[1]

Calderan-Rodrigues MJ, de Barros Dantas LL, Cheavegatti Gianotto A, Caldana C. 2021. Applying molecular phenotyping tools to explore sugarcane carbon potential. Frontiers in Plant Science 12:637166

doi: 10.3389/fpls.2021.637166
[2]

Zhao L, Ran M, Zhang J, Zhao P, Zan F, et al. 2025. Comparative analysis of ratoon-competent and ratoon-deficient sugarcane by hormonal and transcriptome profiling. Agronomy 15:1669

doi: 10.3390/agronomy15071669
[3]

Dlamini NE, Franke AC, Zhou M. 2024. Impact of soil type and harvest season on the ratooning ability of sugarcane varieties. Experimental Agriculture 60:e15

doi: 10.1017/s0014479724000127
[4]

Singh D, Prasad G, Saluja HPS. 2024. Comparative study of ratoon crop and plant crop of sugarcane cultivation. ShodhKosh: Journal of Visual and Performing Arts 5:966−974

doi: 10.29121/shodhkosh.v5.i6.2024.1994
[5]

Ramburan S, Wettergreen T, Berry SD, Shongwe B. 2013. Genetic, environmental and management contributions to ratoon decline in sugarcane. Field Crops Research 146:105−112

doi: 10.1016/j.fcr.2013.03.011
[6]

Qin W, Yang K, Zhao LP, Zhao Y, Zhang J, et al. 2023. Evaluation analysis of sugarcane rooting and its key influencing factors under drought. Sugarcane and Canesugar 52:22−27 (in Chinese)

doi: 10.3969/j.issn.1005-9695.2023.03.005
[7]

Otto R, Altarugio LM, Moretti SML, Tenelli S, Soares JR, et al. 2023. Multisite potassium fertilization effects on sugarcane ratoon yield and economic return in South-Central Brazil. Nutrient Cycling in Agroecosystems 127:393−408

doi: 10.1007/s10705-023-10324-7
[8]

Varala V, Sowjanya B, Devi IS, Prashanth P. 2025. Comparative profitability of plant and ratoon methods of sugarcane cultivation in kamareddy district of telangana, India. Archives of Current Research International 25:818−825

doi: 10.9734/acri/2025/v25i71381
[9]

Botha FC, Marquardt A. 2024. Metabolic control of sugarcane internode elongation and sucrose accumulation. Agronomy 14:1487

doi: 10.3390/agronomy14071487
[10]

Tippayawat A, Jogloy S, Vorasoot N, Songsri P, Kimbeng CA, et al. 2023. Differential physiological responses to different drought durations among a diverse set of sugarcane genotypes. Agronomy 13:2594

doi: 10.3390/agronomy13102594
[11]

Zeng W, He J, Han S, Li R, Meng S, et al. 2025. Mechanisms of ratoon sugarcane nitrogen accumulation and yield formation under intercropping with Fenlong tillage "145" mode. Journal of Soil Science and Plant Nutrition 25:7018−7035

doi: 10.1007/s42729-025-02578-7
[12]

Ball-Coelho B, Sampaio EVSB, Tiessen H, Stewart JWB. 1992. Root dynamics in plant and ratoon crops of sugar cane. Plant and Soil 142:297−305

doi: 10.1007/BF00010975
[13]

Lovera LH, de Souza ZM, Esteban DAA, de Oliveira IN, Farhate CVV, et al. 2021. Sugarcane root system: variation over three cycles under different soil tillage systems and cover crops. Soil and Tillage Research 208:104866

doi: 10.1016/j.still.2020.104866
[14]

Giannelli G, Luche S, Righetti L, Galaverna G, Bonini P, et al. 2025. Unveiling the root–rhizosphere environment of perennial wheat: a metabolomic perspective. BMC Plant Biology 25:942

doi: 10.1186/s12870-025-07008-5
[15]

Zhao D, de Voil P, Sadras VO, Palta JA, Rodriguez D. 2025. The plasticity of root traits and their effects on crop yield and yield stability. Plant and Soil 513:367−382

doi: 10.1007/s11104-024-07185-6
[16]

Liang B, Sun Y, Li Z, Zhang X, Yin B, et al. 2020. Crop load influences growth and hormone changes in the roots of "Red Fuji" apple. Frontiers in Plant Science 11:665

doi: 10.3389/fpls.2020.00665
[17]

