MdHY5 positively regulates cold tolerance via CBF-dependent and CBF-independent pathways in apple. J Plant Physiol. 2017; 218: 275-81

[21] An J, Li R, Qu F, et al. R2R3-MYB transcription factor MdMYB23 is involved in the cold tolerance and proanthocyanidin accumulation in apple. Plant J. 2018; 96: 562-77

[22] Xie Y, Chen P, Yan Y, et al. An atypical R2R3 MYB transcription factor increases cold hardiness by CBF-dependent and CBF-independent pathways in apple. New Phytol. 2018; 218: 201-18

[23] Wang Y, Mao Z, Jiang H, et al. A feedback loop involving MdMYB108L and MdHY5 controls apple cold tolerance. Biochem Biophys Res Commun. 2019; 512: 381-6

[24] Mei C, Yang J, Mei Q, et al. MdNAC104 positively regulates apple cold tolerance via CBF-dependent and CBF-independent pathways. Plant Biotechnol J. 2023; 21: 2057-73

[25] Liu W, Wang T, Liang X, et al. MbWRKY53, a M. baccata WRKY transcription factor, contributes to cold and drought stress tolerance in transgenic Arabidopsis thaliana. Int J Mol Sci. 2024; 25: 7626

[26] Zhang X, An X, Xu R, et al. The MdGLK1-MdBZR1 Module Integrates Ethylene and Strigolactone signals to regulate cold tolerance via a CBF-Dependent pathway in apple. Plant Biotechnol J. 2025; 23: 5550-69

[27] Jing Y, Pei T, Li C, et al. Overexpression of the FERONIA receptor kinase MdMRLK2 enhances apple cold tolerance. Plant J. 2023; 115: 236-52

[28] An J, Li R, Qu F, et al. An apple NAC transcription factor negatively regulates cold tolerance via CBF-dependent pathway. J Plant Physiol. 2018; 221: 74-80

[29] Xu H, Yang G, Zhang J, et al. Overexpression of a repressor MdMYB15L negatively regulates anthocyanin and cold tolerance in red-fleshed callus. Biochem Biophys Res Commun. 2018; 500: 405-10

[30] Eremina M, Unterholzner S, Rathnayake A, et al. Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants. Proc Natl Acad Sci USA. 2016; 113: 5982-91

[31] Shen J, Liu J, Yuan Y, et al. The mechanism of abscisic acid regulation of wild Fragaria species in response to cold stress. BMC Genomics. 2022; 23: 670

[32] Qian Z, He L, Li F . Understanding cold stress response mechanisms in plants: an overview. Front Plant Sci. 2024; 15: 1443317

[33] Huang X, Chen M, Yang L, et al. Effects of exogenous abscisic acid on cell membrane and endogenous hormone contents in leaves of sugarcane seedlings under cold stress. Sugar Tech. 2015; 17: 59-64

[34] Li M, Wang C, Shi J, et al. Abscisic acid and putrescine synergistically regulate the cold tolerance of melon seedlings. Plant Physiol Biochem. 2021; 166: 1054-64

[35] Liu X, Wei J, Li S, et al. MdHY5 positively regulates cold tolerance in apple by integrating the auxin and abscisic acid pathways. New Phytol. 2025; 246: 2155-73

[36] Kagale S, Divi U, Krochko J, et al. Brassinosteroid confers tolerance in Arabidopsis thaliana and Brassica napus to a range of abiotic stresses. Planta. 2007; 225: 353-64

[37] Ye K, Li H, Ding Y, et al. BRASSINOSTEROID-INSENSITIVE2 negatively regulates the stability of transcription factor ICE1 in response to cold stress in Arabidopsis. Plant Cell. 2019; 31: 2682-96

[38] Li H, Ye K, Shi Y, et al. BZR1 positively regulates freezing tolerance via CBF-Dependent and CBF-Independent Pathways in Arabidopsis. Mol Plant. 2017; 10: 545-59

[39] Dong Y, Tang M, Huang Z, et al. The miR164a-NAM3 module confers cold tolerance by inducing ethylene production in tomato. Plant J. 2022; 111: 440-56

