doi:10.48130/forres-0026-0011

[1]

Ma X, Wang W, Zhang J, Jiang Z, Xu C, et al. 2025. NRT1.1B acts as an abscisic acid receptor in integrating compound environmental cues for plants. Cell 188:5231−5248

doi: 10.1016/j.cell.2025.07.027

[2]

Kidokoro S, Shinozaki K, Yamaguchi-Shinozaki K. 2022. Transcriptional regulatory network of plant cold-stress responses. Trends in Plant Science 27:922−935

doi: 10.1016/j.tplants.2022.01.008

[3]

Fang X, Yang D, Deng L, Zhang Y, Lin Z, et al. 2024. Phosphorus uptake, transport, and signaling in woody and model plants. Forestry Research 4:e017

doi: 10.48130/forres-0024-0014

[4]

Nilsson O. 2022. Winter dormancy in trees. Current Biology 32:R630−R634

doi: 10.1016/j.cub.2022.04.011

[5]

Wang H, Cao Y, Mansfield SD, Zhang P, Lin X, et al. 2025. Integrative transcriptome and metabolome evaluation of melanin biosynthesis in Phyllostachys nigra during low-temperature growth. Forestry Research 5:e020

doi: 10.48130/forres-0025-0020

[6]

Larran AS, Pajoro A, Qüesta JI. 2023. Is winter coming? Impact of the changing climate on plant responses to cold temperature. Plant, Cell & Environment 46:3175−3193

doi: 10.1111/pce.14669

[7]

Dai X, Lin Y, Zhou T, Li Y, Liao X, et al. 2023. Natural annual transcriptome dynamics of Eucalyptus reveal seasonal adaptation of tropical/sub-tropical trees. Tree Physiology 43:658−674

doi: 10.1093/treephys/tpac136

[8]

Ding Y, Shi Y, Yang S. 2024. Regulatory networks underlying plant responses and adaptation to cold stress. Annual Review of Genetics 58:43−65

doi: 10.1146/annurev-genet-111523-102226

[9]

Manasa SL, Panigrahy M, Panigrahi KCS, Rout GR. 2022. Overview of cold stress regulation in plants. The Botanical Review 88:359−387

doi: 10.1007/s12229-021-09267-x

[10]

Zhang X, Li M, Zhang X, Zeng R, Peng Y, et al. 2025. A receptor–kinase cascade confers cold-induced root growth inhibition in Arabidopsis. Nature Plants 11:1441−1454

doi: 10.1038/s41477-025-02034-5

[11]

Qian Z, He L, Li F. 2024. Understanding cold stress response mechanisms in plants: an overview. Frontiers in Plant Science 15:1443317

doi: 10.3389/fpls.2024.1443317

[12]

Wu J, Sun W, Sun C, Xu C, Li S, et al. 2023. Cold stress induces malformed tomato fruits by breaking the feedback loops of stem cell regulation in floral meristem. New Phytologist 237:2268−2283

doi: 10.1111/nph.18699

[13]

Shen X, Ping Y, Bao C, Liu C, Tahir MM, et al. 2023. Mdm-miR160–MdARF17–MdWRKY33 module mediates freezing tolerance in apple. The Plant Journal 114:262−278

doi: 10.1111/tpj.16132

[14]

Ding Y, Jia Y, Shi Y, Zhang X, Song C, et al. 2018. OST1-mediated BTF3L phosphorylation positively regulates CBFs during plant cold responses. The EMBO Journal 37:EMBJ201798228

doi: 10.15252/embj.201798228

[15]

Ding Y, Lv J, Shi Y, Gao J, Hua J, et al. 2019. EGR2 phosphatase regulates OST1 kinase activity and freezing tolerance in Arabidopsis. The EMBO Journal 38:EMBJ201899819

doi: 10.15252/embj.201899819

[16]

Lv J, Liu J, Ming Y, Shi Y, Song C, et al. 2021. Reciprocal regulation between the negative regulator PP2CG1 phosphatase and the positive regulator OST1 kinase confers cold response in Arabidopsis. Journal of Integrative Plant Biology 63:1568−1587

doi: 10.1111/jipb.13100

[17]

Ding Y, Li H, Zhang X, Xie Q, Gong Z, et al. 2015. OST1 kinase modulates freezing tolerance by enhancing ICE1 stability in Arabidopsis. Developmental Cell 32:278−289

doi: 10.1016/j.devcel.2014.12.023

[18]

Dong CH, Agarwal M, Zhang Y, Xie Q, Zhu JK. 2006. The negative regulator of plant cold responses, HOS1, is a RING E3 ligase that mediates the ubiquitination and degradation of ICE1. Proceedings of the National Academy of Sciences of the United States of America 103:8281−8286

doi: 10.3410/f.1033009.374627

[19]

