Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Abdelraheem, A., Elassbli, H., Zhu, Y., Kuraparthy, V., Hinze, L., Stelly, D., Wedegaertner, T., and Zhang, J. (2020). A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton. Theor Appl Genet 133, 563–577.
Afifi, A., Bary, A.A., Kamel, S.A., and Heikal, I. (1966). Bahtim 110, a new strain of egyptian cotton free from gossypol. Empire Cotton Grow Rev 43, 112–120.
Ahmed, H., Nazir, M.F., Pan, Z., Gong, W., Iqbal, M.S., He, S., and Du, X. (2020a). Genoty** by sequencing revealed QTL hotspots for trichome-based plant defense in Gossypium hirsutum. Genes 11, 368.
Ahmed, M., Iqbal, A., Latif, A., Din, S., Sarwar, M.B., Wang, X., Rao, A. Q., Husnain, T., and Ali Shahid, A. (2020b). Overexpression of a sucrose synthase gene indirectly improves cotton fiber quality through sucrose cleavage. Front Plant Sci 11, 476251.
Ahmed, M., Shahid, A.A., Akhtar, S., Latif, A., Din, S., Fanglu, M., Rao, A.Q., Sarwar, M.B., Husnain, T., and Xuede, W. (2018). Sucrose synthase genes: a way forward for cotton fiber improvement. Biologia 73, 703–713.
Aleman, L., Kitamura, J., Abdel-mageed, H., Lee, J., Sun, Y., Nakajima, M., Ueguchi-Tanaka, M., Matsuoka, M., and Allen, R.D. (2008). Functional analysis of cotton orthologs of GA signal transduction factors GID1 and SLR1. Plant Mol Biol 68, 1–16.
Andres, R.J., Coneva, V., Frank, M.H., Tuttle, J.R., Samayoa, L.F., Han, S. W., Kaur, B., Zhu, L., Fang, H., Bowman, D.T., et al. (2017). Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.). Proc Natl Acad Sci USA 114, E57–E66.
Anzalone, A.V., Koblan, L.W., and Liu, D.R. (2020). Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 38, 824–844.
Bai, W.Q., **ao, Y.H., Zhao, J., Song, S.Q., Hu, L., Zeng, J.Y., Li, X.B., Hou, L., Luo, M., Li, D.M., et al. (2014). Gibberellin overproduction promotes sucrose synthase expression and secondary cell wall deposition in cotton fibers. PLoS ONE 9, e96537.
Bao, Y., Hu, G., Grover, C.E., Conover, J., Yuan, D., and Wendel, J.F. (2019). Unraveling cis and trans regulatory evolution during cotton domestication. Nat Commun 10, 5399.
Baum, J.A., Bogaert, T., Clinton, W., Heck, G.R., Feldmann, P., Ilagan, O., Johnson, S., Plaetinck, G., Munyikwa, T., Pleau, M., et al. (2007). Control of coleopteran insect pests through RNA interference. Nat Biotechnol 25, 1322–1326.
Benjamin Franklin, S., and Arul, R. (2021). Experimental investigation on EGR technique and performance evaluation of diesel engine using diesel blend cotton seed oil as renewable fuel. Mater Today Proc 45, 828–835.
Binyameen, B., Khan, Z., Khan, S.H., Ahmad, A., Munawar, N., Mubarik, M.S., Riaz, H., Ali, Z., Khan, A.A., Qusmani, A.T., et al. (2021). Using multiplexed CRISPR/Cas9 for suppression of cotton leaf curl virus. Int J Mol Sci 22, 12543.
Blázquez, M.A., and Weigel, D. (2000). Integration of floral inductive signals in Arabidopsis. Nature 404, 889–892.
Bohra, A., Kilian, B., Sivasankar, S., Caccamo, M., Mba, C., McCouch, S. R., and Varshney, R.K. (2022). Reap the crop wild relatives for breeding future crops. Trends Biotechnol 40, 412–431.
Bowman, J.L., and Smyth, D.R. (1999). CRABS CLAW, a gene that regulates carpel and nectary development in Arabidopsis, encodes a novel protein with zinc finger and helix-loop-helix domains. Development 126, 2387–2396.
Brill, E., van Thournout, M., White, R.G., Llewellyn, D., Campbell, P.M., Engelen, S., Ruan, Y.L., Arioli, T., and Furbank, R.T. (2011). A novel isoform of sucrose synthase is targeted to the cell wall during secondary cell wall synthesis in cotton fiber. Plant Physiol 157, 40–54.
Cai, Y., Cai, X., Wang, Q., Wang, P., Zhang, Y., Cai, C., Xu, Y., Wang, K., Zhou, Z., Wang, C., et al. (2020). Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis. Plant Biotechnol J 18, 814–828.
Campos, M.L. (2020). A novel role for a phospholipase D in plant immunity. Plant Physiol 183, 33–34.
Cao, J.F., Zhao, B., Huang, C.C., Chen, Z.W., Zhao, T., Liu, H.R., Hu, G.J., Shangguan, X.X., Shan, C.M., Wang, L.J., et al. (2020). The miR319-targeted GhTCP4 promotes the transition from cell elongation to wall thickening in cotton fiber. Mol Plant 13, 1063–1077.
Chan, J. (2012). Microtubule and cellulose microfibril orientation during plant cell and organ growth. J Microsc 247, 23–32.
Chang, L., Fang, L., Zhu, Y., Wu, H., Zhang, Z., Liu, C., Li, X., and Zhang, T. (2016). Insights into interspecific hybridization events in allotetraploid cotton formation from characterization of a gene-regulating leaf shape. Genetics 204, 799–806.
Chatt, E.C., Mahalim, S.N., Mohd-Fadzil, N.A., Roy, R., Klinkenberg, P. M., Horner, H.T., Hampton, M., Carter, C.J., and Nikolau, B.J. (2021). Nectar biosynthesis is conserved among floral and extrafloral nectaries. Plant Physiol 185, 1595–1616.
Chen, B., Zhang, Y., Sun, Z., Liu, Z., Zhang, D., Yang, J., Wang, G., Wu, J., Ke, H., Meng, C., et al. (2021a). Tissue-specific expression of GhnsLTPs identified via GWAS sophisticatedly coordinates disease and insect resistance by regulating metabolic flux redirection in cotton. Plant J 107, 831–846.
Chen, C.Y., Liu, Y.Q., Song, W.M., Chen, D.Y., Chen, F.Y., Chen, X.Y., Chen, Z.W., Ge, S.X., Wang, C.Z., Zhan, S., et al. (2019a). An effector from cotton bollworm oral secretion impairs host plant defense signaling. Proc Natl Acad Sci USA 116, 14331–14338.
Chen, F.Y., Chen, X.Y., and Mao, Y.B. (2019b). Heterogeneous signals in plant-biotic interactions and their applications. Sci China Life Sci 62, 1707–1709.
Chen, P.J., and Liu, D.R. (2022). Prime editing for precise and highly versatile genome manipulation. Nat Rev Genet doi: https://doi.org/10.1038/s41576-022-00541-1.
Chen, R., Deng, Y., Ding, Y., Guo, J., Qiu, J., Wang, B., Wang, C., **e, Y., Zhang, Z., Chen, J., et al. (2022). Rice functional genomics: decades’ efforts and roads ahead. Sci China Life Sci 65, 33–92.
Chen, W., Yao, J., Chu, L., Yuan, Z., Li, Y., and Zhang, Y. (2015). Genetic map** of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. Theor Appl Genet 128, 539–547.
Chen, X., Liu, Y.Q., Wu, M.N., Yan, L., Chen, C.Y., Mu, Y.P., Liu, Y.J., Wang, M.Y., Chen, X.Y., and Mao, Y.B. (2023). A highly accumulated secretory protein from cotton bollworm interacts with basic helix-loop-helix transcription factors to dampen plant defense. New Phytol 237, 265–278.
Chen, W., Yao, J., Li, Y., Zhao, L., Liu, J., Guo, Y., Wang, J., Yuan, L., Liu, Z., Lu, Y., et al. (2019c). Nulliplex-branch, a TERMINAL FLOWER 1 ortholog, controls plant growth habit in cotton. Theor Appl Genet 132, 97–112.
Chen, X., Wang, D.D., Fang, X., Chen, X.Y., and Mao, Y.B. (2019d). Plant specialized metabolism regulated by jasmonate signaling. Plant Cell Physiol 60, 2638–2647.
Chen, X., Lu, X., Shu, N., Wang, S., Wang, J., Wang, D., Guo, L., and Ye, W. (2017). Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system. Sci Rep 7, 44304.
Chen, X. (2020). Extrafloral nectary-the slee** beauty of plant science. J Cotton Res 3, 7.
Chen, X.Y., Chen, Y., Heinstein, P., and Davisson, V.J. (1995). Cloning, expression, and characterization of (+)-δ-cadinene synthase: a catalyst for cotton phytoalexin biosynthesis. Arch Biochem Biophys 324, 255–266.
Chen, Y.H., Wang, N.N., Zhang, J.B., Zheng, Y., and Li, X.B. (2020a). Genome-wide identification of the mitogen-activated protein kinase (MAPK) family in cotton (Gossypium hirsutum) reveals GhMPK6 involved in fiber elongation. Plant Mol Biol 103, 391–407.
Chen, Y., Fu, M., Li, H., Wang, L., Liu, R., Liu, Z., Zhang, X., and **, S. (2021b). High-oleic acid content, nontransgenic allotetraploid cotton (Gossypium hirsutum L.) generated by knockout of GhFAD2 genes with CRISPR/Cas9 system. Plant Biotechnol J 19, 424–426.
Chen, Z.J., and Guan, X. (2011). Auxin boost for cotton. Nat Biotechnol 29, 407–409.
Chen, Z.J., Sreedasyam, A., Ando, A., Song, Q., De Santiago, L.M., Hulse-Kemp, A.M., Ding, M., Ye, W., Kirkbride, R.C., Jenkins, J., et al. (2020b). Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet 52, 525–533.
Cheng, A.X., Lou, Y.G., Mao, Y.B., Lu, S., Wang, L.J., and Chen, X.Y. (2007). Plant terpenoids: biosynthesis and ecological functions. J Integr Plant Biol 49, 179–186.
Cheng, S., Chen, P., Su, Z., Ma, L., Hao, P., Zhang, J., Ma, Q., Liu, G., Liu, J., Wang, H., et al. (2021). High-resolution temporal dynamic transcriptome landscape reveals a GhCAL-mediated flowering regulatory pathway in cotton (Gossypium hirsutum L.). Plant Biotechnol J 19, 153–166.
Clark, G., Torres, J., Finlayson, S., Guan, X., Handley, C., Lee, J., Kays, J. E., Chen, Z.J., and Roux, S.J. (2010). Apyrase (nucleoside triphosphate-diphosphohydrolase) and extracellular nucleotides regulate cotton fiber elongation in cultured ovules. Plant Physiol 152, 1073–1083.
Comadran, J., Kilian, B., Russell, J., Ramsay, L., Stein, N., Ganal, M., Shaw, P., Bayer, M., Thomas, W., Marshall, D., et al. (2012). Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley. Nat Genet 44, 1388–1392.
Conti, L., and Bradley, D. (2007). TERMINAL FLOWER1 is a mobile signal controlling Arabidopsis architecture. Plant Cell 19, 767–778.
Corbesier, L., Vincent, C., Jang, S., Fornara, F., Fan, Q., Searle, I., Giakountis, A., Farrona, S., Gissot, L., Turnbull, C., et al. (2007). FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316, 1030–1033.
Dai, P., Sun, G., Jia, Y., Pan, Z., Tian, Y., Peng, Z., Li, H., He, S., and Du, X. (2020). Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum). Theor Appl Genet 133, 3273–3285.
Deng, F., Tu, L., Tan, J., Li, Y., Nie, Y., and Zhang, X. (2012). GbPDF1 is involved in cotton fiber initiation via the core cis-element HDZIP2ATATHB2. Plant Physiol 158, 890–904.
Deng, S., Wei, T., Tan, K., Hu, M., Li, F., Zhai, Y., Ye, S., **ao, Y., Hou, L., Pei, Y., et al. (2016). Phytosterol content and the campesterol: sitosterol ratio influence cotton fiber development: role of phytosterols in cell elongation. Sci China Life Sci 59, 183–193.
Diao, Y., Zhan, J., Zhao, Y., Liu, L., Liu, P., Wei, X., Ding, Y., Sajjad, M., Hu, W., Wang, P., et al. (2019). GhTIE1 regulates branching through modulating the transcriptional activity of TCPs in cotton and Arabidopsis. Front Plant Sci 10, 1348.
Ding, J., Wu, S., Cai, C.P., and Guo, W.Z. (2015). Genome-wide identification of lysophosphatidic acid acyltransferase gene family and their expression analysis in cotton. Acta Agron Sin 41, 378.
Ding, M., Cao, Y., He, S., Sun, J., Dai, H., Zhang, H., Sun, C., Jiang, Y., Paterson, A.H., and Rong, J. (2020). GaHD1, a candidate gene for the Gossypium arboreum SMA-4 mutant, promotes trichome and fiber initiation by cellular H2O2 and Ca2+ signals. Plant Mol Biol 103, 409–423.
Dixit, G., Srivastava, A., Rai, K.M., Dubey, R.S., Srivastava, R., and Verma, P.C. (2020). Distinct defensive activity of phenolics and phenylpropanoid pathway genes in different cotton varieties toward chewing pests. Plant Signal Behav 15, 1747689.