[40] Feng J, Wang M, Chen X, et al. EIL (ethylene-insensitive 3-like) transcription factors in apple affect both ethylene- and cold response-dependent fruit ripening. Plant J. 2025; 121: e70059

[41] Hu Y, Jiang Y, Han X, et al. Jasmonate regulates leaf senescence and tolerance to cold stress: crosstalk with other phytohormones. J Exp Bot. 2017; 68: 1361-9

[42] Hu Y, Jiang L, Wang F, et al. Jasmonate regulates the inducer of cbf expression-C-repeat binding factor/DRE binding factor1 cascade and freezing tolerance in Arabidopsis. Plant Cell. 2013; 25: 2907-24

[43] Peng C, Hua W, Liu J . Unraveling the signaling pathways of plant cold stress: current insights and future directions. Front Plant Sci. 2025; 16: 1666852

[44] Gill S, Tuteja N . Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem. 2010; 48: 909-30

[45] Wang P, Liu W, Han C, et al. Reactive oxygen species: multi-dimensional regulators of plant adaptation to abiotic stress and development. J Integr Plant Biol. 2024; 66: 330-67

[46] Yang J, Li N, Li M, et al. The MdHB7L-MdICE1L-MdHOS1 module fine-tunes apple cold response via CBF-dependent and CBF-independent pathways. Adv Sci (Weinh). 2025; 12: e2501524

[47] Hichri I, Barrieu F, Bogs J, et al. Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. J Exp Bot. 2011; 62: 2465-83

[48] Wang N, Qu C, Jiang S, et al. The proanthocyanidin-specific transcription factor MdMYBPA1 initiates anthocyanin synthesis under low-temperature conditions in red-fleshed apples. Plant J. 2018; 96: 39-55

[49] Xie X, Li S, Zhang R, et al. The bHLH transcription factor MdbHLH3 promotes anthocyanin accumulation and fruit colouration in response to low temperature in apples. Plant Cell Environ. 2012; 35: 1884-97

[50] Ma L, Xing L, Li Z, et al. Epigenetic control of plant abiotic stress responses. J Genet Genomics. 2025; 52: 129-44

[51] Xue Y, Cao X, Chen X, et al. Epigenetics in the modern era of crop improvements. China Life Sci. 2025; 68: 1570-609

[52] Zhang H, Lang Z, Zhu J . Dynamics and function of DNA methylation in plants. Nat Rev Mol Cell Biol. 2018; 19: 489-506

[53] Kumar A, Mushtaq M, Kumar P, et al. Insights into flowering mechanisms in apple (Malus × domestica Borkh.) amidst climate change: an exploration of genetic and epigenetic factors. Biochim Biophys Acta Gen Subj. 2024; 1868: 130593

[54] Xu J, Zhou S, Gong X, et al. Single-base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple. Plant Biotechnol J. 2018; 16: 672-87

[55] Niu C, Jiang L, Cao F, et al. Methylation of a MITE insertion in the MdRFNR1-1 promoter is positively associated with its allelic expression in apple in response to drought stress. Plant Cell. 2022; 34: 3983-4006

[56] Li W, Ning G, Mao J, et al. Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin. Planta. 2019; 250: 1833-47

[57] Kumar G, Rattan U, Singh A . Chilling-mediated DNA methylation changes during dormancy and its release reveal the importance of epigenetic regulation during winter dormancy in apple (Malus x domestica Borkh.). PLoS One. 2016; 11: e0149934

[58] Yu L, Sun Y, Zhang X, et al. ROS1 promotes low temperature-induced anthocyanin accumulation in apple by demethylating the promoter of anthocyanin-associated genes. Hortic Res. 2022; 9: uhac007

[59] Howe F, Fischl H, Murray S, et al. Is H3K4me3 instructive for transcription activation? Bioessays. 2017; 39: 1-12

[60] Zhang X, Clarenz O, Cokus S, et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007;5:e129

[61] Zeng Z, Zhang W, Marand A, et al. Cold stress induces enhanced chromatin accessibility and bivalent histone modifications H3K4me3 and H3K27me3 of active genes in potato. Genome Biol. 2019; 20: 123