Prats-Llinàs MT, García-Tejera O, Marsal J, Girona J. 2019. Water stress during the post-harvest period affects new root formation but not starch concentration and content in Chardonnay grapevine (Vitis vinifera L.) perennial organs. Scientia Horticulturae 249:461−470

doi: 10.1016/j.scienta.2019.02.027
[18]

Zhang Y, Luo J, Peng F, Xiao Y, Du A. 2021. Application of bag-controlled release fertilizer facilitated new root formation, delayed leaf, and root senescence in peach trees and improved nitrogen utilization efficiency. Frontiers in Plant Science 12:627313

doi: 10.3389/fpls.2021.627313
[19]

Zhang S, Zhao F, Yang Z, Yang T, Li Y, et al. 2026. Transcriptome time-course analysis unravels the regulatory networks governing ratooning decline in sugarcane. Frontiers in Plant Science 16:1739058

doi: 10.3389/fpls.2025.1739058
[20]

Islam MS, Corak K, McCord P, Hulse-Kemp AM, Lipka AE. 2023. A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane. Frontiers in Plant Science 14:1205999

doi: 10.3389/fpls.2023.1205999
[21]

Zhang B, Horvath S. 2005. A general framework for weighted gene co-expression network analysis. Statistical Applications in Genetics and Molecular Biology 4:17

doi: 10.2202/1544-6115.1128
[22]

Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9:559

doi: 10.1186/1471-2105-9-559
[23]

Perlo V, Margarido GRA, Botha FC, Furtado A, Hodgson-Kratky K, et al. 2022. Transcriptome changes in the developing sugarcane culm associated with high yield and early-season high sugar content. Theoretical and Applied Genetics 135:1619−1636

doi: 10.1007/s00122-022-04058-3
[24]

Ponsuksili S, Siengdee P, Du Y, Trakooljul N, Murani E, et al. 2015. Identification of common regulators of genes in co-expression networks affecting muscle and meat properties. PLoS One 10:e0123678

doi: 10.1371/journal.pone.0123678
[25]

Tang Y, Li J, Song Q, Cheng Q, Tan Q, et al. 2023. Transcriptome and WGCNA reveal hub genes in sugarcane tiller seedlings in response to drought stress. Scientific Reports 13:12823

doi: 10.1038/s41598-023-40006-x
[26]

Du L, Huang X, Ding L, Wang Z, Tang D, et al. 2023. TaERF87 and TaAKS1 synergistically regulate TaP5CS1/TaP5CR1-mediated proline biosynthesis to enhance drought tolerance in wheat. New Phytologist 237:232−250

doi: 10.1111/nph.18549
[27]

Kaderbek T, Huang L, Yue Y, Wang Z, Lian J, et al. 2025. Identification of the maize drought-resistant gene Zinc-finger Inflorescence Meristem 23 through high-resolution temporal transcriptome analysis. International Journal of Biological Macromolecules 308:142347

doi: 10.1016/j.ijbiomac.2025.142347
[28]

Ku W, Su Y, Peng X, Wang R, Li H, et al. 2024. Comparative transcriptome analysis reveals inhibitory roles of strigolactone in axillary bud outgrowth in ratoon rice. Plants 13:899

doi: 10.3390/plants13060899
[29]

Li A, Wu Q, Yang S, Liu J, Zhao Y, et al. 2024. Dissection of genetic architecture for desirable traits in sugarcane by integrated transcriptomics and metabolomics. International Journal of Biological Macromolecules 280:136009

doi: 10.1016/j.ijbiomac.2024.136009
[30]

Wu Q, Pan YB, Su Y, Zou W, Xu F, et al. 2022. WGCNA identifies a comprehensive and dynamic gene co-expression network that associates with smut resistance in sugarcane. International Journal of Molecular Sciences 23:10770

doi: 10.3390/ijms231810770
[31]

Proost S, Krawczyk A, Mutwil M. 2017. LSTrAP: efficiently combining RNA sequencing data into co-expression networks. BMC Bioinformatics 18:444

doi: 10.1186/s12859-017-1861-z
[32]

Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCᴛ Method. Methods 25:402−408

doi: 10.1006/meth.2001.1262
[33]