Dong, H.Z., Zhang, Y.J., Zhang, D.M., Dai, J.L., and Zhang, W. (2018). New grouped harvesting-based population structures of cotton (in Chinese). Sci Agric Sin 51, 4615–4624.
Dong, J., Yin, M.H., Yang, F., Zhao, J., Qin, S., Hou, L., Luo, M., Pei, Y., and **ao, Y.H. (2009). Cloning and expression profile of gibberellin insensitive dwarf GID1 homologous genes from cotton. Acta Agron Sin 35, 1822–1830.
Doroshkov, A.V., Konstantinov, D.K., Afonnikov, D.A., and Gunbin, K.V. (2019). The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development. BMC Plant Biol 19, 53.
Dowd, M.K., McCarty Jr., J.C., Shockey, J., and Jenkins, J.N. (2020). Registration of four Upland cotton germplasm lines with elevated levels of seed oil oleic acid. J Plant regist 14, 64–71.
Du, X., Huang, G., He, S., Yang, Z., Sun, G., Ma, X., Li, N., Zhang, X., Sun, J., Liu, M., et al. (2018). Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nat Genet 50, 796–802.
Duman, Z., Eliyahu, A., Abu-Abied, M., and Sadot, E. (2020). The contribution of cell wall remodeling and signaling to lateral organs formation. Israel J Plant Sci 67, 110–127.
Effenberger, I., Harport, M., Pfannstiel, J., Klaiber, I., and Schaller, A. (2017). Expression in Pichia pastoris and characterization of two novel dirigent proteins for atropselective formation of gossypol. Appl Microbiol Biotechnol 101, 2021–2032.
Fang, L., Wang, Q., Hu, Y., Jia, Y., Chen, J., Liu, B., Zhang, Z., Guan, X., Chen, S., Zhou, B., et al. (2017). Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits. Nat Genet 49, 1089–1098.
Feng, H., Li, X., Chen, H., Deng, J., Zhang, C., Liu, J., Wang, T., Zhang, X., and Dong, J. (2018). GhHUB2, a ubiquitin ligase, is involved in cotton fiber development via the ubiquitin-26S proteasome pathway. J Exp Bot 69, 5059–5075.
Feng, H., Li, Y., Wang, S., Zhang, L., Liu, Y., Xue, F., Sun, Y., Wang, Y., and Sun, J. (2014). Molecular analysis of proanthocyanidins related to pigmentation in brown cotton fibre (Gossypium hirsutum L.). J Exp Bot 65, 5759–5769.
Foston, M. (2014). Advances in solid-state NMR of cellulose. Curr Opin Biotechnol 27, 176–184.
Gao, F., Zhang, B.S., Zhao, J.H., Huang, J.F., Jia, P.S., Wang, S., Zhang, J., Zhou, J.M., and Guo, H.S. (2019a). Deacetylation of chitin oligomers increases virulence in soil-borne fungal pathogens. Nat Plants 5, 1167–1176.
Gao, J., Shen, L., Yuan, J., Zheng, H., Su, Q., Yang, W., Zhang, L., Nnaemeka, V.E., Sun, J., Ke, L., et al. (2019b). Functional analysis of GhCHS, GhANR and GhLAR in colored fiber formation of Gossypium hirsutum L. BMC Plant Biol 19, 455.
Gao, L., Chen, W., Xu, X., Zhang, J., Singh, T.K., Liu, S., Zhang, D., Tian, L., White, A., Shrestha, P., et al. (2020a). Engineering trienoic fatty acids into cottonseed oil improves low-temperature seed germination, plant photosynthesis and cotton fiber quality. Plant Cell Physiol 61, 1335–1347.
Gao, W., Long, L., Tian, X., Xu, F., Liu, J., Singh, P.K., Botella, J.R., and Song, C. (2017). Genome editing in cotton with the CRISPR/Cas9 system. Front Plant Sci 8, 1364.
Gao, W., Xu, F.C., Long, L., Li, Y., Zhang, J.L., Chong, L., Botella, J.R., and Song, C.P. (2020b). The gland localized CGP1 controls gland pigmentation and gossypol accumulation in cotton. Plant Biotechnol J 18, 1573–1584.
Gao, W., Zhu, X., Ding, L., Xu, B., Gao, Y., Cheng, Y., Dai, F., Liu, B., Si, Z., Fang, L., et al. (2022). Development of the engineered “glanded plant and glandless seed” cotton. Food Chem Mol Sci 5, 100130.
Gong, J., Peng, Y., Yu, J., Pei, W., Zhang, Z., Fan, D., Liu, L., **ao, X., Liu, R., Lu, Q., et al. (2022). Linkage and association analyses reveal that hub genes in energy-flow and lipid biosynthesis pathways form a cluster in Upland cotton. Comput Struct Biotechnol J 20, 1841–1859.
Gong, S.Y., Huang, G.Q., Sun, X., Qin, L.X., Li, Y., Zhou, L., and Li, X.B. (2014). Cotton KNL1, encoding a class II KNOX transcription factor, is involved in regulation of fibre development. J Exp Bot 65, 4133–4147.
Gotmare, V., Singh, P., Mayee, C.D., Deshpande, V., and Bhagat, C. (2004). Genetic variability for seed oil content and seed index in some wild species and perennial races of cotton. Plant Breeding 123, 207–208.
Gou, J.Y., Wang, L.J., Chen, S.P., Hu, W.L., and Chen, X.Y. (2007). Gene expression and metabolite profiles of cotton fiber during cell elongation and secondary cell wall synthesis. Cell Res 17, 422–434.
Grover, C.E., Arick II, M.A., Conover, J.L., Thrash, A., Hu, G., Sanders, W. S., Hsu, C.Y., Naqvi, R.Z., Farooq, M., Li, X., et al. (2017). Comparative genomics of an unusual biogeographic disjunction in the cotton tribe (Gossypieae) yields insights into genome downsizing. Genome Biol Evol 9, 3328–3344.
Grover, C.E., Pan, M., Yuan, D., Arick, M.A., Hu, G., Brase, L., Stelly, D. M., Lu, Z., Schmitz, R.J., Peterson, D.G., et al. (2020). The Gossypium longicalyx genome as a resource for cotton breeding and evolution. G3 10, 1457–1467.
Grover, C.E., Yuan, D., Arick, M.A., Miller, E.R., Hu, G., Peterson, D.G., Wendel, J.F., and Udall, J.A. (2021). The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. G3 11, jkab319.
Guan, X.Y., Li, Q.J., Shan, C.M., Wang, S., Mao, Y.B., Wang, L.J., and Chen, X.Y. (2008). The HD-Zip IV gene GaHOX1 from cotton is a functional homologue of the Arabidopsis GLABRA2. Physiol Plant 134, 174–182.
Gul, A., Hussain, G., Iqbal, A., Rao, A.Q., Din, S., Yasmeen, A., Shahid, N., Ahad, A., Latif, A., Azam, S., et al. (2020). Constitutive expression of Asparaginase in Gossypium hirsutum triggers insecticidal activity against Bemisia tabaci. Sci Rep 10, 8958.
Guo, D., Hao, C., Hou, J., Zhao, G., Shan, W., Guo, H., Wang, C., and Guo, X. (2022a). The protein phosphatase GhAP2C1 interacts together with GhMPK4 to synergistically regulate the immune response to Fusarium oxysporum in cotton. Int J Mol Sci 23, 2014.
Guo, Y., Chen, F., Luo, J., Qiao, M., Zeng, W., Li, J., and Xu, W. (2022b). The DUF288 domain containing proteins GhSTLs participate in cotton fiber cellulose synthesis and impact on fiber elongation. Plant Sci 316, 111168.
Haas, K.T., Wightman, R., Meyerowitz, E.M., and Peaucelle, A. (2020). Pectin homogalacturonan nanofilament expansion drives morphogenesis in plant epidermal cells. Science 367, 1003–1007.
Haigler, C.H., Betancur, L., Stiff, M.R., and Tuttle, J.R. (2012). Cotton fiber: a powerful single-cell model for cell wall and cellulose research. Front Plant Sci 3, 104.
Hammond, D. (1941). The expression of genes for leaf shape in Gossypium hirsutum L. and Gossypium arboreum L. I. The expression of genes for leaf shape in Gossypium hirsutum L. Am J Bot 28, 124–138.
Han, J., Pan, Y., Wang, X., Zhang, Y., and Ma, Z. (2016). Antisense expression of Gossypium barbadense UGD6 in Arabidopsis thaliana significantly alters cell wall composition. Sci China Life Sci 59, 213–218.
Han, J., Lopez-Arredondo, D., Yu, G., Wang, Y., Wang, B., Wall, S.B., Zhang, X., Fang, H., Barragán-Rosillo, A.C., Pan, X., et al. (2022). Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton. Proc Natl Acad Sci USA 119, e2209743119.
Han, L.B., Li, Y.B., Wang, F.X., Wang, W.Y., Liu, J., Wu, J.H., Zhong, N. Q., Wu, S.J., Jiao, G.L., Wang, H.Y., et al. (2019). The cotton apoplastic protein CRR1 stabilizes chitinase 28 to facilitate defense against the fungal pathogen Verticillium dahliae. Plant Cell 31, 520–536.
Han, L.B., Li, Y.B., Wang, H.Y., Wu, X.M., Li, C.L., Luo, M., Wu, S.J., Kong, Z.S., Pei, Y., Jiao, G.L., et al. (2013). The dual functions of WLIM1a in cell elongation and secondary wall formation in develo** cotton fibers. Plant Cell 25, 4421–4438.
Han, X., Xu, X., Fang, D.D., Zhang, T., and Guo, W. (2012). Cloning and expression analysis of novel Aux/IAA family genes in Gossypium hirsutum. Gene 503, 83–91.
Harmer, S., Orford, S., and Timmis, J. (2002). Characterisation of six α-expansin genes in Gossypium hirsutum (upland cotton). Mol Gen Genomics 268, 1–9.
Hawkins, J.S., Proulx, S.R., Rapp, R.A., and Wendel, J.F. (2009). Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc Natl Acad Sci USA 106, 17811–17816.
He, P., Zhang, Y., Li, H., Fu, X., Shang, H., Zou, C., Friml, J., and **ao, G. (2021a). GhARF16-1 modulates leaf development by transcriptionally regulating the GhKNOX2-1 gene in cotton. Plant Biotechnol J 19, 548–562.
He, S., Sun, G., Geng, X., Gong, W., Dai, P., Jia, Y., Shi, W., Pan, Z., Wang, J., Wang, L., et al. (2021b). The genomic basis of geographic differentiation and fiber improvement in cultivated cotton. Nat Genet 53, 916–924.
He, X., Wang, T., Xu, Z., Liu, N., Wang, L., Hu, Q., Luo, X., Zhang, X., and Zhu, L. (2018). The cotton HD-Zip transcription factor GhHB12 regulates flowering time and plant architecture via the GhmiR157-GhSPL pathway. Commun Biol 1, 1–8.
He, Y. (2009). Control of the transition to flowering by chromatin modifications. Mol Plant 2, 554–564.
He, Y.Z., Wang, Y.M., Yin, T.Y., Fiallo-Olivé, E., Liu, Y.Q., Hanley-Bowdoin, L., and Wang, X.W. (2020). A plant DNA virus replicates in the salivary glands of its insect vector via recruitment of host DNA synthesis machinery. Proc Natl Acad Sci USA 117, 16928–16937.
Heil, M. (2011). Nectar: generation, regulation and ecological functions. Trends Plant Sci 16, 191–200.
Heinstein, P.F., Smith, F.H., and Tove, S.B. (1962). Biosynthesis of C14-labeled gossypol. J Biol Chem 237, 2643–2646.
Hernandez-Gomez, M.C., Runavot, J.L., Guo, X., Bourot, S., Benians, T.A. S., Willats, W.G.T., Meulewaeter, F., and Knox, J.P. (2015). Heteromannan and heteroxylan cell wall polysaccharides display different dynamics during the elongation and secondary cell wall deposition phases of cotton fiber cell development. Plant Cell Physiol 56, 1786–1797.
Hu, G., Hao, M., Wang, L., Liu, J., Zhang, Z., Tang, Y., Peng, Q., Yang, Z., and Wu, J. (2020a). The cotton miR477-CBP60A module participates in plant defense against Verticillium dahlia. Mol Plant Microbe Interact 33, 624–636.
Hu, H., Zhang, R., Dong, S., Li, Y., Fan, C., Wang, Y., **a, T., Chen, P., Wang, L., Feng, S., et al. (2018). AtCSLD3 and GhCSLD3 mediate root growth and cell elongation downstream of the ethylene response pathway in Arabidopsis. J Exp Bot 69, 1065–1080.
Hu, H., Zhang, R., Tang, Y., Peng, C., Wu, L., Feng, S., Chen, P., Wang, Y., Du, X., and Peng, L. (2019a). Cotton CSLD3 restores cell elongation and cell wall integrity mainly by enhancing primary cellulose production in the Arabidopsis cesa6 mutant. Plant Mol Biol 101, 389–401.
Hu, H., He, X., Tu, L., Zhu, L., Zhu, S., Ge, Z., and Zhang, X. (2016). GhJAZ2 negatively regulates cotton fiber initiation by interacting with the R2R3-MYB transcription factor GhMYB25-like. Plant J 88, 921–935.