[62] Faivre L, Kinscher N, Kuhlmann A, et al. Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana. Front Plant Sci. 2024; 15: 1390144

[63] Di Q, Zhou M, Li Y, et al. Respiratory burst oxidase homolog 5.1 regulates H3K4me3 deposition and transcription after cold priming in cucumber. Plant Physiol. 2025; 197: kiae461

[64] Nishiyama S, Matsushita M, Yamane H, et al. Functional and expressional analyses of apple FLC-like in relation to dormancy progress and flower bud development. Tree Physiol. 2021; 41: 562-70

[65] Zhu H, Chen P, Zhong S, et al. Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds. Hortic Res. 2020;7:114

[66] Chen W, Tamada Y, Yamane H, et al. H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. Plant J. 2022; 111: 1015-31

[67] Guo M, Wang S, Liu H, et al. Histone deacetylase MdHDA6 is an antagonist in regulation of transcription factor MdTCP15 to promote cold tolerance in apple. Plant Biotechnol J. 2023; 21: 2254-72

[68] Liang Z, Huang Y, Hao Y, et al. The histone acetyltransferase 1 interacts with constans to promote flowering in Arabidopsis. J Genet Genomics. 2025; 52: 1627-37

[69] Kumar V, Thakur J, Prasad M . Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci. 2021; 78: 4467-86

[70] Servet C, Conde e Silva N, Zhou D . Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Mol Plant. 2010; 3: 670-7

[71] Park J, Lim C, Shen M, et al. Epigenetic switch from repressive to permissive chromatin in response to cold stress. Proc Natl Acad Sci USA. 2018; 115: 5400-9

[72] Kamble N. Histone deacetylase OsHDA716 chilling out with OsbZIP46: antagonistically regulating cold stress tolerance in rice. Plant Cell. 2024; 36: 1592-3

[73] Park K, Kim M, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proc Natl Acad Sci USA. 2016; 113: 15138-43

[74] Hu Y, Zhang L, Zhao L, et al. Trichostatin a selectively suppresses the cold-induced transcription of the ZmDREB1 gene in maize. PLoS One. 2011; 6: e22132

[75] Jiang W, Hong F, Niu B, et al. Genome-wide analysis of apple histone acetyltransferases reveals the regulatory roles of MdHAG1 and MdHAM1 in response to abiotic stresses. Plant Sci. 2025; 355: 112441

[76] Tang J, Chen S, Jia G . Detection, regulation, and functions of RNA N6-methyladenosine modification in plants. Plant Commun. 2023; 4: 100546

[77] Roundtree I, Evans M, Pan T, et al. Dynamic RNA modifications in gene expression regulation. Cell. 2017; 169: 1187-200

[78] Yue H, Nie X, Yan Z, et al. N6-methyladenosine regulatory machinery in plants: composition, function and evolution. Plant Biotechnol J. 2019; 17: 1194-208

[79] Shen L. Epitranscriptomic regulation through phase separation in plants. Trends Plant Sci. 2025; 30: 629-41

[80] Hou N, He J, Bao C, et al. MdDSK2a-like-MdMTA module functions in apple cold response via regulating ROS detoxification and cell wall deposition. Adv Sci (Weinh). 2025; 12: e2504405

[81] Jha U, Nayyar H, Roychowdhury R, et al. Non-coding RNAs (ncRNAs) in plant: master regulators for adapting to extreme temperature conditions. Plant Physiol Biochem. 2023; 205: 108164

[82] Cao W, Yang L, Zhuang M, et al. Plant non-coding RNAs: the new frontier for the regulation of plant development and adaptation to stress. Plant Physiol Biochem. 2024; 208: 108435

[83] Gleave A, Ampomah-Dwamena C, Berthold S, et al. Identification and characterisation of primary microRNAs from apple (Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genet Genomes. 2008; 4: 343-58

[84] Varkonyi-Gasic E, Gould N, Sandanayaka M, et al. Characterisation of microRNAs from apple (Malus domestica ’Royal Gala’) vascular tissue and phloem sap. BMC Plant Biol. 2010; 10: 159

