Abdelraheem A, Esmaeili N, O’Connell M, Zhang J. 2019. Progress and perspective on drought and salt stress tolerance in cotton. Industrial Crops and Products, 130, 118–129.

Aluko O O, Ninkuu V, Liu Z, Qin A, Liu H, Yang J, Hu M, Ma X, Sun X. 2025. Recent advances in cotton transformation and genome editing techniques: The prospects and challenges. Modern Agriculture, 3, e70014.

Bai C, Cao Y, Zhao S, Wu Z, Dai S, Wang H, Fu C. 2023. Generation of CRISPR/Cas9-mediated mutants in Monochasma savatieri using a hairy root system. Industrial Crops and Products, 191, 116008.

Bhaumik S R. 2021. Fluorescence resonance energy transfer in revealing protein-protein interactions in living cells. Emerging Topics in Life Sciences, 5, 49–59.

Cao X, Xie H, Song M, Zhao L, Liu H, Li G, Zhu J K. 2023. Simple method for transformation and gene editing in medicinal plants. Journal of Integrative Plant Biology, 66, 17–19. 

Chattopadhyay T, Roy S, Mitra A, Maiti M K. 2011. Development of a transgenic hairy root system in jute (Corchorus capsularis L.) with gusA reporter gene through Agrobacterium rhizogenes mediated co-transformation. Plant Cell Reports, 30, 485–493.

Chen Y, Fu M, Li H, Wang L, Liu R, Liu Z, Zhang X, Jin S. 2021. High-oleic acid content, nontransgenic allotetraploid cotton (Gossypium hirsutum L.) generated by knockout of GhFAD2 genes with CRISPR/Cas9 system. Plant Biotechnology Journal, 19, 424–426.

Cheng Y, Wang X, Cao L, Ji J, Liu T, Duan K. 2021. Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation for gene functional and gene editing analysis in soybean. Plant Methods, 17, 1–12.

Clough S J, Bent A F. 1998. Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant Journal, 16, 735–743.

Collings D A. 2013. Subcellular localization of transiently expressed fluorescent fusion proteins. Methods in Molecular Biology, 1069, 227–258.

Cui M L, Liu C, Piao C L, Liu C L. 2020. A Stable Agrobacterium rhizogenes-mediated transformation of cotton (Gossypium hirsutum L.) and plant regeneration from transformed hairy root via embryogenesis. Frontiers of Plant Science, 11, 604255.

Dangol S, Singh R, Chen Y, Jwa N S. 2017. Visualization of multicolored in vivo organelle markers for co-localization studies in Oryza sativa. Molecules and Cells, 40, 828–836.

Estrada-Navarrete G, Alvarado-Affantranger X, Olivares J E, Guillén G, Díaz-Camino C, Campos F, Quinto C, Gresshoff P M, Sanchez F. 2007. Fast, efficient and reproducible genetic transformation of Phaseolus spp. by Agrobacterium rhizogenes. Nature Protocols, 2, 1819–1824.

Fan Y L, Zhang X H, Zhong L J, Wang X Y, Jin L S, Lyu S H. 2020. One-step generation of composite soybean plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation. BMC Plant Biology, 20, 208.

Faraz R, Gokhale M, Gothalwa R. 2020. Hairy root culture through Agrobacterium rhizogenes for enhancement of secondary metabolites production in medicinal plants: A review. Journal of Advanced Microbiology, 4, 45–58.

Ferreira L M, Henschel J M, Mendes J, Araujo D J, Ribeiro J E S, Ferreira V, da Cruz O N, Batista D S. 2024. Pre-harvest application of sodium nitroprusside enhances storage root quality in red beet cultivated under normal and drought conditions. Journal of the Science of Food and Agriculture, 104, 9540–9547.

Firoozabady E, Deboer D L, Merlo D J, Halk E L, Amerson L N, Rashka K E, Murray E E. 1987. Transformation of cotton (Gossypium hirsutum L.) by Agrobacterium tumefaciens and regeneration of transgenic plants. Plant Molecular Biology, 10, 105–116.

Frankfater C R, Dowd M K, Triplett B A. 2009. Effect of elicitors on the production of gossypol and methylated gossypol in cotton hairy roots. Plant Cell, Tissue and Organ Culture, 98, 341–349.

Friesen M L, Porter S S, Stark S C, von Wettberg E J, Sachs J L, Martinez-Romero E. 2011. Microbially mediated plant functional traits. Annual Review of Ecology, Evolution and Systematics, 42, 23–46.