Hu, L., Pan, X., Wang, X., Hu, Q., Wang, X., Zhang, H., Xue, Q., and Song, M. (2021). Cotton photosynthetic productivity enhancement through uniform row-spacing with optimal plant density in **njiang, China. Crop Sci 61, 2745–2758.
Hu, W., Qin, W., **, Y., Wang, P., Yan, Q., Li, F., and Yang, Z. (2020b). Genetic and evolution analysis of extrafloral nectary in cotton. Plant Biotechnol J 18, 2081–2095.
Hu, Y., Chen, J., Fang, L., Zhang, Z., Ma, W., Niu, Y., Ju, L., Deng, J., Zhao, T., Lian, J., et al. (2019b). Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nat Genet 51, 739–748.
Huang, G.Q., Gong, S.Y., Xu, W.L., Li, W., Li, P., Zhang, C.J., Li, D.D., Zheng, Y., Li, F.G., and Li, X.B. (2013a). A fasciclin-like arabinogalactan protein, GhFLA1, is involved in fiber initiation and elongation of cotton. Plant Physiol 161, 1278–1290.
Huang, G., Huang, J.Q., Chen, X.Y., and Zhu, Y.X. (2021a). Recent advances and future perspectives in cotton research. Annu Rev Plant Biol 72, 437–462.
Huang, G., Wu, Z., Percy, R.G., Bai, M., Li, Y., Frelichowski, J.E., Hu, J., Wang, K., Yu, J.Z., and Zhu, Y. (2020a). Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nat Genet 52, 516–524.
Huang, G., and Zhu, Y.X. (2019). Plant polyploidy and evolution. J Integr Plant Biol 61, 4–6.
Huang, G., and Zhu, Y.X. (2021). Breeding cotton with superior fiber quality: identification and utilization of multiple elite loci and exotic genetic resources. Sci China Life Sci 64, 1197–1198.
Huang, G.Q., Xu, W.L., Gong, S.Y., Li, B., Wang, X.L., Xu, D., and Li, X. B. (2008a). Characterization of 19 novel cotton FLA genes and their expression profiling in fiber development and in response to phytohormones and salt stress. Physiol Plant 134, 348–359.
Huang, J., Chen, F., Guo, Y., Gan, X., Yang, M., Zeng, W., Persson, S., Li, J., and Xu, W. (2021b). GhMYB7 promotes secondary wall cellulose deposition in cotton fibres by regulating GhCesA gene expression through three distinct cis-elements. New Phytol 232, 1718–1737.
Huang, J., Guo, Y., Sun, Q., Zeng, W., Li, J., Li, X., and Xu, W. (2019). Genome-wide identification of R2R3-MYB transcription factors regulating secondary cell wall thickening in cotton fiber development. Plant Cell Physiol 60, 687–701.
Huang, J.Q., Lin, J.L., Guo, X.X., Tian, X., Tian, Y., Shangguan, X.X., Wang, L.J., Fang, X., and Chen, X.Y. (2020b). RES transformation for biosynthesis and detoxification. Sci China Life Sci 63, 1297–1302.
Huang, Q.S., Wang, H.Y., Gao, P., Wang, G.Y., and **a, G.X. (2008b). Cloning and characterization of a calcium dependent protein kinase gene associated with cotton fiber development. Plant Cell Rep 27, 1869–1875.
Huang, X., Tian, X., Pei, L., Luo, X., Zhang, Y., Zhang, X., Zhang, X., Zhu, L., and Wang, M. (2022). Multi-omics map** of chromatin interaction resolves the fine hierarchy of 3D genome in allotetraploid cotton. Plant Biotechnol J 20, 1639–1641.
Huang, X.Z., Chen, J.Y., **ao, H.J., **ao, Y.T., Wu, J., Wu, J.X., Zhou, J.J., Zhang, Y.J., and Guo, Y.Y. (2015). Dynamic transcriptome analysis and volatile profiling of Gossypium hirsutum in response to the cotton bollworm Helicoverpa armigera. Sci Rep 5, 11867.
Huang, Y., Deng, T., and Zuo, K. (2013b). Cotton annexin proteins participate in the establishment of fiber cell elongation scaffold. Plant Signal Behav 8, e25601.
Huang, Y., Wang, J., Zhang, L., and Zuo, K. (2013c). A cotton annexin protein AnxGb6 regulates fiber elongation through its interaction with Actin 1. PLoS ONE 8, e66160.
Humphries, J.A., Walker, A.R., Timmis, J.N., and Orford, S.J. (2005). Two WD-repeat genes from cotton are functional homologues of the Arabidopsis thalianaTRANSPARENT TESTA GLABRA1 (TTG1) gene. Plant Mol Biol 57, 67–81.
Janga, M.R., Campbell, L.A.M., and Rathore, K.S. (2017). CRISPR/Cas9-mediated targeted mutagenesis in Upland cotton (Gossypium hirsutum L.). Plant Mol Biol 94, 349–360.
Janga, M.R., Pandeya, D., Campbell, L.A.M., Konganti, K., Villafuerte, S. T., Puckhaber, L., Pepper, A., Stipanovic, R.D., Scheffler, J.A., and Rathore, K.S. (2019). Genes regulating gland development in the cotton plant. Plant Biotechnol J 17, 1142–1153.
Ji, G., Liang, C., Cai, Y., Pan, Z., Meng, Z., Li, Y., Jia, Y., Miao, Y., Pei, X., Gong, W., et al. (2021). A copy number variant at the HPDA-D12 locus confers compact plant architecture in cotton. New Phytol 229, 2091–2103.
Jia, Q., Liu, N., **e, K., Dai, Y., Han, S., Zhao, X., Qian, L., Wang, Y., Zhao, J., Gorovits, R., et al. (2016). CLCuMuB betaC1 subverts ubiquitination by interacting with NbSKP1s to enhance geminivirus infection in Nicotiana benthamiana. PLoS Pathog 12, e1005668.
Jiang, Y., Guo, W., Zhu, H., Ruan, Y.L., and Zhang, T. (2012). Overexpression of GhSusA1 increases plant biomass and improves cotton fiber yield and quality. Plant Biotechnol J 10, 301–312.
**, X., Li, Q., **ao, G., and Zhu, Y.X. (2013). Using genome-referenced expressed sequence tag assembly to analyze the origin and expression patterns of Gossypium hirsutum transcripts. J Integr Plant Biol 55, 576–585.
Johnson, K.L. (2020). From fuzz to fiber: identification of genes involved in cotton fiber elongation. Plant Physiol 183, 23–24.
Ju, F., Liu, S., Zhang, S., Ma, H., Chen, J., Ge, C., Shen, Q., Zhang, X., Zhao, X., Zhang, Y., et al. (2019). Transcriptome analysis and identification of genes associated with fruiting branch internode elongation in Upland cotton. BMC Plant Biol 19, 1–6.
Kim, H.J., and Triplett, B.A. (2001). Cotton fiber growth in planta and in vitro. Models for plant cell elongation and cell wall biogenesis. Plant Physiol 127, 1361–1366.
Kim, H.J., and Triplett, B.A. (2004). Characterization of GhRac1 GTPase expressed in develo** cotton (Gossypium hirsutum L.) fibers. Biochim Biophys Acta 1679, 214–221.
Kim, H.J., Triplett, B.A., Zhang, H.B., Lee, M.K., Hinchliffe, D.J., Li, P., and Fang, D.D. (2012). Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum L.). Gene 494, 181–189.
Kohel, R.J. (1978). Survey of Gossypium hirsutum L. Germplasm Collections for Seed-Oil Percentage and Seed Characteristics. London: Agricultural Research Service Publication.
Konukan, D., Yilmaztekin, M., Mert, M., Gener, O., and Dergisi, K.J.T.B. (2017). Tarm bilimleri dergisi physico-chemical characteristic and fatty acids compositions of cottonseed oils. Tarim Bilimleri Dergisi 23.
Krakhmalev, V.A., and Paiziev, A.A. (2006). Spiral structures of cotton fiber. Cellulose 13, 45–52.
Kram, B.W., and Carter, C.J. (2009). Arabidopsis thaliana as a model for functional nectary analysis. Sex Plant Reprod 22, 235–246.
Kumar, V., Singh, B., Singh, S.K., Rai, K.M., Singh, S.P., Sable, A., Pant, P., Saxena, G., and Sawant, S.V. (2018). Role of GhHDA5 in H3K9 deacetylation and fiber initiation in Gossypium hirsutum. Plant J 95, 1069–1083.
Lee, J., Burns, T.H., Light, G., Sun, Y., Fokar, M., Kasukabe, Y., Fujisawa, K., Maekawa, Y., and Allen, R.D. (2010). Xyloglucan endotransglycosylase/hydrolase genes in cotton and their role in fiber elongation. Planta 232, 1191–1205.
Lam, E. (2018). Mixing genomes alters nuclear architecture. Nat Plants 4, 65–66.
Lee, K.H., Du, Q., Zhuo, C., Qi, L., and Wang, H. (2019). LBD29-involved auxin signaling represses nac master regulators and fiber wall biosynthesis. Plant Physiol 181, 595–608.
Li, A., **a, T., Xu, W., Chen, T., Li, X., Fan, J., Wang, R., Feng, S., Wang, Y., Wang, B., et al. (2013a). An integrative analysis of four CESA isoforms specific for fiber cellulose production between Gossypium hirsutum and Gossypium barbadense. Planta 237, 1585–1597.
Li, B., Fu, C., Zhou, J., Hui, F., Wang, Q., Wang, F., Wang, G., Xu, Z., Che, L., Yuan, D., et al. (2022a). Highly efficient genome editing using Geminivirus-Based CRISPR/Cas9 system in cotton plant. Cells 11, 2902.
Li, B., Li, D.D., Zhang, J., **a, H., Wang, X.L., Li, Y., and Li, X.B. (2013b). Cotton AnnGh3 encoding an annexin protein is preferentially expressed in fibers and promotes initiation and elongation of leaf trichomes in transgenic Arabidopsis. J Integr Plant Biol 55, 902–916.
Li, B., Rui, H., Li, Y., Wang, Q., Alariqi, M., Qin, L., Sun, L., Ding, X., Wang, F., Zou, J., et al. (2019a). Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnol J 17, 1862–1864.
Li, B., Zhang, L., **, J., Hou, L., Fu, X., Pei, Y., and Zhang, M. (2022b). An unexpected regulatory sequence from Rho-related GTPase6 confers fiber-specific expression in Upland cotton. Int J Mol Sci 23, 1087.
Li, C., He, Q., Zhang, F., Yu, J., Li, C., Zhao, T., Zhang, Y., **e, Q., Su, B., Mei, L., et al. (2019b). Melatonin enhances cotton immunity to Verticillium wilt via manipulating lignin and gossypol biosynthesis. Plant J 100, 784–800.
Li, C., Unver, T., and Zhang, B. (2017a). A high-efficiency CRISPR/Cas9 system for targeted mutagenesis in cotton (Gossypium hirsutum L.). Sci Rep 7, 43902.
Li, C., Wang, X., Dong, N., Zhao, H., **a, Z., Wang, R., Converse, R.L., and Wang, Q. (2013c). QTL analysis for early-maturing traits in cotton using two upland cotton (Gossypium hirsutum L.) crosses. Breed Sci 63, 154–163.
Li, C., Wang, Y., Ai, N., Li, Y., and Song, J. (2018a). A genome-wide association study of early-maturation traits in Upland cotton based on the CottonSNP80K array. J Integr Plant Biol 60, 970–985.
Li, C., Zhang, Y., Zhang, K., Guo, D., Cui, B., Wang, X., and Huang, X. (2015a). Promoting flowering, lateral shoot outgrowth, leaf development, and flower abscission in tobacco plants overexpressing cotton FLOWERING LOCUS T (FT)-like gene GhFT1. Front Plant Sci 6.
Li, D.D., Ruan, X.M., Zhang, J., Wu, Y.J., Wang, X.L., and Li, X.B. (2013d). Cotton plasma membrane intrinsic protein 2s (PIP2s) selectively interact to regulate their water channel activities and are required for fibre development. New Phytol 199, 695–707.
Li, F., Fan, G., Lu, C., **ao, G., Zou, C., Kohel, R.J., Ma, Z., Shang, H., Ma, X., Wu, J., et al. (2015b). Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33, 524–530.
Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G., Li, Q., Ma, Z., Lu, C., Zou, C., et al. (2014a). Genome sequence of the cultivated cotton Gossypium arboreum. Nat Genet 46, 567–572.
Li, H.B., Qin, Y.M., Pang, Y., Song, W.Q., Mei, W.Q., and Zhu, Y.X. (2007). A cotton ascorbate peroxidase is involved in hydrogen peroxide homeostasis during fibre cell development. New Phytol 175, 462–471.
Li, I.X., **ao, Y.H., Luo, M., Hou, L., Li, D.M., Luo, X.Y., and Pei, Y. (2005a). Cloning and expression analysis of two Rac genes from cotton (Gossypium hirsutum L.) (in Chinese). Acta Genet Sin 32, 72–78.
Li, J., Fan, S.L., Song, M.Z., Pang, C.Y., Wei, H.L., Li, W., Ma, J., Wei, J. H., **g, J., and Yu, S.X. (2013e). Cloning and characterization of a FLO/LFY ortholog in Gossypium hirsutum L. Plant Cell Rep 32, 1675–1686.
Li, J., Zhu, L., Hull, J.J., Liang, S., Daniell, H., **, S., and Zhang, X. (2016a). Transcriptome analysis reveals a comprehensive insect resistance response mechanism in cotton to infestation by the phloem feeding insect Bemisia tabaci (whitefly). Plant Biotechnol J 14, 1956–1975.