[85] Xia R, Zhu H, An Y, et al. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol. 2012; 13: R47

[86] Visser M, van der Walt A, Maree H, et al. Extending the sRNAome of apple by next-generation sequencing. PLoS One. 2014; 9: e95782

[87] Liu F, Tang J, Li T, et al. The microRNA miR482 regulates NBS-LRR genes in response to ALT1 infection in apple. Plant Sci. 2024; 343: 112078

[88] Liu X, Dai H, Zhang F, et al. The miR7125-MdARF1 module enhances the resistance of apple to Colletotrichum gloeosporioides by promoting lignin synthesis in response to salicylic acid signalling. Plant Biotechnol J. 2024; 22: 2741-55

[89] Zhang Z, Li Z, Zhang F, et al. A viroid-derived small interfering RNA targets bHLH transcription factor MdPIF1 to regulate anthocyanin biosynthesis in Malus domestica. Plant Cell Environ. 2024; 47: 4664-82

[90] Feng C, Zhang X, Du B, et al. MicroRNA156ab regulates apple plant growth and drought tolerance by targeting transcription factor MsSPL13. Plant Physiol. 2023; 192: 1836-57

[91] Ma Y, Xue H, Zhang F, et al. The miR156/SPL module regulates apple salt stress tolerance by activating MdWRKY100 expression. Plant Biotechnol J. 2021; 19: 311-23

[92] Yu X, Lin X, Zhou T, et al. Host-induced gene silencing in wild apple germplasm Malus hupehensis confers resistance to the fungal pathogen Botryosphaeria dothidea. Plant J. 2024; 118: 1174-93

[93] Li Z, Liu W, Chen Q, et al. Mdm-miR858 targets MdMYB9 and MdMYBPA1 to participate anthocyanin biosynthesis in red-fleshed apple. Plant J. 2023; 113: 1295-309

[94] Shen X, Ping Y, Bao C, et al. Mdm-miR160-MdARF17-MdWRKY33 module mediates freezing tolerance in apple. Plant J. 2023; 114: 262-78

[95] Shen X, Song Y, Ping Y, et al. The RNA-binding protein MdHYL1 modulates cold tolerance and disease resistance in apple. Plant Physiol. 2023; 192: 2143-60

[96] Ding Y, Shi Y, Yang S . Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants. New Phytol. 2019; 222: 1690-704

[97] Zhao C, Wang P, Si T, et al. MAP kinase cascades regulate the cold response by modulating ICE1 protein stability. Dev Cell. 2017; 43: 618-29

[98] Liu Z, Jia Y, Ding Y, et al. Plasma membrane CRPK1-mediated phosphorylation of 14-3-3 proteins induces their nuclear import to fine-tune CBF signaling during cold response. Mol Cell. 2017; 66: 117-28

[99] Teige M, Scheikl E, Eulgem T, et al. The MKK2 pathway mediates cold and salt stress signaling in Arabidopsis. Mol Cell. 2004; 15: 141-52

[100] Haimi P, Vinskiene J, Stepulaitiene I, et al. Patterns of low temperature induced accumulation of dehydrins in Rosaceae crops -evidence for post-translational modification in apple. J Plant Physiol. 2017; 218: 175-81

[101] Wang D, Zhang X, Xu R, et al. Apple U-box-type E3 ubiquitin ligase MdPUB23 reduces cold-stress tolerance by degrading the cold-stress regulatory protein MdICE1. Hortic Res. 2022; 9: uhac171

[102] Zhi F, Fan T, Zhang Y, et al. MdKIN10-mediated phosphorylation of the E3 ubiquitin ligase MdMIEL1 leads to its autophagic degradation under cold stress. Plant Cell. 2025; 38: koaf284

[103] Jiang H, Zhou L, Gao H, et al. The transcription factor MdMYB2 influences cold tolerance and anthocyanin accumulation by activating SUMO E3 ligase MdSIZ1 in apple. Plant Physiol. 2022; 189: 2044-60

[104] Yadav A, Singh D, Lingwan M, et al. Light signaling and UV-B-mediated plant growth regulation. J Integr Plant Biol. 2020; 62: 1270-92