Ge X, Xu J, Yang Z, Yang X, Wang Y, Chen Y, Wang P, Li F. 2023. Efficient genotype‐independent cotton genetic transformation and genome editing. Journal of Integrative Plant Biology, 65, 907–917.

Geldner N, Dénervaud-Tendon V, Hyman D L, Mayer U, Stierhof Y D, Chory J. 2009. Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set. Plant Journal, 59, 169–178.

Gelvin S B. 2010. Plant proteins involved in Agrobacterium-mediated genetic transformation. Annual Review of Phytopathology, 48, 45–68.

Gong J, Chen Y, Xu Y, Gu M, Ma H, Hu X, Li X, Jiao C, Sun X. 2024. Tracking organelle activities through efficient and stable root genetic transformation system in woody plants. Horticulture Research, 11, uhad262.

Gu Z, Huang C, Li F, Zhou X. 2014. A versatile system for functional analysis of genes and microRNAs in cotton. Plant Biotechnology Journal, 12, 638–649. 

Gutierrez-Valdes N, Hakkinen S T, Lemasson C, Guillet M, Oksman-Caldentey K M, Ritala A, Cardon F. 2020. Hairy root cultures-A versatile tool with multiple applications. Frontiers of Plant Science, 11, 33.

Hanson A D, Roje S. 2001. One-carbon metabolism in higher plants. Annual Review of Plant Physiology and Plant Molecular Biology, 52, 119–137. 

Huang G, Huang J Q, Chen X Y, Zhu Y X. 2021. Recent advances and future perspectives in cotton research. Annual Review of Plant Biology, 72, 437–462. 

Hwang H H, Yu M, Lai E M. 2017. Agrobacterium-mediated plant transformation: Biology and applications. The Arabidopsis Book, 15, e0186.

Jian B, Hou W, Wu C, Liu B, Liu W, Song S, Bi Y, Han T. 2009. Agrobacterium rhizogenes-mediated transformation of Superroot-derived Lotus corniculatus plants: A valuable tool for functional genomics. BMC Plant Biology, 9, 78. 

Kalbande B B, Patil A S. 2016. Plant tissue culture independent Agrobacterium tumefaciens mediated In-planta transformation strategy for upland cotton (Gossypium hirsutum). Journal, Genetic Engineering & Biotechnology, 14, 9–18. 

Kim H J. 2013. Agrobacterium rhizogenes-induced cotton hairy root culture as an alternative tool for cotton functional genomics. Methods in Molecular Biology, 958, 179–187.

Kokkirala V R, Yonggang P, Abbagani S, Zhu Z, Umate P. 2010. Subcellular localization of proteins of Oryza sativa L. in the model tobacco and tomato plants. Plant Signaling & Behavior, 5, 1336–1341.

Li F, Fan G, Lu C, Xiao G, Zou C, Kohel R J, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy R G, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, et al. 2015. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nature Biotechnology, 33, 524–530.

Li M, Wang H, Zhao X, Feng W, Ding G, Quan W. 2023. Effect of ectomycorrhizal fungi on the drought resistance of Pinus massoniana seedlings. Journal of Fungi, 9, 471.

Limpens E, Ramos J, Franken C, Raz V, Compaan B, Franssen H, Bisseling T, Geurts R. 2004. RNA interference in Agrobacterium rhizogenes-transformed roots of Arabidopsis and Medicago truncatula. Journal of Experimental Botany, 55, 983–992.

Lin J, Wi D, Ly M, Jahan M A, Pullano S, Martirosyan I, Kovinich N. 2023. Soybean hairy root transformation for the analysis of gene function. Journal of Visualized Experiments, 195, e65485.

Lin J S, Lai E M. 2017. Protein-protein interactions: Co-immunoprecipitation. Methods in Molecular Biology, 1615, 211–219. 

Liu L, Yu Z, Xu Y, Guo C, Zhang L, Wu C, Yang G, Huang J, Yan K, Shu H, Zheng C, Zhang S. 2020. Function identification of MdTIR1 in apple root growth benefited from the predicted MdPPI network. Journal of Integrative Plant Biology, 63, 723–739.

Luo C, Shi Y, Xiang Y. 2022. SNAREs regulate vesicle trafficking during root growth and development. Frontiers of Plant Science, 13, 853251. 