Li, J., Hull, J.J., Liang, S., Wang, Q., Chen, L., Zhang, Q., Wang, M., Mansoor, S., Zhang, X., and **, S. (2019c). Genome-wide analysis of cotton miRNAs during whitefly infestation offers new insights into plant-herbivore interaction. Int J Mol Sci 20, 5357.
Li, J., Manghwar, H., Sun, L., Wang, P., Wang, G., Sheng, H., Zhang, J., Liu, H., Qin, L., Rui, H., et al. (2019d). Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants. Plant Biotechnol J 17, 858–868.
Li, J., Wang, M., Li, Y., Zhang, Q., Lindsey, K., Daniell, H., **, S., and Zhang, X. (2019e). Multi-omics analyses reveal epigenomics basis for cotton somatic embryogenesis through successive regeneration acclimation process. Plant Biotechnol J 17, 435–450.
Li, J., Yuan, D., Wang, P., Wang, Q., Sun, M., Liu, Z., Si, H., Xu, Z., Ma, Y., Zhang, B., et al. (2021a). Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biol 22, 119.
Li, L., Huang, J., Qin, L., Huang, Y., Zeng, W., Rao, Y., Li, J., Li, X., and Xu, W. (2014b). Two cotton fiber-associated glycosyltransferases, GhGT43A1 and GhGT43C1, function in hemicellulose glucuronoxylan biosynthesis during plant development. Physiol Plant 152, 367–379.
Li, L., Zhang, C., Huang, J., Liu, Q., Wei, H., Wang, H., Liu, G., Gu, L., and Yu, S. (2021b). Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.). Plant Biotechnol J 19, 109–123.
Li, P., Wang, M., Lu, Q., Ge, Q., Rashid, M.H., Liu, A., Gong, J., Shang, H., Gong, W., Li, J., et al. (2017b). Comparative transcriptome analysis of cotton fiber development of Upland cotton (Gossypium hirsutum) and chromosome segment substitution lines from G. hirsutum × G. barbadense. BMC Genomics 18, 705.
Li, Q., **, X., and Zhu, Y.X. (2012). Identification and analyses of miRNA genes in allotetraploid Gossypium hirsutum fiber cells based on the sequenced diploid G. raimondii genome. J Genet Genomics 39, 351–360.
Li, Q., ** of the Gossypium raimondii transcriptome reveals a new mechanism for alternative splicing of introns. Mol Plant 7, 829–840.
Li, S., Bashline, L., Zheng, Y., **n, X., Huang, S., Kong, Z., Kim, S.H., Cosgrove, D.J., and Gu, Y. (2016b). Cellulose synthase complexes act in a concerted fashion to synthesize highly aggregated cellulose in secondary cell walls of plants. Proc Natl Acad Sci USA 113, 11348–11353.
Li, W., Li, D.D., Han, L.H., Tao, M., Hu, Q.Q., Wu, W.Y., Zhang, J.B., Li, X.B., and Huang, G.Q. (2017c). Genome-wide identification and characterization of TCP transcription factor genes in Upland cotton (Gossypium hirsutum). Sci Rep 7, 10118.
Li, W., Shang, H., Ge, Q., Zou, C., Cai, J., Wang, D., Fan, S., Zhang, Z., Deng, X., Tan, Y., et al. (2016c). Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development. BMC Genomics 17, 1000.
Li, X., Liu, N., Sun, Y., Wang, P., Ge, X., Pei, Y., Liu, D., Ma, X., Li, F., and Hou, Y. (2019f). The cotton GhWIN2 gene activates the cuticle biosynthesis pathway and influences the salicylic and jasmonic acid biosynthesis pathways. BMC Plant Biol 19, 379.
Li, X., Ouyang, X., Zhang, Z., He, L., Wang, Y., Li, Y., Zhao, J., Chen, Z., Wang, C., Ding, L., et al. (2019g). Over-expression of the red plant gene R1 enhances anthocyanin production and resistance to bollworm and spider mite in cotton. Mol Genet Genomics 294, 469–478.
Li, X., Zhang, Y., Ding, C., Xu, W., and Wang, X. (2017d). Temporal patterns of cotton Fusarium and Verticillium wilt in Jiangsu coastal areas of China. Sci Rep 7, 12581.
Li, X.B., Fan, X.P., Wang, X.L., Cai, L., and Yang, W.C. (2005b). The cotton ACTIN1 gene is functionally expressed in fibers and participates in fiber elongation. Plant Cell 17, 859–875.
Li, X.B., Xu, D., Wang, X.L., Huang, G.Q., Luo, J., Li, D.D., Zhang, Z.T., and Xu, W.L. (2010). Three cotton genes preferentially expressed in flower tissues encode actin-depolymerizing factors which are involved in F-actin dynamics in cells. J Exp Bot 61, 41–53.
Li, X.Y., Liu, W., Ren, Z.Y., Wang, X.X., Liu, J., Yang, Z.R., Zhao, J.J., Pei, X.Y., Liu, Y.A., He, K.L., et al. (2022c). Glucose regulates cotton fiber elongation by interacting with brassinosteroid. J Exp Bot 73, 711–726.
Li, Y., Hallerman, E.M., Wu, K., and Peng, Y. (2020a). Insect-resistant genetically engineered crops in China: development, application, and prospects for use. Annu Rev Entomol 65, 273–292.
Li, Y., Tu, L., Pettolino, F.A., Ji, S., Hao, J., Yuan, D., Deng, F., Tan, J., Hu, H., Wang, Q., et al. (2016d). GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring. Plant Biotechnol J 14, 951–963.
Li, Y., Wang, N.N., Wang, Y., Liu, D., Gao, Y., Li, L., and Li, X.B. (2018b). The cotton XLIM protein (GhXLIM6) is required for fiber development via maintaining dynamic F-actin cytoskeleton and modulating cellulose biosynthesis. Plant J 96, 1269–1282.
Li, Z., Wang, P., You, C., Yu, J., Zhang, X., Yan, F., Ye, Z., Shen, C., Li, B., Guo, K., et al. (2020b). Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. New Phytol 226, 1738–1752.
Liang, A., Zhao, J., Li, X., Yan, F., Chen, Z., Chen, X., Wang, Y., Li, Y., Wang, C., and **ao, Y. (2020). Up-regulation of GhPAP1A results in moderate anthocyanin accumulation and pigmentation in sub-red cotton. Mol Genet Genomics 295, 1393–1400.
Liang, S., Luo, J., Alariqi, M., Xu, Z., Wang, A., Zafar, M.N., Ren, J., Wang, F., Liu, X., **n, Y., et al. (2021). Silencing of a LIM gene in cotton exhibits enhanced resistance against Apolygus lucorum. J Cell Physiol 236, 5921–5936.
Lifschitz, E., Eviatar, T., Rozman, A., Shalit, A., Goldshmidt, A., Amsellem, Z., Alvarez, J.P., and Eshed, Y. (2006). The tomato FT ortholog triggers systemic signals that regulate growth and flowering and substitute for diverse environmental stimuli. Proc Natl Acad Sci USA 103, 6398–6403.
Liu, B., Zhu, Y., and Zhang, T. (2015a). The R3-MYB gene GhCPC negatively regulates cotton fiber elongation. PLoS ONE 10, e0116272.
Liu, D., Tu, L., Wang, L., Li, Y., Zhu, L., and Zhang, X. (2008). Characterization and expression of plasma and tonoplast membrane aquaporins in elongating cotton fibers. Plant Cell Rep 27, 1385–1394.
Liu, G.J., **ao, G.H., Liu, N.J., Liu, D., Chen, P.S., Qin, Y.M., and Zhu, Y. X. (2015b). Targeted lipidomics studies reveal that linolenic acid promotes cotton fiber elongation by activating phosphatidylinositol and phosphatidylinositol monophosphate biosynthesis. Mol Plant 8, 911–921.
Liu, H., Shi, R., Wang, X., Pan, Y., Li, Z., Yang, X., Zhang, G., and Ma, Z. (2013). Characterization and expression analysis of a fiber differentially expressed fasciclin-like arabinogalactan protein gene in sea island cotton fibers. PLoS ONE 8, e70185.
Liu, L., Wang, Y.M., Zhao, Y.P., Wang, D., Zhao, P., Liu, Z.J., and Hua, J.P. (2016). Construction of expression vectors and a preliminary functional analysis of fatty acid synthetase genes of GhKAR and GhENR in Upland cotton (in Chinses). Cotton Sci 28, 527–537.
Liu, L., Wang, Z., Li, J., Wang, Y., Yuan, J., Zhan, J., Wang, P., Lin, Y., Li, F., and Ge, X. (2021a). Verticillium dahliae secreted protein Vd424Y is required for full virulence, targets the nucleus of plant cells, and induces cell death. Mol Plant Pathol 22, 1109–1120.
Liu, Q., Wu, M., Zhang, B., Shrestha, P., Petrie, J., Green, A.G., and Singh, S.P. (2017). Genetic enhancement of palmitic acid accumulation in cotton seed oil through RNAi down-regulation of ghKAS2 encoding β-ketoacyl-ACP synthase II (KASII). Plant Biotechnol J 15, 132–143.
Liu, R., ** for plant height and fruit branch number based on RIL population of Upland cotton. J Cotton Res 3, 5.
Liu, S., Zhang, X., **ao, S., Ma, J., Shi, W., Qin, T., **, H., Nie, X., You, C., Xu, Z., et al. (2021b). A single-nucleotide mutation in a GLUTAMATE RECEPTOR-LIKE gene confers resistance to fusarium wilt in Gossypium hirsutum. Adv Sci 8, 2002723.
Liu, T., Chen, T., Kan, J., Yao, Y., Guo, D., Yang, Y., Ling, X., Wang, J., and Zhang, B. (2022). The GhMYB36 transcription factor confers resistance to biotic and abiotic stress by enhancing PR1 gene expression in plants. Plant Biotechnol J 20, 722–735.
Liu, Y., Chen, X., Xue, S., Quan, T., Cui, D., Han, L., Cong, W., Li, M., Yun, D.J., Liu, B., et al. (2021c). SET DOMAIN GROUP 721 protein functions in saline-alkaline stress tolerance in the model rice variety Kitaake. Plant Biotechnol J 19, 2576–2588.
Liu, Z., Qanmber, G., Lu, L., Qin, W., Liu, J., Li, J., Ma, S., Yang, Z., and Yang, Z. (2018). Genome-wide analysis of BES1 genes in Gossypium revealed their evolutionary conserved roles in brassinosteroid signaling. Sci China Life Sci 61, 1566–1582.
Liu, Z.H., Chen, Y., Wang, N.N., Chen, Y.H., Wei, N., Lu, R., Li, Y., and Li, X.B. (2020b). A basic helix-loop-helix protein (GhFP1) promotes fibre elongation of cotton (Gossypium hirsutum) by modulating brassinosteroid biosynthesis and signalling. New Phytol 225, 2439–2452.
Long, Y., Liu, Z., Wang, P., Yang, H., Wang, Y., Zhang, S., Zhang, X., and Wang, M. (2021). Disruption of topologically associating domains by structural variations in tetraploid cottons. Genomics 113, 3405–3414.
Lu, R., Li, Y., Zhang, J., Wang, Y., Zhang, J., Li, Y., Zheng, Y., and Li, X.B. (2022). The bHLH/HLH transcription factors GhFP2 and GhACE1 antagonistically regulate fiber elongation in cotton. Plant Physiol 189, 628–643.
Lu, R., Zhang, J., Liu, D., Wei, Y.L., Wang, Y., and Li, X.B. (2018). Characterization of bHLH/HLH genes that are involved in brassinosteroid (BR) signaling in fiber development of cotton (Gossypium hirsutum). BMC Plant Biol 18, 304.
Luo, M., **ao, Y., Li, X., Lu, X., Deng, W., Li, D., Hou, L., Hu, M., Li, Y., and Pei, Y. (2007). GhDET2, a steroid 5α-reductase, plays an important role in cotton fiber cell initiation and elongation. Plant J 51, 419–430.
Luo, P., Wang, Y.H., Wang, G.D., Essenberg, M., and Chen, X.Y. (2001). Molecular cloning and functional identification of (+)-δ-cadinene-8-hydroxylase, a cytochrome P450 mono-oxygenase (CYP706B1) of cotton sesquiterpene biosynthesis. Plant J 28, 95–104.
Luo, S., Naranjo, S.E., and Wu, K. (2014). Biological control of cotton pests in China. Biol Control 68, 6–14.
Lv, F., Wang, H., Wang, X., Han, L., Ma, Y., Wang, S., Feng, Z., Niu, X., Cai, C., Kong, Z., et al. (2015). GhCFE1A, a dynamic linker between the ER network and actin cytoskeleton, plays an important role in cotton fibre cell initiation and elongation. J Exp Bot 66, 1877–1889.
Ma, D., Hu, Y., Yang, C., Liu, B., Fang, L., Wan, Q., Liang, W., Mei, G., Wang, L., Wang, H., et al. (2016). Genetic basis for glandular trichome formation in cotton. Nat Commun 7, 10456.
Ma, Z., He, S., Wang, X., Sun, J., Zhang, Y., Zhang, G., Wu, L., Li, Z., Liu, Z., Sun, G., et al. (2018). Resequencing a core collection of Upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet 50, 803–813.