[105] Zhang X, Zhang L, Sun Y, et al. Hydrogen peroxide is involved in strigolactone induced low temperature stress tolerance in rape seedlings (Brassica rapa L.) Plant Physiol Biochem. 2020; 157: 402-5

[106] Lee C, Thomashow M . Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2012; 109: 15054-9

[107] Prerostova S, Cerny M, Dobrev P, et al. Light regulates the cytokinin-dependent cold stress responses in Arabidopsis. Front Plant Sci. 2021; 11: 608711

[108] Fang H, Dong Y, Yue X, et al. The B-box zinc finger protein MdBBX20 integrates anthocyanin accumulation in response to ultraviolet radiation and low temperature. Plant Cell Environ. 2019; 42: 2090-104

[109] Haak D, Fukao T, Grene R, et al. Multilevel regulation of abiotic stress responses in plants. Front Plant Sci. 2017; 8: 1564

[110] Wang Y, Zheng L, Song J, et al. Drought priming-induced low temperature stress tolerance in wheat: insight into stress memory dynamics. Crop Environ. 2025; 4: 118-29

[111] Li X, Li M, Zhou B, et al. Transcriptome analysis provides insights into the stress response crosstalk in apple (Malus × domestica) subjected to drought, cold and high salinity. Sci Rep. 2019; 9: 9071

[112] Li X, Meng D, Li M, et al. Transcription factors MhDREB2A/MhZAT10 play a role in drought and cold stress response crosstalk in apple. Plant Physiol. 2023; 192: 2203-20

[113] Zhang Y, Li X . Salicylic acid: biosynthesis, perception, and contributions to plant immunity. Curr Opin Plant Biol. 2019; 50: 29-36

[114] Li S, He L, Yang Y, et al. INDUCER OF CBF EXPRESSION 1 promotes cold-enhanced immunity by directly activating salicylic acid signaling. Plant Cell. 2024; 36: 2587-606

[115] Li W, Sun G, Yang W, et al. Living with temperature changes: Salicylic acid at the crossroads of plant immunity and temperature resilience. Sci Adv. 2025; 11: eady3327

[116] Geng D, Shen X, Xie Y, et al. Regulation of phenylpropanoid biosynthesis by MdMYB88 and MdMYB124 contributes to pathogen and drought resistance in apple. Hortic Res. 2020; 7: 102

[117] Li W, Chu C, Zhang T, et al. Pan-genome analysis reveals the evolution and diversity of Malus. Nat Genet. 2025; 57: 1274-86

[118] Zhang L, Xu Y, Lv L, et al. MbbHLH93, a transcription factor associated with cold and drought tolerance in Malus baccata. Fruit Res. 2024; 4: e038

[119] Celton J, Martinez S, Jammes M, et al. Deciphering the genetic determinism of bud phenology in apple progenies: a new insight into chilling and heat requirement effects on flowering dates and positional candidate genes. New Phytol. 2011; 192: 378-92

[120] Allard A, Bink M, Martinez S, et al. Detecting QTLs and putative candidate genes involved in budbreak and flowering time in an apple multiparental population. J Exp Bot. 2016; 67: 2875-88

[121] Liu J, Artlip T, Sherif S, et al. Genetics and genomics of cold hardiness and dormancy. Compend Plant Genomes 2021; 30: 74681

[122] Watson A, Guitton B, Soriano A, et al. Target enrichment sequencing coupled with GWAS identifies MdPRX10 as a candidate gene in the control of budbreak in apple. Front Plant Sci. 2024; 15: 1352757

[123] Xu G, Yan S, He M, et al. Advances in the research on cold resistance of apple. Acta Horticulturae Sinica. 2025; 52: 2021-45

[124] Xu G, He M, Yan S, et al. Galactinol synthase gene 5 (MdGolS5) enhances the cold resistance of apples by promoting raffinose family oligosaccharide accumulation. Plant Physiol Biochem. 2025; 220: 109416