Shi Q, Xia Y, Xue N, Wang Q, Tao Q, et al. 2024. Modulation of starch synthesis in Arabidopsis via phytochrome B-mediated light signal transduction. Journal of Integrative Plant Biology 66:973−985

doi: 10.1111/jipb.13630
[34]

Zhang Y, Liu X, Shi Y, Lang L, Tao S, et al. 2024. The B‐box transcription factor BnBBX22. A07 enhances salt stress tolerance by indirectly activating BnWRKY33.C03. Plant, Cell & Environment 47:5424−5442

doi: 10.1111/pce.15119
[35]

Dokladny K, Myers OB, Moseley PL. 2015. Heat shock response and autophagy—cooperation and control. Autophagy 11:200−213

doi: 10.1080/15548627.2015.1009776
[36]

Himanen SV, Puustinen MC, Da Silva AJ, Vihervaara A, Sistonen L. 2022. HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock. Nucleic Acids Research 50:6102−6115

doi: 10.1093/nar/gkac493
[37]

Chaumont F, Tyerman SD. 2014. Aquaporins: highly regulated channels controlling plant water relations. Plant Physiology 164:1600−1618

doi: 10.1104/pp.113.233791
[38]

Gillaspy GE. 2011. The cellular language of myo-inositol signaling. New Phytologist 192:823−839

doi: 10.1111/j.1469-8137.2011.03939.x
[39]

Cheng WH, Endo A, Zhou L, Penney J, Chen HC, et al. 2002. A unique short-chain dehydrogenase/reductase in Arabidopsis glucose signaling and abscisic acid biosynthesis and functions. The Plant Cell 14:2723−2743

doi: 10.1105/tpc.006494
[40]

Garcia ME, Lynch T, Peeters J, Snowden C, Finkelstein R. 2008. A small plant-specific protein family of ABI five binding proteins (AFPs) regulates stress response in germinating Arabidopsis seeds and seedlings. Plant Molecular Biology 67:643−658

doi: 10.1007/s11103-008-9344-2
[41]

Zhang Y, Tian H, Chen D, Zhang H, Sun M, et al. 2023. Cysteine-rich receptor-like protein kinases: emerging regulators of plant stress responses. Trends in Plant Science 28:776−794

doi: 10.1016/j.tplants.2023.03.028
[42]

Dunwell JM, Culham A, Carter CE, Sosa-Aguirre CR, Goodenough PW. 2001. Evolution of functional diversity in the cupin superfamily. Trends in Biochemical Sciences 26:740−746

doi: 10.1016/s0968-0004(01)01981-8
[43]

Hu F, Ye Z, Dong K, Zhang W, Fang D, et al. 2023. Divergent structures and functions of the Cupin proteins in plants. International Journal of Biological Macromolecules 242:124791

doi: 10.1016/j.ijbiomac.2023.124791
[44]

Banerjee J, Das N, Dey P, Maiti MK. 2010. Transgenically expressed rice germin-like protein1 in tobacco causes hyper-accumulation of H2O2 and reinforcement of the cell wall components. Biochemical and Biophysical Research Communications 402:637−643

doi: 10.1016/j.bbrc.2010.10.073
[45]

Govindan G, K, R, S, Alphonse V, Somasundram S. 2024. Role of germin-like proteins (GLPs) in biotic and abiotic stress responses in major crops: a review on plant defense mechanisms and stress tolerance. Plant Molecular Biology Reporter 42:450−468

doi: 10.1007/s11105-024-01434-9
[46]

Rietz S, Bernsdorff FEM, Cai D. 2012. Members of the germin-like protein family in Brassica napus are candidates for the initiation of an oxidative burst that impedes pathogenesis of Sclerotinia sclerotiorum. Journal of Experimental Botany 63:5507−5519

doi: 10.1093/jxb/ers203
[47]

Wu Q, Li A, Zhao P, Xia H, Zhang Y, et al. 2024. Theory to practice: a success in breeding sugarcane variety YZ08–1609 known as the King of Sugar. Frontiers in Plant Science 15:21413108

doi: 10.3389/fpls.2024.1413108
[48]

Jia X, Gong X, Jia X, Li X, Wang Y, et al. 2021. Overexpression of MdATG8i enhances drought tolerance by alleviating oxidative damage and promoting water uptake in transgenic apple. International Journal of Molecular Sciences 22:5517

doi: 10.3390/ijms22115517
[49]