Ma, Z., Zhang, Y., Wu, L., Zhang, G., Sun, Z., Li, Z., Jiang, Y., Ke, H., Chen, B., Liu, Z., et al. (2021). High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. Nat Genet 53, 1385–1391.
Machado, A., Wu, Y., Yang, Y., Llewellyn, D.J., and Dennis, E.S. (2009). The MYB transcription factor GhMYB25 regulates early fibre and trichome development. Plant J 59, 52–62.
Manghwar, H., Lindsey, K., Zhang, X., and **, S. (2019). CRISPR/Cas system: Recent advances and future prospects for genome editing. Trends Plant Sci 24, 1102–1125.
Mansoor, S., Briddon, R.W., Zafar, Y., and Stanley, J. (2003). Geminivirus disease complexes: an emerging threat. Trends Plant Sci 8, 128–134.
Mao, Y.B., Lu, S., Wang, L.J., and Chen, X.Y. (2007a). Biosynthesis of gossypol in cotton. CABI Rev 2006, 12.
Mao, Y.B., Cai, W.J., Wang, J.W., Hong, G.J., Tao, X.Y., Wang, L.J., Huang, Y.P., and Chen, X.Y. (2007b). Silencing a cotton bollworm P450 monooxygenase gene by plant-mediated RNAi impairs larval tolerance of gossypol. Nat Biotechnol 25, 1307–1313.
Mao, Y.B., Liu, Y.Q., Chen, D.Y., Chen, F.Y., Fang, X., Hong, G.J., Wang, L.J., Wang, J.W., and Chen, X.Y. (2017). Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance. Nat Commun 8, 13925.
McGarry, R.C., and Ayre, B.G. (2012). Geminivirus-mediated delivery of florigen promotes determinate growth in aerial organs and uncouples flowering from photoperiod in cotton. PLoS ONE 7, e36746.
McGarry, R.C., and Ayre, B.G. (2021). Cotton architecture: examining the roles of single flower truss and self-pruning in regulating growth habits of a woody perennial crop. Curr Opin Plant Biol 59, 101968.
McGarry, R.C., Prewitt, S.F., Culpepper, S., Eshed, Y., Lifschitz, E., and Ayre, B.G. (2016). Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF-PRUNING orthologs. New Phytol 212, 244–258.
McMichael, S.C. (1959). Hopi cotton, a source of cottonseed free of gossypol pigments. Agron J 51, 630.
Mei, W., Qin, Y., Song, W., Li, J., and Zhu, Y. (2009). Cotton GhPOX1 encoding plant class III peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation. J Genet Genomics 36, 141–150.
Mello, V.M. (2013). Resenha do livro “OECD-FAO Agricultural Outlook 2012–2021”. Rev Virtual Quím 5, 123.
Michailidis, G., Argiriou, A., Darzentas, N., and Tsaftaris, A. (2009). Analysis of xyloglucan endotransglycosylase/hydrolase (XTH) genes from allotetraploid (Gossypium hirsutum) cotton and its diploid progenitors expressed during fiber elongation. J Plant Physiol 166, 403–416.
Min, Y., Bunn, J.I., and Kramer, E.M. (2019). Homologs of the STYLISH gene family control nectary development in Aquilegia. New Phytol 221, 1090–1100.
Molina, A., Miedes, E., Bacete, L., Rodríguez, T., Mélida, H., Denancé, N., Sánchez-Vallet, A., Rivière, M.P., López, G., Freydier, A., et al. (2021). Arabidopsis cell wall composition determines disease resistance specificity and fitness. Proc Natl Acad Sci USA 118, e2010243118.
Naoumkina, M., Zeng, L., Fang, D.D., Wang, M., Thyssen, G.N., Florane, C.B., Li, P., and Delhom, C.D. (2020). Map** and validation of a fiber length QTL on chromosome D11 using two independent F2 populations of Upland cotton. Mol Breeding 40, 31.
Niu, E., Shang, X., Cheng, C., Bao, J., Zeng, Y., Cai, C., Du, X., and Guo, W. (2015). Comprehensive analysis of the COBRA-Like (COBL) gene family in Gossypium identifies two COBLs potentially associated with fiber quality. PLoS ONE 10, e0145725.
Pang, C.Y., Wang, H., Pang, Y., Xu, C., Jiao, Y., Qin, Y.M., Western, T.L., Yu, S.X., and Zhu, Y.X. (2010a). Comparative proteomics indicates that biosynthesis of pectic precursors is important for cotton fiber and Arabidopsis root hair elongation. Mol Cell Proteomics 9, 2019–2033.
Pang, Y., Wang, H., Song, W.Q., and Zhu, Y.X. (2010b). The cotton ATP synthase δ1 subunit is required to maintain a higher ATP/ADP ratio that facilitates rapid fibre cell elongation. Plant Biol 12, 903–909.
Paradez, A., Wright, A., and Ehrhardt, D.W. (2006). Microtubule cortical array organization and plant cell morphogenesis. Curr Opin Plant Biol 9, 571–578.
Park, Y.B., and Cosgrove, D.J. (2015). Xyloglucan and its interactions with other components of the growing cell wall. Plant Cell Physiol 56, 180–194.
Paterson, A.H., Wendel, J.F., Gundlach, H., Guo, H., Jenkins, J., **, D., Llewellyn, D., Showmaker, K.C., Shu, S., Udall, J., et al. (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492, 423–427.
Pei, L., Huang, X., Liu, Z., Tian, X., You, J., Li, J., Fang, D.D., Lindsey, K., Zhu, L., Zhang, X., et al. (2022). Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biol 23, 45.
Pei, L., Li, G., Lindsey, K., Zhang, X., and Wang, M. (2021a). Plant 3D genomics: the exploration and application of chromatin organization. New Phytol 230, 1772–1786.
Pei, Y. (2015). The homeodomain-containing transcription factor, GhHOX3, is a key regulator of cotton fiber elongation. Sci China Life Sci 58, 309–310.
Pei, Y., Zhang, J., Wu, P., Ye, L., Yang, D., Chen, J., Li, J., Hu, Y., Zhu, X., Guo, X., et al. (2021b). GoNe encoding a class VIIIb AP2/ERF is required for both extrafloral and floral nectary development in Gossypium. Plant J 106, 1116–1127.
Peng, R., Xu, Y., Tian, S., Unver, T., Liu, Z., Zhou, Z., Cai, X., Wang, K., Wei, Y., Liu, Y., et al. (2022). Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons. Proc Natl Acad Sci USA 119, e2208496119.
Peng, Z., Li, H., Sun, G., Dai, P., Geng, X., Wang, X., Zhang, X., Wang, Z., Jia, Y., Pan, Z., et al. (2021). CottonGVD: A comprehensive genomic variation database for cultivated cottons. Front Plant Sci 12.
Pien, S., Wyrzykowska, J., McQueen-Mason, S., Smart, C., and Fleming, A. (2001). Local expression of expansin induces the entire process of leaf development and modifies leaf shape. Proc Natl Acad Sci USA 98, 11812–11817.
Preuss, M.L., Delmer, D.P., and Liu, B. (2003). The cotton kinesin-like calmodulin-binding protein associates with cortical microtubules in cotton fibers. Plant Physiol 132, 154–160.
Preuss, M.L., Kovar, D.R., Lee, Y.R.J., Staiger, C.J., Delmer, D.P., and Liu, B. (2004). A plant-specific kinesin binds to actin microfilaments and interacts with cortical microtubules in cotton fibers. Plant Physiol 136, 3945–3955.
Pu, L., Li, Q., Fan, X., Yang, W., and Xue, Y. (2008). The R2R3 MYB transcription factor GhMYB109 is required for cotton fiber development. Genetics 180, 811–820.
Qanmber, G., Lu, L., Liu, Z., Yu, D., Zhou, K., Huo, P., Li, F., and Yang, Z. (2019). Genome-wide identification of GhAAI genes reveals that GhAAI66 triggers a phase transition to induce early flowering. J Exp Bot 70, 4721–4736.
Qin, L., Li, J., Wang, Q., Xu, Z., Sun, L., Alariqi, M., Manghwar, H., Wang, G., Li, B., Ding, X., et al. (2020). High-efficient and precise base editing of C·G to T·A in the allotetraploid cotton (Gossypium hirsutum) genome using a modified CRISPR/Cas9 system. Plant Biotechnol J 18, 45–56.
Qin, L.X., Chen, Y., Zeng, W., Li, Y., Gao, L., Li, D.D., Bacic, A., Xu, W. L., and Li, X.B. (2017). The cotton β-galactosyltransferase 1 (GalT1) that galactosylates arabinogalactan proteins participates in controlling fiber development. Plant J 89, 957–971.
Qin, Y., Sun, M., Li, W., Xu, M., Shao, L., Liu, Y., Zhao, G., Liu, Z., Xu, Z., You, J., et al. (2022). Single-cell RNA-seq reveals fate determination control of an individual fibre cell initiation in cotton (Gossypium hirsutum). Plant Biotechnol J 20, 2372–2388.
Qin, Y.M., and Zhu, Y.X. (2011). How cotton fibers elongate: a tale of linear cell-growth mode. Curr Opin Plant Biol 14, 106–111.
Qin, Y.M., Hu, C.Y., Pang, Y., Kastaniotis, A.J., Hiltunen, J.K., and Zhu, Y. X. (2007a). Saturated very-long-chain fatty acids promote cotton fiber and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell 19, 3692–3704.
Qin, Y.M., Hu, C.Y., and Zhu, Y.X. (2008). The ascorbate peroxidase regulated by H2O2 and ethylene is involved in cotton fiber cell elongation by modulating ROS homeostasis. Plant Signal Behav 3, 194–196.
Qin, Y.M., Pujol, F.M., Hu, C.Y., Feng, J.X., Kastaniotis, A.J., Hiltunen, J. K., and Zhu, Y.X. (2007b). Genetic and biochemical studies in yeast reveal that the cotton fibre-specific GhCER6 gene functions in fatty acid elongation. J Exp Bot 58, 473–481.
Qiu, F., **ng, S., Xue, C., Liu, J., Chen, K., Chai, T., and Gao, C. (2022). Transient expression of a TaGRF4-TaGIF1 complex stimulates wheat regeneration and improves genome editing. Sci China Life Sci 65, 731–738.
Ramadan, M., Alariqi, M., Ma, Y., Li, Y., Liu, Z., Zhang, R., **, S., Min, L., and Zhang, X. (2021). Efficient CRISPR/Cas9 mediated pooledsgRNAs assembly accelerates targeting multiple genes related to male sterility in cotton. Plant Methods 17, 16.
Ramli, U.S., Baker, D.S., Quant, P.A., and Harwood, J.L. (2002). Use of control analysis to study the regulation of plant lipid biosynthesis. Biochem Soc Trans 30, 1043–1046.
Ramos-Sobrinho, R., Adegbola, R.O., Lawrence, K., Schrimsher, D.W., Isakeit, T., Alabi, O.J., and Brown, J.K. (2021). Cotton leafroll dwarf virus US genomes comprise divergent subpopulations and harbor extensive variability. Viruses 13, 2230.
Ren, J., Meng, X., Hu, F., Liu, Q., Cao, Y., Li, H., Yan, C., Li, J., Wang, K., Yu, H., et al. (2021). Expanding the scope of genome editing with SpG and SpRY variants in rice. Sci China Life Sci 64, 1784–1787.
Ruan, Y.L., Llewellyn, D.J., and Furbank, R.T. (2001). The control of single-celled cotton fiber elongation by developmentally reversible gating of plasmodesmata and coordinated expression of sucrose and K+ transporters and expansin. Plant Cell 13, 47–60.
Ruan, Y.L., Llewellyn, D.J., and Furbank, R.T. (2003). Suppression of sucrose synthase gene expression represses cotton fiber cell initiation, elongation, and seed development. Plant Cell 15, 952–964.
Ruan, Y.L., Llewellyn, D.J., Furbank, R.T., and Chourey, P.S. (2005). The delayed initiation and slow elongation of fuzz-like short fibre cells in relation to altered patterns of sucrose synthase expression and plasmodesmata gating in a lintless mutant of cotton. J Exp Bot 56, 977–984.
Ruan, Y.L., Xu, S.M., White, R., and Furbank, R.T. (2004). Genotypic and developmental evidence for the role of plasmodesmatal regulation in cotton fiber elongation mediated by callose turnover. Plant Physiol 136, 4104–4113.
Salvador, R., Niz, J.M., Nakaya, P.A., Pedarros, A., and Hopp, H.E. (2021). Midgut genes knockdown by oral dsRNA administration produces a lethal effect on cotton boll weevil. Neotrop Entomol 50, 121–128.
Sankoh, A.F., and Burch-Smith, T.M. (2021). Approaches for investigating plasmodesmata and effective communication. Curr Opin Plant Biol 64, 102143.
Scheller, H.V., and Ulvskov, P. (2010). Hemicelluloses. Annu Rev Plant Biol 61, 263–289.
Schrick, K., DeBolt, S., and Bulone, V. (2012). Deciphering the molecular functions of sterols in cellulose biosynthesis. Front Plant Sci 3, 84.
Schuler, M.A. (2012). Insect P450s: mounted for battle in their war against toxins. Mol Ecol 21, 4157–4159.
Shan, C.M., Shangguan, X.X., Zhao, B., Zhang, X.F., Chao, L.M., Yang, C. Q., Wang, L.J., Zhu, H.Y., Zeng, Y.D., Guo, W.Z., et al. (2014). Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3. Nat Commun 5, 5519.