Ma H, Meng X, Xu K, Li M, Gmitter Jr F G, Liu N, Gai Y, Huang S, Wang M, Wang M, Wang N, Xu H, Liu J, Sun X, Duan S. 2022. Highly efficient hairy root genetic transformation and applications in citrus. Frontiers of Plant Science, 13, 1039094.

Marion J, Bach L, Bellec Y, Meyer C, Gissot L, Faure J D. 2008. Systematic analysis of protein subcellular localization and interaction using high-throughput transient transformation of Arabidopsis seedlings. Plant Journal, 56, 169–179.

Marjamaa K, Hildén K, Kukkola E, Lehtonen M, Holkeri H, Haapaniemi P, Koutaniemi S, Teeri T H, Fagerstedt K, Lundell T. 2006. Cloning, characterization and localization of three novel class III peroxidases in lignifying xylem of Norway spruce (Picea abies). Plant Molecular Biology, 61, 719–732.

Matsuoka K, Matsumoto S, Hattori T, Machida Y, Nakamura K. 1990. Vacuolar targeting and posttranslational processing of the precursor to the sweet potato tuberous root storage protein in heterologous plant cells. Journal of Biological Chemistry, 265, 19750–19757.

Mei G, Chen A, Wang Y, Li S, Wu M, Hu Y, Liu X, Hou X. 2024. A simple and efficient in planta transformation method based on the active regeneration capacity of plants. Plant Communications, 5, 100822.

Meng D, Yang Q, Dong B, Song Z, Niu L, Wang L, Cao H, Li H, Fu Y. 2019. Development of an efficient root transgenic system for pigeon pea and its application to other important economically plants. Plant Biotechnology Journal, 17, 1804–1813. 

Meng S, Chao S, Xiong M, Cheng L, Sun Y, Wang L, Chen Y, Jane S J, Luo C, Chen J. 2025. CaSun1, a SUN family protein, governs the pathogenicity of Colletotrichum camelliae by recruiting CaAtg8 to promote mitophagy. Horticulture Research, 12, uhaf121.

Millar A H, Carrie C, Pogson B, Whelan J. 2009. Exploring the function-location nexus: Using multiple lines of evidence in defining the subcellular location of plant proteins. The Plant Cell, 21, 1625–1631.

Moreno-Valenzuela O A, Minero-García Y, Brito-Argáez L, Carbajal-Mora E, Echeverría O, Vázquez-Nin G, Loyola-Vargas V M. 2003. Immunocytolocalization of tryptophan decarboxylase in Catharanthus roseus hairy roots. Molecular Biotechnology, 23, 11–18.

Mustafa R, Shafiq M, Mansoor S, Briddon R W, Scheffler B E, Scheffler J, Amin I. 2015. Virus-induced gene silencing in cultivated cotton (Gossypium spp.) using tobacco rattle virus. Molecular Biotechnology, 58, 65–72.

Nakato R, Sakata T. 2021. Methods for ChIP-seq analysis: A practical workflow and advanced applications. Methods, 187, 44–53.

Niu X, Song L, Xiao Y, Ge W. 2017. Drought-tolerant plant growth-promoting rhizobacteria associated with foxtail millet in a semi-arid agroecosystem and their potential in alleviating drought stress. Frontiers in Microbiology, 8, 2580.

Nontachaiyapoom S, Scott P T, Men A E, Kinkema M, Schenk P M, Gresshoff P M. 2007. Promoters of orthologous Glycine max and Lotus japonicus nodulation autoregulation genes interchangeably drive phloem-specific expression in transgenic plants. Molecular Plant-Microbe Interactions, 20, 769–780.

Pendin D, Greotti E, Lefkimmiatis K, Pozzan T. 2017. Exploring cells with targeted biosensors. Journal of General Physiology, 149, 1–36.

Raman V, Rojas C M, Vasudevan B, Dunning K, Kolape J, Oh S, Yun J, Yang L, Li G, Pant B D. 2022. Agrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation. Nature Communications, 13, 2581.

Ron M, Kajala K, Pauluzzi G, Wang D, Reynoso M A, Zumstein K, Garcha J, Winte S, Masson H, Inagaki S, Federici F, Sinha N, Deal R B, Bailey-Serres J, Brady S M. 2014. Hairy root transformation using Agrobacterium rhizogenes as a tool for exploring cell type-specific gene expression and function using tomato as a model. Plant Physiology, 166, 455–469.

Ruan Y L. 2013. Boosting seed development as a new strategy to increase cotton fiber yield and quality. Journal of Integrative Plant Biology, 55, 572–575.