Rodriguez-Izquierdo A, Carrasco D, Valledor L, Bota J, López-Hidalgo C, et al. 2025. The scion-driven transcriptomic changes guide the resilience of grafted near-isohydric grapevines under water deficit. Horticulture Research 12:uhae291

doi: 10.1093/hr/uhae291
[50]

Wang X, Chai X, Gao B, Deng C, Günther CS, et al. 2023. Multi-omics analysis reveals the mechanism of bHLH130 responding to low-nitrogen stress of apple rootstock. Plant Physiology 191:1305−1323

doi: 10.1093/plphys/kiac519
[51]

Kim T, Kang K, Kim SH, An G, Paek NC. 2019. OsWRKY5 promotes rice leaf senescence via senescence-associated NAC and abscisic acid biosynthesis pathway. International Journal of Molecular Sciences 20:4437

doi: 10.3390/ijms20184437
[52]

Lee S, Masclaux-Daubresse C. 2021. Current understanding of eaf senescence in rice. International Journal of Molecular Sciences 22:4515

doi: 10.3390/ijms22094515
[53]

Xie W, Li X, Wang S, Yuan M. 2022. OsWRKY53 promotes abscisic acid accumulation to accelerate leaf senescence and inhibit seed germination by downregulating abscisic acid catabolic genes in rice. Frontiers in Plant Science 12:816156

doi: 10.3389/fpls.2021.816156
[54]

Niu JP, Zhao J, Guo Q, Wang SH, Zhao JZ, et al. 2025. Identification and induced expression analysis of transcription factors NAC in soybean resistance to soybean mosaic virus based on WGCNA. Biotechnology Bulletin 41:95−105 (in Chinese)

doi: 10.13560/j.cnki.biotech.bull.1985.2025-0109
[55]

Jiang L, Wang Y, Li QF, Björn LO, He JX, et al. 2012. Arabidopsis STO/BBX24 negatively regulates UV-B signaling by interacting with COP1 and repressing HY5 transcriptional activity. Cell Research 22:1046−1057

doi: 10.1038/cr.2012.34
[56]

Habibi F, Liu T, Shahid MA, Schaffer B, Sarkhosh A. 2023. Physiological, biochemical, and molecular responses of fruit trees to root zone hypoxia. Environmental and Experimental Botany 206:105179

doi: 10.1016/j.envexpbot.2022.105179
[57]

Li P, Yang R, Liu J, Huang C, Huang G, et al. 2025. Coexpression regulation of new and ancient genes in the dynamic transcriptome landscape of stem and rhizome development in "Bainianzhe" —an ancient Chinese sugarcane variety ratooned for nearly 300 years. Plant, Cell & Environment 48:1621−1642

doi: 10.1111/pce.15232
[58]

Zhou H, Liu L, Zhou J, He A, Wu Z. 2025. Biological agents and plant growth regulator promote rice growth and regenerative capacity. BMC Plant Biology 25:1540

doi: 10.1186/s12870-025-06751-z
[59]

Sabir F, Zarrouk O, Noronha H, Loureiro-Dias MC, Soveral G, et al. 2021. Grapevine aquaporins: diversity, cellular functions, and ecophysiological perspectives. Biochimie 188:61−76

doi: 10.1016/j.biochi.2021.06.004
[60]

Vandeleur RK, Sullivan W, Athman A, Jordans C, Gilliham M, et al. 2014. Rapid shoot-to-root signalling regulates root hydraulic conductance via aquaporins. Plant, Cell & Environment 37:520−538

doi: 10.1111/pce.12175
[61]

Boneh U, Biton I, Schwartz A, Ben-Ari G. 2012. Characterization of the ABA signal transduction pathway in Vitis vinifera. Plant Science 187:89−96

doi: 10.1016/j.plantsci.2012.01.015
[62]

Wong DCJ, Zhang L, Merlin I, Castellarin SD, Gambetta GA. 2018. Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine. BMC Genomics 19:248

doi: 10.1186/s12864-018-4638-5
[63]

He Y, Li Y, Bai Z, Xie M, Zuo R, et al. 2022. Genome-wide identification and functional analysis of cupin_1 domain-containing members involved in the responses to Sclerotinia sclerotiorum and abiotic stress in Brassica napus. Frontiers in Plant Science 13:983786

doi: 10.3389/fpls.2022.983786