Shang, X., Zhu, L., Duan, Y., and Guo, W. (2020). A cotton α1,3-/4-fucosyltransferase-encoding gene, FucT4, plays an important role in cell elongation and is significantly associated with fiber quality. Mol Genet Genomics 295, 1141–1153.
Shangguan, X.X., Yang, C.Q., Zhang, X.F., and Wang, L.J. (2016). Functional characterization of a basic helix-loop-helix (bHLH) transcription factor GhDEL65 from cotton (Gossypium hirsutum). Physiol Plant 158, 200–212.
Shen, C.Y. (1985). Integrated management of Fusarium and Verticillum wilts of cotton in China. Crop Protection 4, 337–345.
Shen, E., Chen, T., Zhu, X., Fan, L., Sun, J., Llewellyn, D.J., Wilson, I., and Zhu, Q.H. (2020). Expansion of MIR482/2118 by a class-II transposable element in cotton. Plant J 103, 2084–2099.
Sheng, K., Sun, Y., Liu, M., Cao, Y., Han, Y., Li, C., Muhammad, U., Daud, M.K., Wang, W., Li, H., et al. (2023). A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol. Plant Commun 4, 100421.
Shi, Y.H., Zhu, S.W., Mao, X.Z., Feng, J.X., Qin, Y.M., Zhang, L., Cheng, J., Wei, L.P., Wang, Z.Y., and Zhu, Y.X. (2006). Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18, 651–664.
Shockey, J., Dowd, M., Mack, B., Gilbert, M., Scheffler, B., Ballard, L., Frelichowski, J., and Mason, C. (2017). Naturally occurring high oleic acid cottonseed oil: identification and functional analysis of a mutant allele of Gossypium barbadense fatty acid desaturase-2. Planta 245, 611–622.
Singh, B., Avci, U., Eichler Inwood, S.E., Grimson, M.J., Landgraf, J., Mohnen, D., Sørensen, I., Wilkerson, C.G., Willats, W.G.T., and Haigler, C.H. (2009). A specialized outer layer of the primary cell wall joins elongating cotton fibers into tissue-like bundles. Plant Physiol 150, 684–699.
Snelders, N.C., Rovenich, H., Petti, G.C., Rocafort, M., van den Berg, G.C. M., Vorholt, J.A., Mesters, J.R., Seidl, M.F., Nijland, R., and Thomma, B.P.H.J. (2020). Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins. Nat Plants 6, 1365–1374.
Song, Q., Guan, X., and Chen, Z.J. (2015). Dynamic roles for small RNAs and DNA Methylation during ovule and fiber development in allote-traploid cotton. PLoS Genet 11, e1005724.
Song, Q., Zhang, T., Stelly, D.M., and Chen, Z.J. (2017). Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biol 18, 1–4.
Song, W.Q., Qin, Y.M., Saito, M., Shirai, T., Pujol, F.M., Kastaniotis, A.J., Hiltunen, J.K., and Zhu, Y.X. (2009). Characterization of two cotton cDNAs encoding trans-2-enoyl-CoA reductase reveals a putative novel NADPH-binding motif. J Exp Bot 60, 1839–1848.
Song, X., Li, Y., Cao, X., and Qi, Y. (2019). MicroRNAs and their regulatory roles in plant-environment interactions. Annu Rev Plant Biol 70, 489–525.
Stansbury, M.F., Cucullu, A.F., and Den Hartog, G.T. (1954). Cottonseed contents variation, influence of variety and environment on oil content of cottonseed kernels. J Agric Food Chem 2, 692–696.
Stiff, M.R., and Haigler, C.H. (2016). Cotton fiber tips have diverse morphologies and show evidence of apical cell wall synthesis. Sci Rep 6, 27883.
Sturtevant, D., Horn, P., Kennedy, C., Hinze, L., Percy, R., and Chapman, K. (2017). Lipid metabolites in seeds of diverse Gossypium accessions: molecular identification of a high oleic mutant allele. Planta 245, 595–610.
Su, C.H., Li, Y.S., Wang, J.W., Zhang, W.M., and Fan, Z.J. (1993). Studies on combined cultural techniques by higher planting density, growth regulatore, application of fertilizer and irrigation for obtaining high yield in cotton (in Chinese). Acta Gossypii Sin 5, 57–64.
Su, J., Li, L., Zhang, C., Wang, C., Gu, L., Wang, H., Wei, H., Liu, Q., Huang, L., and Yu, S. (2018). Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese Upland cotton. Theor Appl Genet 131, 1299–1314.
Su, J., Pang, C., Wei, H., Li, L., Liang, B., Wang, C., Song, M., Wang, H., Zhao, S., Jia, X., et al. (2016). Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in Upland cotton. BMC Genomics 17, 687.
Sumathi, S., and Shakina, J. (2021). Synthesis and characterisation of novel crosslinked biopolyurethane from cotton seed oil as eco-friendly bio-degradable material. Heterocycl Lett 11, 45–52.
Sun, H., Hu, M., Li, J., Chen, L., Li, M., Zhang, S., Zhang, X., and Yang, X. (2018). Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton. BMC Plant Biol 18, 150.
Sun, Q., Huang, J., Guo, Y., Yang, M., Guo, Y., Li, J., Zhang, J., and Xu, W. (2020). A cotton NAC domain transcription factor, GhFSN5, negatively regulates secondary cell wall biosynthesis and anther development in transgenic Arabidopsis. Plant Physiol Biochem 146, 303–314.
Sun, Q., **e, Y., Li, H., Liu, J., Geng, R., Wang, P., Chu, Z., Chang, Y., Li, G., Zhang, X., et al. (2022a). Cotton GhBRC1 regulates branching, flowering, and growth by integrating multiple hormone pathways. Crop J 10, 75–87.
Sun, W., Gao, Z., Wang, J., Huang, Y., Chen, Y., Li, J., Lv, M., Wang, J., Luo, M., and Zuo, K. (2019a). Cotton fiber elongation requires the transcription factor GhMYB212 to regulate sucrose transportation into expanding fibers. New Phytol 222, 864–881.
Sun, Y., and Allen, R.D. (2005). Functional analysis of the BIN2 genes of cotton. Mol Genet Genomics 274, 51–59.
Sun, Y., Fokar, M., Asami, T., Yoshida, S., and Allen, R.D. (2004). Characterization of the brassinosteroid insensitive 1 genes of cotton. Plant Mol Biol 54, 221–232.
Sun, Y., Liang, W., Shen, W., Feng, H., Chen, J., Si, Z., Hu, Y., and Zhang, T. (2019b). G65V substitution in actin disturbs polymerization leading to inhibited cell elongation in cotton. Front Plant Sci 10, 1486.
Sun, Y., Veerabomma, S., Abdel-Mageed, H.A., Fokar, M., Asami, T., Yoshida, S., and Allen, R.D. (2005). Brassinosteroid regulates fiber development on cultured cotton ovules. Plant Cell Physiol 46, 1384–1391.
Sun, Y., Zhang, D., Zheng, H., Wu, Y., Mei, J., Ke, L., Yu, D., and Sun, Y. (2022b). Biochemical and expression analyses revealed the involvement of proanthocyanidins and/or their derivatives in fiber pigmentation of Gossypium stocksii. Int J Mol Sci 23, 1008.
Sun, Y., Zhong, M., Li, Y., Zhang, R., Su, L., **a, G., and Wang, H. (2021). GhADF6-mediated actin reorganization is associated with defence against Verticillium dahliae infection in cotton. Mol Plant Pathol 22, 1656–1667.
Sunilkumar, G., Campbell, L.A.M., Puckhaber, L., Stipanovic, R.D., and Rathore, K.S. (2006). Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. Proc Natl Acad Sci USA 103, 18054–18059.
Taliercio, E.W., and Boykin, D. (2007). Analysis of gene expression in cotton fiber initials. BMC Plant Biol 7, 22.
Tan, J., Tu, L., Deng, F., Wu, R., and Zhang, X. (2012). Exogenous jasmonic acid inhibits cotton fiber elongation. J Plant Growth Regul 31, 599–605.
Tanaka, Y., Sasaki, N., and Ohmiya, A. (2008). Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J 54, 733–749.
Tang, D., Jia, Y., Zhang, J., Li, H., Cheng, L., Wang, P., Bao, Z., Liu, Z., Feng, S., Zhu, X., et al. (2022). Genome evolution and diversity of wild and cultivated potatoes. Nature 606, 535–541.
Tang, K., and Liu, J.Y. (2017). Molecular characterization of GhPLDα1 and its relationship with secondary cell wall thickening in cotton fibers. Acta Biochim Biophys Sin 49, 33–43.
Tang, W., Tu, L., Yang, X., Tan, J., Deng, F., Hao, J., Guo, K., Lindsey, K., and Zhang, X. (2014). The calcium sensor GhCaM7 promotes cotton fiber elongation by modulating reactive oxygen species (ROS) production. New Phytol 202, 509–520.
Tao, X., Li, M., Zhao, T., Feng, S., Zhang, H., Wang, L., Han, J., Gao, M., Lu, K., Chen, Q., et al. (2021). Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation. Plant Physiol 186, 2152–2168.
Tao, X.Y., Xue, X.Y., Huang, Y.P., Chen, X.Y., and Mao, Y.B. (2012). Gossypol-enhanced P450 gene pool contributes to cotton bollworm tolerance to a pyrethroid insecticide. Mol Ecol 21, 4371–4385.
Taylor-Teeples, M., Lin, L., de Lucas, M., Turco, G., Toal, T.W., Gaudinier, A., Young, N.F., Trabucco, G.M., Veling, M.T., Lamothe, R., et al. (2015). An Arabidopsis gene regulatory network for secondary cell wall synthesis. Nature 517, 571–575.
Taylor, N.G. (2008). Cellulose biosynthesis and deposition in higher plants. New Phytol 178, 239–252.
Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Mattison, C. P., and Naoumkina, M. (2017). A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F-actin organization resulting in dwarf, lintless cotton plants. Plant J 90, 111–121.
Thyssen, G.N., Jenkins, J.N., McCarty, J.C., Zeng, L., Campbell, B.T., Delhom, C.D., Islam, M.S., Li, P., Jones, D.C., Condon, B.D., et al. (2019). Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in Upland cotton (Gossypium hirsutum L.). Theor Appl Genet 132, 989–999.
Tian, X., Ruan, J., Huang, J., Fang, X., Mao, Y., Wang, L., Chen, X., and Yang, C. (2016). Gossypol: phytoalexin of cotton. Sci China Life Sci 59, 122–129.
Tian, X., Ruan, J.X., Huang, J.Q., Yang, C.Q., Fang, X., Chen, Z.W., Hong, H., Wang, L.J., Mao, Y.B., Lu, S., et al. (2018). Characterization of gossypol biosynthetic pathway. Proc Natl Acad Sci USA 115, E5410–E5418.
Tian, Y., Du, J.J., Wu, H.T., Guan, X.Y., Chen, W.H., Hu, Y., Fang, L., Ding, L.Y., Li, M.L., Yang, D.F., et al. (2020). The transcription factor MML4_D12 regulates fiber development through interplay with the WD40-repeat protein WDR in cotton. J Exp Bot 71, 3499–3511.
Tian, Z., Wang, X., Lee, R., Li, Y., Specht, J.E., Nelson, R.L., McClean, P. E., Qiu, L., and Ma, J. (2010). Artificial selection for determinate growth habit in soybean. Proc Natl Acad Sci USA 107, 8563–8568.
Tong, S., Yuan, M., Liu, Y., Li, X., **, D., Cheng, X., Lin, D., Ling, H., Yang, D., Wang, Y., et al. (2021). Ergosterol-targeting fusion antifungal peptide significantly increases the Verticillium wilt resistance of cotton. Plant Biotechnol J 19, 926–936.
Udall, J.A., Long, E., Hanson, C., Yuan, D., Ramaraj, T., Conover, J.L., Gong, L., Arick, M.A., Grover, C.E., Peterson, D.G., et al. (2019a). De novo genome sequence assemblies of Gossypium raimondii and Gossypium turneri. G3 9, 3079–3085.
Udall, J.A., Long, E., Ramaraj, T., Conover, J.L., Yuan, D., Grover, C.E., Gong, L., Arick Ii, M.A., Masonbrink, R.E., Peterson, D.G., et al. (2019b). The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants. Front Plant Sci 10.
Wagner, D., Sablowski, R.W.M., and Meyerowitz, E.M. (1999). Transcriptional activation of APETALA1 by LEAFY. Science 285, 582–584.
Wagner, T.A., Duke, S.E., Davie, S.M., Magill, C., and Liu, J. (2022). Interaction of fusarium wilt race 4 with root-knot nematode increases disease severity in cotton. Plant Dis 106, 2558–2562.
Walford, S.A., Wu, Y., Llewellyn, D.J., and Dennis, E.S. (2011). GhMYB25-like: a key factor in early cotton fibre development. Plant J 65, 785–797.
Walford, S.A., Wu, Y., Llewellyn, D.J., and Dennis, E.S. (2012). Epidermal cell differentiation in cotton mediated by the homeodomain leucine zipper gene, GhHD-1. Plant J 71, 464–478.
Wang, B., Smith, S.M., and Li, J. (2018a). Genetic regulation of shoot architecture. Annu Rev Plant Biol 69, 437–468.
Wang, C., Guo, H., He, X., Zhang, S., Wang, J., Wang, L., Guo, D., and Guo, X. (2020a). Scaffold protein GhMORG1 enhances the resistance of cotton to Fusarium oxysporum by facilitating the MKK6-MPK4 cascade. Plant Biotechnol J 18, 1421–1433.