Li H, Ding Y, Shi Y, Zhang X, Zhang S, et al. 2017. MPK3- and MPK6-mediated ICE1 phosphorylation negatively regulates ICE1 stability and freezing tolerance in Arabidopsis. Developmental Cell 43:630−642.e4

doi: 10.1016/j.devcel.2017.09.025

[20]

Zhao C, Wang P, Si T, Hsu CC, Wang L, et al. 2017. MAP kinase cascades regulate the cold response by modulating ICE1 protein stability. Developmental Cell 43:618−629.e5

doi: 10.1016/j.devcel.2017.09.024

[21]

Song Y, Zhang X, Li M, Yang H, Fu D, et al. 2021. The direct targets of CBFs: in cold stress response and beyond. Journal of Integrative Plant Biology 63:1874−1887

doi: 10.1111/jipb.13161

[22]

Ding Y, Yang H, Wu S, Fu D, Li M, et al. 2022. CPK28-NLP7 module integrates cold-induced Ca²⁺ signal and transcriptional reprogramming in Arabidopsis. Science Advances 8:eabn7901

doi: 10.1126/sciadv.abn7901

[23]

Doherty CJ, Van Buskirk HA, Myers SJ, Thomashow MF. 2009. Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance. The Plant Cell 21:972−984

doi: 10.1105/tpc.108.063958

[24]

Kidokoro S, Yoneda K, Takasaki H, Takahashi F, Shinozaki K, et al. 2017. Different cold-signaling pathways function in the responses to rapid and gradual decreases in temperature. The Plant Cell 29:760−774

doi: 10.1105/tpc.16.00669

[25]

Li Z, Fu D, Wang X, Zeng R, Zhang X, et al. 2022. The transcription factor bZIP68 negatively regulates cold tolerance in maize. The Plant Cell 34:2833−2851

doi: 10.1093/plcell/koac137

[26]

Agarwal M, Hao Y, Kapoor A, Dong CH, Fujii H, et al. 2006. A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. Journal of Biological Chemistry 281:37636−37645

doi: 10.1074/jbc.M605895200

[27]

Jiang B, Shi Y, Peng Y, Jia Y, Yan Y, et al. 2020. Cold-induced CBF–PIF3 interaction enhances freezing tolerance by stabilizing the phyB thermosensor in Arabidopsis. Molecular Plant 13:894−906

doi: 10.1016/j.molp.2020.04.006

[28]

Kidokoro S, Hayashi K, Haraguchi H, Ishikawa T, Soma F, et al. 2021. Posttranslational regulation of multiple clock-related transcription factors triggers cold-inducible gene expression in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 118:e2021048118

doi: 10.3410/f.739665053.793583716

[29]

Zhou C, Yuan Z, Ma X, Yang H, Wang P, et al. 2021. Accessible chromatin regions and their functional interrelations with gene transcription and epigenetic modifications in sorghum genome. Plant Communications 2:100140

doi: 10.1016/j.xplc.2020.100140

[30]

Klemm SL, Shipony Z, Greenleaf WJ. 2019. Chromatin accessibility and the regulatory epigenome. Nature Reviews Genetics 20:207−220

doi: 10.1038/s41576-018-0089-8

[31]

Grandi FC, Modi H, Kampman L, Corces MR. 2022. Chromatin accessibility profiling by ATAC-seq. Nature Protocols 17:1518−1552

doi: 10.1038/s41596-022-00692-9

[32]

Liu X, Bie XM, Lin X, Li M, Wang H, et al. 2023. Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation. Nature Plants 9:908−925

doi: 10.1038/s41477-023-01406-z

[33]

Li M, Li J, Zhang Y, Zhai Y, Chen Y, et al. 2024. Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa. Molecular Plant Pathology 25:e13446

doi: 10.1111/mpp.13446

[34]

Zhang SY, Zhao BG, Shen Z, Mei YC, Li G, et al. 2023. Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves. Plant Molecular Biology 113:59−74

doi: 10.1007/s11103-023-01375-z

[35]

Guo M, Yang F, Zhu L, Wang L, Li Z, et al. 2024. Loss of cold tolerance is conferred by absence of the WRKY34 promoter fragment during tomato evolution. Nature Communications 15:6667

doi: 10.1038/s41467-024-51036-y

[36]

Wang P, Jin S, Chen X, Wu L, Zheng Y, et al. 2021. Chromatin accessibility and translational landscapes of tea plants under chilling stress. Horticulture Research 8:96

doi: 10.1038/s41438-021-00529-8

[37]