[125] Wang Y, Yang Y, Chen M, et al. The MpbZIP46-MpERF105 module responds to ABA and ethylene signalling to promote anthocyanin synthesis in Malus ’profusion’ under rust stress. Plant Cell Environ. 2025; 49: 193-208

[126] Wang N, Liu W, Mei Z, et al. A functional InDel in the WRKY10 promoter controls the degree of flesh red pigmentation in apple. Adv Sci (Weinh). 2024; 11: e2400998

[127] Zhang S, Wang H, Wang T, et al. MdMYB305-MdbHLH33-MdMYB10 regulates sugar and anthocyanin balance in red-fleshed apple fruits. Plant J. 2023; 113: 1062-79

[128] Zhou H, Bai S, Wang N, et al. CRISPR/Cas9-mediated mutagenesis of MdCNGC2 in apple callus and VIGS-mediated silencing of MdCNGC2 in fruits improve resistance to Botryosphaeria dothidea. Front Plant Sci. 2020; 11: 575477

[129] Pompili V, Dalla Costa L, Piazza S, et al. Reduced fire blight susceptibility in apple cultivars using a high-efficiency CRISPR/Cas9-FLP/FRT-based gene editing system. Plant Biotechnol J. 2020; 18: 845-58

[130] Yue Y, Yu D, Tang J, et al. Enhancing somatic embryogenesis and genetic transformation through overexpression of MdWOX4 in apple. Hortic Plant J. 2025

[131] Wada M, Nishitani C, Komori S . Stable and efficient transformation of apple. Plant Biotechnol (Tokyo). 2020; 37: 163-70

[132] Liu L, Qu J, Wang C, et al. An efficient genetic transformation system mediated by Rhizobium rhizogenes in fruit trees based on the transgenic hairy root to shoot conversion. Plant Biotechnol J. 2024; 22: 2093-103

[133] Yang Q, Liu Y, Zhou J, et al. The transcription factor MhZAT10 enhances antioxidant capacity by directly activating the antioxidant genes MhMSD1, MhAPX3a and MhCAT1 in apple rootstock SH6 (Malus honanensis × M. domestica). Tree Physiol. 2024; 44: tpae077

[134] Wang Y, Hu Y, Chen B, et al. Physiological mechanisms of resistance to cold stress associated with 10 elite apple rootstocks. J Integr Agric. 2018: 857-66

[135] Fazio G, Robinson T . Apple rootstocks can modulate the chilling requirements of grafted scions. Acta Hortic Sin. 2022: 723-28

[136] Lee Y, Hoang N, Do V, et al. Identification of genes associated with the regulation of cold tolerance and the RNA movement in the grafted apple. Sci Rep. 2023; 13: 11583

[137] Zhang X, Wang L, Wang J, et al. Seasonal variations in rhizosphere bacterial communities and potential functions of different Osmanthus fragrans cultivars. Plant Soil. 2025; 516: 673-88

[138] Zhang J, Song K, Jin F, et al. A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress. Sci Total Environ. 2024; 949: 175184.

[139] Wang J, Wu H, Wang Y, et al. Small particles, big effects: How nanoparticles can enhance plant growth in favorable and harsh conditions. J Integr Plant Biol. 2024; 66: 1274-94

[140] Magana-Lopez E, Palos-Barba V, Zuverza-Mena N, et al. Nanostructured mesoporous silica materials induce hormesis on chili pepper (Capsicum annuum L.) under greenhouse conditions. Heliyon. 2022; 8: e09049

[141] Mahmoudi R, Razavi F, Rabiei V, et al. Application of glycine betaine coated chitosan nanoparticles alleviate chilling injury and maintain quality of plum (Prunus domestica L.) fruit. Int J Biol Macromol. 2022; 207: 965-77

[142] Ratajczak K, Sulewska H, Panasiewicz K, et al. Phytostimulator application after cold stress for better maize (Zea mays L.) Plant Recover. Agric. 2023; 13: 569

[143] Borella M, Baghdadi A, Bertoldo G, et al. Transcriptomic and physiological approaches to decipher cold stress mitigation exerted by brown-seaweed extract application in tomato. Front Plant Sci. 2023; 14: 1232421