Wang, D., Fan, W., Guo, X., Wu, K., Zhou, S., Chen, Z., Li, D., Wang, K., Zhu, Y., and Zhou, Y. (2020b). MaGenDB: a functional genomics hub for Malvaceae plants. Nucleic Acids Res 48, D1076–D1084.
Wang, G., Xu, J., Li, L., Guo, Z., Si, Q., Zhu, G., Wang, X., and Guo, W. (2020c). GbCYP86A1-1 from Gossypium barbadense positively regulates defence against Verticillium dahliae by cell wall modification and activation of immune pathways. Plant Biotechnol J 18, 222–238.
Wang, G., Zhao, G.H., Jia, Y.H., and Du, X.M. (2013a). Identification and characterization of cotton genes involved in fuzz-fiber development. J Integr Plant Biol 55, 619–630.
Wang, G., Xu, Z., Wang, F., Huang, Y., **n, Y., Liang, S., Li, B., Si, H., Sun, L., Wang, Q., et al. (2022a). Development of an efficient and precise adenine base editor (ABE) with expanded target range in allotetraploid cotton (Gossypium hirsutum). BMC Biol 20, 45.
Wang, G.D., Li, Q.J., Luo, B., and Chen, X.Y. (2004a). Ex planta phytoremediation of trichlorophenol and phenolic allelochemicals via an engineered secretory laccase. Nat Biotechnol 22, 893–897.
Wang, H., Mei, W., Qin, Y., and Zhu, Y. (2011). 1-Aminocyclopropane-1-carboxylic acid synthase 2 is phosphorylated by calcium-dependent protein kinase 1 during cotton fiber elongation. Acta Biochim Biophys Sin 43, 654–661.
Wang, H., Guo, Y., Lv, F., Zhu, H., Wu, S., Jiang, Y., Li, F., Zhou, B., Guo, W., and Zhang, T. (2010a). The essential role of GhPEL gene, encoding a pectate lyase, in cell wall loosening by depolymerization of the deesterified pectin during fiber elongation in cotton. Plant Mol Biol 72, 397–406.
Wang, H.Y., Wang, J., Gao, P., Jiao, G.L., Zhao, P.M., Li, Y., Wang, G.L., and **a, G.X. (2009). Down-regulation of GhADF1 gene expression affects cotton fibre properties. Plant Biotechnol J 7, 13–23.
Wang, J., Wang, H.Y., Zhao, P.M., Han, L.B., Jiao, G.L., Zheng, Y.Y., Huang, S.J., and **a, G.X. (2010b). Overexpression of a profilin (GhPFN2) promotes the progression of developmental phases in cotton fibers. Plant Cell Physiol 51, 1276–1290.
Wang, K., Huang, G., and Zhu, Y. (2016a). Transposable elements play an important role during cotton genome evolution and fiber cell development. Sci China Life Sci 59, 112–121.
Wang, K., Wang, D., Zheng, X., Qin, A., Zhou, J., Guo, B., Chen, Y., Wen, X., Ye, W., Zhou, Y., et al. (2019a). Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nat Commun 10, 4714.
Wang, K., Wang, Z., Li, F., Ye, W., Wang, J., Song, G., Yue, Z., Cong, L., Shang, H., Zhu, S., et al. (2012). The draft genome of a diploid cotton Gossypium raimondii. Nat Genet 44, 1098–1103.
Wang, L., Cook, A., Patrick, J.W., Chen, X.Y., and Ruan, Y.L. (2014). Silencing the vacuolar invertase gene GhVIN1 blocks cotton fiber initiation from the ovule epidermis, probably by suppressing a cohort of regulatory genes via sugar signaling. Plant J 78, 686–696.
Wang, L., Kartika, D., and Ruan, Y.L. (2021a). Looking into ‘hair tonics’ for cotton fiber initiation. New Phytol 229, 1844–1851.
Wang, L., Li, X.R., Lian, H., Ni, D.A., He, Y., Chen, X.Y., and Ruan, Y.L. (2010c). Evidence that high activity of vacuolar invertase is required for cotton fiber and Arabidopsis root elongation through osmotic dependent and independent pathways, respectively. Plant Physiol 154, 744–756.
Wang, L., Liu, C., Liu, Y., and Luo, M. (2020d). Fumonisin B1-induced changes in cotton fiber elongation revealed by sphingolipidomics and proteomics. Biomolecules 10, 1258.
Wang, L., Cheng, H., **ong, F., Ma, S., Zheng, L., Song, Y., Deng, K., Wu, H., Li, F., and Yang, Z. (2020e). Comparative phosphoproteomic analysis of BR-defective mutant reveals a key role of GhSK13 in regulating cotton fiber development. Sci China Life Sci 63, 1905–1917.
Wang, L., He, S., Dia, S., Sun, G., Liu, X., Wang, X., Pan, Z., Jia, Y., Wang, L., Pang, B., et al. (2021b). Alien genomic introgressions enhanced fiber strength in Upland cotton (Gossypium hirsutum L.). Industrial Crops Products 159, 113028.
Wang, M.Y., Zhao, P.M., Cheng, H.Q., Han, L.B., Wu, X.M., Gao, P., Wang, H.Y., Yang, C.L., Zhong, N.Q., Zuo, J.R., et al. (2013b). The cotton transcription factor TCP14 functions in auxin-mediated epidermal cell differentiation and elongation. Plant Physiol 162, 1669–1680.
Wang, M., Li, J., Qi, Z., Long, Y., Pei, L., Huang, X., Grover, C.E., Du, X., **a, C., Wang, P., et al. (2022b). Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat Genet 54, 1959–1971.
Wang, M., Li, J., Wang, P., Liu, F., Liu, Z., Zhao, G., Xu, Z., Pei, L., Grover, C., Wendel, J., et al. (2021c). Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton. Mol Biol Evol 38, 3621–3636.
Wang, M., Tu, L., Lin, M., Lin, Z., Wang, P., Yang, Q., Ye, Z., Shen, C., Li, J., Zhang, L., et al. (2017a). Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 49, 579–587.
Wang, M., Tu, L., Yuan, D., Zhu, D., Shen, C., Li, J., Liu, F., Pei, L., Wang, P., Zhao, G., et al. (2019b). Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nat Genet 51, 224–229.
Wang, M., Wang, P., Lin, M., Ye, Z., Li, G., Tu, L., Shen, C., Li, J., Yang, Q., and Zhang, X. (2018b). Evolutionary dynamics of 3D genome architecture following polyploidization in cotton. Nat Plants 4, 90–97.
Wang, M., Wang, P., Tu, L., Zhu, S., Zhang, L., Li, Z., Zhang, Q., Yuan, D., and Zhang, X. (2016b). Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res 44, 4067–4079.
Wang, M.X., Zhou, D.Y., Ma, L., Xu, S.J., Wei, S.J., Yang, W.H., Wang, Y. Q., and Du, S.K. (2016c). Aanalysis and evaluation of fatty acid composition in cottonseed (in Chinese). Food Sci 37, 136–141.
Wang, N., Zhang, B., Yao, T., Shen, C., Wen, T., Zhang, R., Li, Y., Le, Y., Li, Z., Zhang, X., et al. (2022c). Re enhances anthocyanin and proanthocyanidin accumulation to produce red foliated cotton and brown fiber. Plant Physiol 189, 1466–1481.
Wang, N.N., Li, Y., Chen, Y.H., Lu, R., Zhou, L., Wang, Y., Zheng, Y., and Li, X.B. (2021d). Phosphorylation of WRKY16 by MPK3-1 is essential for its transcriptional activity during fiber initiation and elongation in cotton (Gossypium hirsutum). Plant Cell 33, 2736–2752.
Wang, P., Dong, N., Wang, M., Sun, G., Jia, Y., Geng, X., Liu, M., Wang, W., Pan, Z., Yang, Q., et al. (2022d). Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense. Plant J 110, 764–780.
Wang, P., Mormile, B., and He, P. (2021e). A ‘GLoRy’ battle for cotton against Fusarium. Trends Plant Sci 26, 671–673.
Wang, P., Zhou, L., Jamieson, P., Zhang, L., Zhao, Z., Babilonia, K., Shao, W., Wu, L., Mustafa, R., Amin, I., et al. (2020f). The cotton wall-associated kinase GhWAK7A mediates responses to fungal wilt pathogens by complexing with the chitin sensory receptors. Plant Cell 32, 3978–4001.
Wang, P., Zhang, J., Sun, L., Ma, Y., Xu, J., Liang, S., Deng, J., Tan, J., Zhang, Q., Tu, L., et al. (2018c). High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system. Plant Biotechnol J 16, 137–150.
Wang, Q., Alariqi, M., Wang, F., Li, B., Ding, X., Rui, H., Li, Y., Xu, Z., Qin, L., Sun, L., et al. (2020g). The application of a heat-inducible CRISPR/Cas12b (C2c1) genome editing system in tetraploid cotton (G. hirsutum) plants. Plant Biotechnol J 18, 2436–2443.
Wang, S., Wang, J.W., Yu, N., Li, C.H., Luo, B., Gou, J.Y., Wang, L.J., and Chen, X.Y. (2004b). Control of plant trichome development by a cotton fiber MYB gene. Plant Cell 16, 2323–2334.
Wang, X., Miao, Y., Cai, Y., Sun, G., Jia, Y., Song, S., Pan, Z., Zhang, Y., Wang, L., Fu, G., et al. (2020h). Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum). Plant Biotechnol J 19, 1110–1124.
Wang, Y., Meng, Z., Liang, C., Meng, Z., Wang, Y., Sun, G., Zhu, T., Cai, Y., Guo, S., Zhang, R., et al. (2017b). Increased lateral root formation by CRISPR/Cas9-mediated editing of arginase genes in cotton. Sci China Life Sci 60, 524–527.
Wang, Z., Yang, Z., and Li, F. (2019c). Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton. Plant Biotechnol J 17, 1706–1722.
Waqas, M.S., Shi, Z., Yi, T.C., **ao, R., Shoaib, A.A., Elabasy, A.S., and **, D.C. (2021). Biology, ecology, and management of cotton mealybug Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae). Pest Manag Sci 77, 5321–5333.
Wen, X., Huang, G., Li, C., and Zhu, Y. (2021). A Malvaceae-specific miRNA targeting the newly duplicated GaZIP1L to regulate Zn2+ ion transporter capacity in cotton ovules. Sci China Life Sci 64, 339–351.
Wen, X., Zhai, Y., Zhang, L., Chen, Y., Zhu, Z., Chen, G., Wang, K., and Zhu, Y. (2022). Molecular studies of cellulose synthase supercomplex from cotton fiber reveal its unique biochemical properties. Sci China Life Sci 65, 1776–1793.
Wendel, J.F., Brubaker, C.L., and Seelanan, T. (2010). The Origin and Evolution of Gossypium. In: Stewart, J.M., Oosterhuis, D.M., Heitholt, J.J., and Mauney, J.R., eds. Physiology of Cotton. Dordrecht: Springer. 1–18.
Wendel, J.F., and Grover, C.E. (2015). Taxonomy and Evolution of the Cotton Genus, Gossypium. In: Fang, D.D., and Percy, R.G., eds. Cotton. Madison: American Society of Agronomy Inc. 25–44.
Woodley, M., Mulvihill, A., Fujita, M., and Wasteneys, G. (2018). Exploring microtubule-dependent cellulose-synthase-complex movement with high precision particle tracking. Plants 7, 53.
Wu, H., Ren, Z., Zheng, L., Guo, M., Yang, J., Hou, L., Qanmber, G., Li, F., and Yang, Z. (2021a). The bHLH transcription factor GhPAS1 mediates BR signaling to regulate plant development and architecture in cotton. Crop J 9, 1049–1059.
Wu, H., Tian, Y., Wan, Q., Fang, L., Guan, X., Chen, J., Hu, Y., Ye, W., Zhang, H., Guo, W., et al. (2018). Genetics and evolution of MIXTA genes regulating cotton lint fiber development. New Phytol 217, 883–895.
Wu, J., Jenkins, J.N., McCarty, J.C., and Thaxton, P. (2009). Seed trait evaluation of Gossypium barbadense L. chromosomes/arms in a G. hirsutum L. background. Euphytica 167, 371–380.
Wu, K.M., and Guo, Y.Y. (2005). The evolution of cotton pest management practices in China. Annu Rev Entomol 50, 31–52.
Wu, P., Xu, X., Li, J., Zhang, J., Chang, S., Yang, X., and Guo, X. (2021b). Seed-specific overexpression of cotton GhDGAT1 gene leads to increased oil accumulation in cottonseed. Crop J 9, 487–490.
Wu, Y., Machado, A.C., White, R.G., Llewellyn, D.J., and Dennis, E.S. (2006). Expression profiling identifies genes expressed early during lint fibre initiation in cotton. Plant Cell Physiol 47, 107–127.
Wu, Z., Yang, Y., Huang, G., Lin, J., **a, Y., and Zhu, Y. (2017). Cotton functional genomics reveals global insight into genome evolution and fiber development. J Genet Genomics 44, 511–518.
**a, Y., Huang, G., and Zhu, Y. (2019). Sustainable plant disease control: biotic information flow and behavior manipulation. Sci China Life Sci 62, 1710–1713.
**ao, G., Zhao, P., and Zhang, Y. (2019). A Pivotal role of hormones in regulating cotton fiber development. Front Plant Sci 10.