Fensham RJ, Laffineur B, Collingwood TD, Beech E, Bell S, et al. 2020. Rarity or decline: key concepts for the red list of Australian eucalypts. Biological Conservation 243:108455

doi: 10.1016/j.biocon.2020.108455

[38]

Wei J, Han Y, Xu H, Deng L, Li L, et al. 2025. AAAP gene family evolution and transcriptional regulation in Eucalyptus grandis under nitrogen, phosphate and boron deficiencies. BMC Plant Biology 25:879

doi: 10.1186/s12870-025-06907-x

[39]

Xing Y, Xu H, Yang D, Deng L, Li G, et al. 2025. Genome-wide identification and gene expression analysis of the malate dehydrogenase (MDH) gene family in Eucalyptus grandis. Frontiers in Plant Science 16:1640247

doi: 10.3389/fpls.2025.1640247

[40]

Xu H, Xing Y, Li G, Wang X, Zhou X, et al. 2025. Decoding PHR-orchestrated stress adaptation: a genome-wide integrative analysis of transcriptional regulation under abiotic stress in Eucalyptus grandis. International Journal of Molecular Sciences 26:2958

doi: 10.3390/ijms26072958

[41]

Aguayo P, Fernández M, Balocchi C, Valenzuela S. 2023. An overview of cold stress responses in Eucalyptus globulus. Trees 37:211−222

doi: 10.1007/s00468-022-02355-4

[42]

Costa e Silva F, Shvaleva A, Broetto F, Ortuño MF, Rodrigues ML, et al. 2009. Acclimation to short-term low temperatures in two Eucalyptus globulus clones with contrasting drought resistance. Tree Physiology 29:77−86

doi: 10.1093/treephys/tpn002

[43]

Costa e Silva F, Shvaleva A, Almeida MH, Chaves MM, Pereira JS. 2007. Responses to chilling of two Eucalyptus globulus clones with contrasting drought resistance. Functional Plant Biology 34:793−802

doi: 10.1071/fp07080

[44]

Shvaleva A, Costa e Silva F, Scotti P, Oufir M, Hausman JF, et al. 2008. Physiological and biochemical responses to low non-freezing temperature of two Eucalyptus globulus clones differing in drought resistance. Annals of Forest Science 65:204

doi: 10.1051/forest:2007087

[45]

Xu J, Li G, Lu Z, Xiang D, Zeng B, et al. 2008. Investigation on eucalypt forest plantations subjected to the freezing catastrophe in Southern China. Scientia Silvae Sinicae 44:103−110

doi: 10.11707/j.1001-7488.20080718

[46]

Duan F, Yan E, Shi T, Kang W, Tian W, et al. 2015. Eucalyptus plantation freezing damage and countermeasure analysis in Chuxiong prefecture. Eucalypt Science & Technology 32:39−44 (in Chinese)

doi: 10.13987/j.cnki.askj.2015.01.008

[47]

Ball MC, Wolfe J, Canny M, Hofmann M, Nicotra AB, et al. 2002. Space and time dependence of temperature and freezing in evergreen leaves. Functional Plant Biology 29:1259−1272

doi: 10.1071/fp02037

[48]

Oberschelp GPJ, Guarnaschelli AB, Teson N, Harrand L, Podestá FE, et al. 2020. Cold acclimation and freezing tolerance in three Eucalyptus species: a metabolomic and proteomic approach. Plant Physiology and Biochemistry 154:316−327

doi: 10.1016/j.plaphy.2020.05.026

[49]

Liu Y, Jiang Y, Lan J, Zou Y, Gao J. 2014. Comparative transcriptomic analysis of the response to cold acclimation in Eucalyptus dunnii. PLoS One 9:e113091

doi: 10.1371/journal.pone.0113091

[50]

Ramírez F, Ryan DP, Grüning B, Bhardwaj V, Kilpert F, et al. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44:W160−W165

doi: 10.1093/nar/gkw257

[51]

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biology 9:R137

doi: 10.1186/gb-2008-9-9-r137

[52]

Wang T, Ye W, Zhang J, Li H, Zeng W, et al. 2023. Alternative 3'-untranslated regions regulate high-salt tolerance of Spartina alterniflora. Plant Physiology 191:2570−2587

doi: 10.1093/plphys/kiad030

[53]

Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, et al. 2019. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research 47:D309−D314

doi: 10.1093/nar/gky1085

[54]

Xu S, Hu E, Cai Y, Xie Z, Luo X, et al. 2024. Using clusterProfiler to characterize multiomics data. Nature Protocols 19:3292−3320

doi: 10.1038/s41596-024-01020-z

[55]

Heinz S, Benner C, Spann N, Bertolino E, Lin YC, et al. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Molecular Cell 38:576−589

doi: 10.1016/j.molcel.2010.05.004

[56]