Sarkar S, Ghosh I, Roychowdhury D, Jha S. 2018. The effects of rol genes of Agrobacterium rhizogenes on morphogenesis and secondary metabolite accumulation in medicinal plants. In: Biotechnological Approaches for Medicinal and Aromatic Plants: Conservation, Genetic Improvement and Utilization. pp. 27–51.

Saud S, Wang L. 2022. Mechanism of cotton resistance to abiotic stress, and recent research advances in the osmoregulation related genes. Frontiers of Plant Science, 13, 972635.

Shang X, Zhu L, Duan Y, He Q, Zhao M, Yu Y, Guo W. 2022. An easy and rapid transformation protocol for transient expression in cotton fiber. Frontiers of Plant Science, 13, 837994.

Shangguan X X, Xu B, Yu Z X, Wang L J, Chen X Y. 2008. Promoter of a cotton fibre MYB gene functional in trichomes of Arabidopsis and glandular trichomes of tobacco. Journal of Experimental Botany, 59, 3533–3542.

Shukla A K, Upadhyay S K, Mishra M, Saurabh S, Singh R, Singh H, Thakur N, Rai P, Pandey P, Hans A L, Srivastava S, Rajapure V, Yadav S K, Singh M K, Kumar J, Chandrashekar K, Verma P C, Singh A P, Nair K N, Bhadauria S, et al. 2016. Expression of an insecticidal fern protein in cotton protects against whitefly. Nature Biotechnology, 34, 1046–1051. 

Sohn E J, Kim E S, Zhao M, Kim S J, Kim H, Kim Y W, Lee Y J, Hillmer S, Sohn U, Jiang L, Hwang I. 2003. Rha1, an Arabidopsis Rab5 homolog, plays a critical role in the vacuolar trafficking of soluble cargo proteins. The Plant Cell, 15, 1057–1070.

Tanz S K, Castleden I, Small I D, Millar A H. 2013. Fluorescent protein tagging as a tool to define the subcellular distribution of proteins in plants. Frontiers of Plant Science, 4, 214.

Triplett B A, Moss S C, Bland J M, Dowd M K. 2008. Induction of hairy root cultures from Gossypium hirsutum and Gossypium barbadense to produce gossypol and related compounds. In Vitro Cellular & Developmental Biology-Plant, 44, 508–517.

Tuttle J R, Haigler C H, Robertson D. 2012. Method: Low-cost delivery of the cotton leaf crumple virus-induced gene silencing system. Plant Methods, 8, 27. 

Umbeck P, Johnson G, Barton K, Swain W. 1987. Genetically transformed cotton (Gossypium hirsutum L.) plants. Nature Biotechnology, 5, 263–266.

Unniyampurath U, Pilankatta R, Krishnan M N. 2016. RNA interference in the age of CRISPR: Will CRISPR interfere with RNAi? International Journal of Molecular Sciences, 17, 291.

Verma P C, Trivedi I, Singh H, Shukla A K, Kumar M, Upadhyay S K, Pandey P, Hans A L, Singh P K. 2009. Efficient production of gossypol from hairy root cultures of cotton (Gossypium hirsutum L.). Current Pharmaceutical Biotechnology, 10, 691–700.

Waadt R, Schmidt L K, Lohse M, Hashimoto K, Bock R, Kudla J. 2008. Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. The Plant Journal, 56, 505–516.

Wang H, Zheng Y, Zhou Q, Li Y, Liu T, Hou X. 2024. Fast, simple, efficient Agrobacterium rhizogenes-mediated transformation system to non-heading Chinese cabbage with transgenic roots. Horticultural Plant Journal, 10, 450–460. 

Wang M, Qin Y Y, Wei N N, Xue H Y, Dai W S. 2023. Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation in citrus seeds and its application in gene functional analysis. Frontiers of Plant Science, 14, 1293374. 

Wang X, Deng Y, Gao L, Kong F, Shen G, Duan B, Wang Z, Dai M, Han Z. 2022. Series-temporal transcriptome profiling of cotton reveals the response mechanism of phosphatidylinositol signaling system in the early stage of drought stress. Genomics, 114, 110465.

Wen L, Li W, Parris S, West M, Lawson J, Smathers M, Li Z, Jones D, Jin S, Saski C A. 2020. Transcriptomic profiles of non-embryogenic and embryogenic callus cells in a highly regenerative upland cotton line (Gossypium hirsutum L.). BMC Developmental Biology, 20, 25.

Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. 2023. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. Science China-Life Sciences, 66, 2214–2256.

Wendel J F, Grover C E. 2015. Taxonomy and evolution of the cotton genus, Gossypium. Cotton, 57, 25–44.

Wu A, Shen T, Lu J, Fu X, Yang M, Sun M, Ma L, Lian B, Wu H, Li Y, Yu S, Wei H, Wang H. 2025. GhMYB102 affects cotton fibre elongation and secondary wall thickening by regulating GhIRX10 in cotton. Plant Biotechnology Journal, 23, 1329–1344.

Wu C A, Yang G D, Meng Q W, Zheng C C. 2004. The cotton GhNHX1 gene encoding a novel putative tonoplast Na⁺/H⁺ antiporter plays an important role in salt stress. Plant & Cell Physiology, 45, 600–607. 

Wu Z, Wang P, Chen G. 2024. Untargeted metabolomic analysis of the metabolites in roots of Pugionium cornutum seedlings under drought stress. Functional Plant Biology, 51, FP22190.

Wubben M J, Callahan F E, Triplett B A, Jenkins J N. 2009. Phenotypic and molecular evaluation of cotton hairy roots as a model system for studying nematode resistance. Plant Cell Reports, 28, 1399–1409. 

Xu Q, Fu H, Zhu B, Hussain HA, Zhang K, Tian X, Duan M, Xie X, Wang L. 2021. Potassium improves drought stress tolerance in plants by affecting root morphology, root exudates and microbial diversity. Metabolites, 11, 131.

Xu S, Lai E, Zhao L, Cai Y, Ogutu C, Cherono S, Han Y, Zheng B. 2020. Development of a fast and efficient root transgenic system for functional genomics and genetic engineering in peach. Scientific Reports, 10, 2836.

Yan M, Chai M, Li L, Dong Z, Jin H, Tan M, Ye Z, Yu S, Feng Z. 2024a. Calcium-dependent protein kinase GhCDPK16 exerts a positive regulatory role in enhancing drought tolerance in cotton. International Journal of Molecular Sciences, 25, 8308.

Yan M, Dong Z, Pan T, Li L, Zhou Z, Li W, Ke Z, Feng Z, Yu S. 2024b. Systematical characterization of Rab7 gene family in Gossypium and potential functions of GhRab7B3-A gene in drought tolerance. BMC Genomics, 25, 1023.

Yan M, Li W, Zhou Z, Pan T, Li L, Chai M, Feng Z, Yu S. 2024c Genome-wide identification of the Serine hydroxymethyltransferase gene revealed the function of GhSHMT11s involved in plant growth development and salt stress tolerance in cotton. Industrial Crops and Products, 222, 119687.

Yan M, Yu X, Zhou G, Sun D, Hu Y, Huang C, Zheng Q, Sun N, Wu J, Fu Z, Li L, Feng Z, Yu S. 2022. GhCDPK60 positively regulates drought stress tolerance in both transgenic Arabidopsis and cotton by regulating proline content and ROS level. Frontiers of Plant Science, 13, 1072584.

Yang J, Kim S R, Lee S K, Choi H, Jeon J S, An G. 2015. Alanine aminotransferase 1 (OsAlaAT1) plays an essential role in the regulation of starch storage in rice endosperm. Plant Science, 240, 79–89.

Zhan J, Chu Y, Wang Y, Diao Y, Zhao Y, Liu L, Wei X, Meng Y, Li F, Ge X. 2021. The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton. Plant Biotechnology Journal, 19, 1839–1851.

Zhang L, Yu Y, Zhang M, Rong K, Wu Y, Zhang M, Hu H. 2023. Genome-wide identification of xylan glucuronosyltransferase family in cotton and function characterization of GhGUX5 in regulating Verticillium wilt resistance. International Journal of Biological Macromolecules, 245, 124795.

Zhang M, Hu S, Yi F, Gao Y, Zhu D, Wang Y, Cai Y, Hou D, Lin X, Shen J. 2021. Organelle visualization with multicolored fluorescent markers in bamboo. Frontiers of Plant Science, 12, 658836.

Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski C A, Scheffler B E, Stelly D M, Hulse-Kemp A M, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, et al. 2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology, 33, 531–537.

Zhou L, Wang Y, Wang P, Wang C, Wang J, Wang X, Cheng H. 2022. Highly efficient Agrobacterium rhizogenes-mediated hairy root transformation for gene editing analysis in cotton. Frontiers of Plant Science, 13, 1059404.