Wang FX, Shang GD, Wu LY, Xu ZG, Zhao XY, et al. 2020. Chromatin accessibility dynamics and a hierarchical transcriptional regulatory network structure for plant somatic embryogenesis. Developmental Cell 54:742−757.e8

doi: 10.1016/j.devcel.2020.07.003

[57]

Zhuang H, Lin E, Xie J, Jiang M, Ni F, et al. 2025. InDel variation and contraction of the C-repeat binding factor family contribute to cold sensitivity in Betula fujianensis. The Plant Cell 37:koaf216

doi: 10.1093/plcell/koaf216

[58]

Mei C, Yang J, Mei Q, Jia D, Yan P, et al. 2023. MdNAC104 positively regulates apple cold tolerance via CBF-dependent and CBF-independent pathways. Plant Biotechnology Journal 21:2057−2073

doi: 10.1111/pbi.14112

[59]

Li P, Zheng T, Li L, Liu W, Qiu L, et al. 2023. Integration of chromatin accessibility and gene expression reveals new regulators of cold hardening to enhance freezing tolerance in Prunus mume. Journal of Experimental Botany 74:2173−2187

doi: 10.1093/jxb/erad027

[60]

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 Physiology 33:866−877

doi: 10.1093/treephys/tpt056

[61]

Vyse K, Schaarschmidt S, Erban A, Kopka J, Zuther E. 2022. Specific CBF transcription factors and cold-responsive genes fine-tune the early triggering response after acquisition of cold priming and memory. Physiologia Plantarum 174:e13740

doi: 10.1111/ppl.13740

[62]

Mathieu J, Yant LJ, Mürdter F, Küttner F, Schmid M. 2009. Repression of flowering by the miR172 target SMZ. PLoS Biology 7:e1000148

doi: 10.1371/journal.pbio.1000148

[63]

Dorca-Fornell C, Gregis V, Grandi V, Coupland G, Colombo L, et al. 2011. The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems. The Plant Journal 67:1006−1017

doi: 10.1111/j.1365-313X.2011.04653.x

[64]

Zhang G, Zhao H, Zhang C, Li X, Lyu Y, et al. 2019. TCP7 functions redundantly with several Class I TCPs and regulates endoreplication in Arabidopsis. Journal of Integrative Plant Biology 61:1151−1170

doi: 10.1111/jipb.12749

[65]

Zhang JJ, Xue HW. 2013. OsLEC1/OsHAP3E participates in the determination of meristem identity in both vegetative and reproductive developments of rice. Journal of Integrative Plant Biology 55:232−249

doi: 10.1111/jipb.12025

[66]

Andersen SU, Algreen-Petersen RG, Hoedl M, Jurkiewicz A, Cvitanich C, et al. 2007. The conserved cysteine-rich domain of a tesmin/TSO1-like protein binds zinc in vitro and TSO1 is required for both male and female fertility in Arabidopsis thaliana. Journal of Experimental Botany 58:3657−3670

doi: 10.1093/jxb/erm215

[67]

Feeney M, Frigerio L, Cui Y, Menassa R. 2013. Following vegetative to embryonic cellular changes in leaves of Arabidopsis overexpressing LEAFY COTYLEDON2. Plant Physiology 162:1881−1896

doi: 10.1104/pp.113.220996

[68]

Basile P, Wallace F, Olivaro C, De Palma N, Borsani O, et al. 2025. Cold-induced biochemical changes in leaves of two commercial clones of Eucalyptus. Frontiers in Molecular Biosciences 12:1584132

doi: 10.3389/fmolb.2025.1584132

[69]

Wang J, Liao X, Wu Z, Sane S, Han S, et al. 2025. Genetic control of seasonal meristem arrest in trees. Proceedings of the National Academy of Sciences of the United States of America 122:e2505641122

doi: 10.1073/pnas.2505641122

[70]

Canton M, Forestan C, Marconi G, Carrera E, Bonghi C, et al. 2022. Evidence of chromatin and transcriptional dynamics for cold development in peach flower bud. New Phytologist 236:974−988

doi: 10.1111/nph.18393

[71]

Zhu JK. 2016. Abiotic stress signaling and responses in plants. Cell 167:313−324

doi: 10.1016/j.cell.2016.08.029

[72]

Ma Y, Dai X, Xu Y, Luo W, Zheng X, et al. 2015. COLD1 confers chilling tolerance in rice. Cell 160:1209−1221

doi: 10.1016/j.cell.2015.01.046

[73]

Shibasaki K, Uemura M, Tsurumi S, Rahman A. 2009. Auxin response in Arabidopsis under cold stress: underlying molecular mechanisms. The Plant Cell 21:3823−3838

doi: 10.1105/tpc.109.069906