**ao, G., He, P., Zhao, P., Liu, H., Zhang, L., Pang, C., and Yu, J. (2018). Genome-wide identification of the GhARF gene family reveals that GhARF2 and GhARF18 are involved in cotton fibre cell initiation. J Exp Bot 69, 4323–4337.
**ao, G.H., Wang, K., Huang, G., and Zhu, Y.X. (2016). Genome-scale analysis of the cotton KCS gene family revealed a binary mode of action for gibberellin A regulated fiber growth. J Integr Plant Biol 58, 577–589.
**ao, J., Liu, B., Yao, Y., Guo, Z., Jia, H., Kong, L., Zhang, A., Ma, W., Ni, Z., Xu, S., et al. (2022). Wheat genomic study for genetic improvement of traits in China. Sci China Life Sci 65, 1718–1775.
**ao, S., Hu, Q., Zhang, X., Si, H., Liu, S., Chen, L., Chen, K., Berne, S., Yuan, D., Lindsey, K., et al. (2021a). Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2. J Exp Bot 72, 4721–4743.
**ao, Y., Li, W., Yang, X., Xu, P., **, M., Yuan, H., Zheng, W., Soberón, M., Bravo, A., Wilson, K., et al. (2021b). Rapid spread of a densovirus in a major crop pest following wide-scale adoption of Bt-cotton in China. eLife 10, e66913.
**ao, Y.H., Li, D.M., Yin, M.H., Li, X.B., Zhang, M., Wang, Y.J., Dong, J., Zhao, J., Luo, M., Luo, X.Y., et al. (2010). Gibberellin 20-oxidase promotes initiation and elongation of cotton fibers by regulating gibberellin synthesis. J Plant Physiol 167, 829–837.
Xu, B., Gou, J.Y., Li, F.G., Shangguan, X.X., Zhao, B., Yang, C.Q., Wang, L.J., Yuan, S., Liu, C.J., and Chen, X.Y. (2013). A cotton BURP domain protein interacts with α-expansin and their co-expression promotes plant growth and fruit production. Mol Plant 6, 945–958.
Xu, F., Chen, Q., Huang, L., and Luo, M. (2021). Advances about the roles of membranes in cotton fiber development. Membranes 11, 471.
Xu, F., Suo, X., Li, F., Bao, C., He, S., Huang, L., and Luo, M. (2020). Membrane lipid raft organization during cotton fiber development. J Cotton Res 3, 13.
Xu, S.M., Brill, E., Llewellyn, D.J., Furbank, R.T., and Ruan, Y.L. (2012). Overexpression of a potato sucrose synthase gene in cotton accelerates leaf expansion, reduces seed abortion, and enhances fiber production. Mol Plant 5, 430–441.
Xu, Y., Li, H.B., and Zhu, Y.X. (2007). Molecular biological and biochemical studies reveal new pathways important for cotton fiber development. J Integr Plant Biol 49, 69–74.
Xu, Y., Zhang, X., Li, H., Zheng, H., Zhang, J., Olsen, M.S., Varshney, R. K., Prasanna, B.M., and Qian, Q. (2022a). Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction. Mol Plant 15, 1664–1695.
Xu, Y.H., Wang, J.W., Wang, S., Wang, J.Y., and Chen, X.Y. (2004). Characterization of GaWRKY1, a cotton transcription factor that regulates the sesquiterpene synthase gene (+)-δ-cadinene synthase-A. Plant Physiol 135, 507–515.
Xu, Z., Chen, J., Meng, S., Xu, P., Zhai, C., Huang, F., Guo, Q., Zhao, L., Quan, Y., Shangguan, Y., et al. (2022b). Genome sequence of Gossypium anomalum facilitates interspecific introgression breeding. Plant Commun 3, 100350.
Xue, Y., Chen, R., Qu, L., and Cao, X. (2020). Noncoding RNA: from dark matter to bright star. Sci China Life Sci 63, 463–468.
Yan, Q., Wang, Y., Li, Q., Zhang, Z., Ding, H., Zhang, Y., Liu, H., Luo, M., Liu, D., Song, W., et al. (2018). Up-regulation of GhTT2-3A in cotton fibres during secondary wall thickening results in brown fibres with improved quality. Plant Biotechnol J 16, 1735–1747.
Yanagisawa, M., Desyatova, A.S., Belteton, S.A., Mallery, E.L., Turner, J. A., and Szymanski, D.B. (2015). Patterning mechanisms of cytoskeletal and cell wall systems during leaf trichome morphogenesis. Nat Plants 1, 15014.
Yang, C., Lu, X., Ma, B., Chen, S.Y., and Zhang, J.S. (2015a). Ethylene signaling in rice and Arabidopsis: conserved and diverged aspects. Mol Plant 8, 495–505.
Yang, C.L., Liang, S., Wang, H.Y., Han, L.B., Wang, F.X., Cheng, H.Q., Wu, X.M., Qu, Z.L., Wu, J.H., and **a, G.X. (2015b). Cotton major latex protein 28 functions as a positive regulator of the ethylene responsive factor 6 in defense against Verticillium dahliae. Mol Plant 8, 399–411.
Yang, J., Wang, X., **e, M., Wang, G., Li, Z., Zhang, Y., Wu, L., Zhang, G., and Ma, Z. (2020a). Proteomic analyses on xylem sap provides insights into the defense response of Gossypium hirsutum against Verticillium dahliae. J Proteomics 213, 103599.
Yang, X., Du, M., Li, S., and Zhou, X. (2021a). Coinfection of cotton plants with watermelon mosaic virus and a novel polerovirus in China. Viruses 13.
Yang, Y., Chen, T., Ling, X., and Ma, Z. (2017). Gbvdr6, a gene encoding a receptor-like protein of cotton (Gossypium barbadense), confers resistance to verticillium wilt in Arabidopsis and Upland cotton. Front Plant Sci 8, 2272.
Yang, Z., Qanmber, G., Wang, Z., Yang, Z., and Li, F. (2020b). Gossypium genomics: trends, scope, and utilization for cotton improvement. Trends Plant Sci 25, 488–500.
Yang, Z., Ge, X., Li, W., **, Y., Liu, L., Hu, W., Liu, F., Chen, Y., Peng, S., and Li, F. (2021b). Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence. BMC Biol 19, 115.
Yang, Z., Ge, X., Yang, Z., Qin, W., Sun, G., Wang, Z., Li, Z., Liu, J., Wu, J., Wang, Y., et al. (2019). Extensive intraspecific gene order and gene structural variations in Upland cotton cultivars. Nat Commun 10, 2989.
Yang, Z., Zhang, C., Yang, X., Liu, K., Wu, Z., Zhang, X., Zheng, W., Xun, Q., Liu, C., Lu, L., et al. (2014). PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation. New Phytol 203, 437–448.
Yang, Z., Wang, J., Huang, Y., Wang, S., Wei, L., Liu, D., Weng, Y., **ang, J., Zhu, Q., Yang, Z., et al. (2023). CottonMD: a multi-omics database for cotton biological study. Nucleic Acids Res 51, D1446–D1456.
Ye, L., Chen, Y., Chen, K., Yang, D., Ding, L., Yang, Q., Xu, C., Chen, J., Zhang, T., and Hu, Y. (2022). Cotton genes GhMML1 and GhMML2 control trichome branching when ectopically expressed in tobacco. Gene 820, 146308.
Yin, Z., Zhu, W., Zhang, X., Chen, X., Wang, W., Lin, H., Wang, J., and Ye, W. (2021). Molecular characterization, expression and interaction of MAPK, MAPKK and MAPKKK genes in Upland cotton. Genomics 113, 1071–1086.
Yoo, M.J., and Wendel, J.F. (2014). Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet 10, e1004073.
You, Q., Xu, W., Zhang, K., Zhang, L., Yi, X., Yao, D., Wang, C., Zhang, X., Zhao, X., Provart, N.J., et al. (2017). ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium. Nucleic Acids Res 45, D1090–D1099.
Yu, D., Ke, L., Zhang, D., Wu, Y., Sun, Y., Mei, J., Sun, J., and Sun, Y. (2021a). Multi-omics assisted identification of the key and species-specific regulatory components of drought-tolerant mechanisms in Gossypium stocksii. Plant Biotechnol J 19, 1690–1692.
Yu, D., Li, X., Li, Y., Ali, F., Li, F., and Wang, Z. (2022a). Dynamic roles and intricate mechanisms of ethylene in epidermal hair development in Arabidopsis and cotton. New Phytol 234, 375–391.
Yu, H., and Li, J. (2022b). Breeding future crops to feed the world through de novo domestication. Nat Commun 13, 1171.
Yu, J., Hui, Y., Chen, J., Yu, H., Gao, X., Zhang, Z., Li, Q., Zhu, S., and Zhao, T. (2021b). Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage. Theor Appl Genet 134, 3249–3261.
Yu, J., Jung, S., Cheng, C.H., Lee, T., Zheng, P., Buble, K., Crabb, J., Humann, J., Hough, H., Jones, D., et al. (2021c). CottonGen: The community database for cotton genomics, genetics, and breeding research. Plants 10, 2805.
Yu, S., Ali, J., Zhou, S., Ren, G., ** the promise of functional genomics research. Mol Plant 15, 9–26.
Yu, Y., Wu, S., Nowak, J., Wang, G., Han, L., Feng, Z., Mendrinna, A., Ma, Y., Wang, H., Zhang, X., et al. (2019). Live-cell imaging of the cytoskeleton in elongating cotton fibres. Nat Plants 5, 498–504.
Yuan, D., Grover, C.E., Hu, G., Pan, M., Miller, E.R., Conover, J.L., Hunt, S.P., Udall, J.A., and Wendel, J.F. (2021). Parallel and intertwining threads of domestication in allopolyploid cotton. Adv Sci 8, 2003634.
Yuan, D., Tang, Z., Wang, M., Gao, W., Tu, L., **, X., Chen, L., He, Y., Zhang, L., Zhu, L., et al. (2015). The genome sequence of Sea-island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Sci Rep 5, 17662.
Zang, Y., Xu, C., Xuan, L., Ding, L., Zhu, J.K., Si, Z., Zhang, T., and Hu, Y. (2021). Identification and characteristics of a novel gland-forming gene in cotton. Plant J 108, 781–792.
Zeng, L., Campbell, B.T., Bechere, E., Dever, J.K., Zhang, J., Jones, A.S., Raper, T.B., Hague, S., Smith, W., Myers, G.O., et al. (2015). Genotypic and environmental effects on cottonseed oil, nitrogen, and gossypol contents in 18 years of regional high quality tests. Euphytica 206, 815–824.
Zhan, J., Chu, Y., Wang, Y., Diao, Y., Zhao, Y., Liu, L., Wei, X., Meng, Y., Li, F., and Ge, X. (2021). The miR164-GhCUC2-GhBRC1 module regulates plant architecture through abscisic acid in cotton. Plant Biotechnol J 19, 1839–1851.
Zhang, B., Chopra, D., Schrader, A., and Hülskamp, M. (2019a). Evolutionary comparison of competitive protein-complex formation of MYB, bHLH, and WDR proteins in plants. J Exp Bot 70, 3197–3209.
Zhang, B., Wang, Y., and Liu, J.Y. (2018a). Genome-wide identification and characterization of phospholipase C gene family in cotton (Gossypium spp.). Sci China Life Sci 61, 88–99.
Zhang, D., Hussain, A., Manghwar, H., **e, K., **e, S., Zhao, S., Larkin, R.M., Qing, P., **, S., and Ding, F. (2021a). Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective. Plant Biotechnol J 18, 1651–1669.
Zhang, D., Zhang, T., and Guo, W. (2010). Effect of H2O2 on fiber initiation using fiber retardation initiation mutants in cotton (Gossypium hirsutum). J Plant Physiol 167, 393–399.
Zhang, H., Wang, Y., Deng, C., Zhao, S., Zhang, P., Feng, J., Huang, W., Kang, S., Qian, Q., **ong, G., et al. (2022a). High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan. Sci China Life Sci 65, 398–411.
Zhang, J., Abdelraheem, A., Ma, J., Zhu, Y., Dever, J., Wheeler, T.A., Hake, K., Wedegaertner, T., and Yu, J. (2022b). Map** of dynamic QTLs for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a backcross inbred line population of Upland cotton. Mol Genet Genomics 297, 319–332.
Zhang, J., Gao, Y., Feng, M., Cui, Y., Li, S., Liu, L., Wang, Y., Xu, W., and Li, F. (2022c). Genome-wide identification of the HD-ZIP III subfamily in Upland cotton reveals the involvement of GhHB8-5D in the biosynthesis of secondary wall in fiber and drought resistance. Front Plant Sci 12, 806195.
Zhang, J., Huang, G.Q., Zou, D., Yan, J.Q., Li, Y., Hu, S., and Li, X.B. (2018b). The cotton (Gossypium hirsutum) NAC transcription factor (FSN1) as a positive regulator participates in controlling secondary cell wall biosynthesis and modification of fibers. New Phytol 217, 625–640.
Zhang, J., and Wedegaertner, T. (2021). Genetics and breeding for glandless Upland cotton with improved yield potential and disease resistance: A review. Front Plant Sci 12, 753426.
Zhang, J., Li, J., Saeed, S., Batchelor, W.D., Alariqi, M., Meng, Q., Zhu, F., Zou, J., Xu, Z., Si, H., et al. (2022d). Identification and functional analysis of lncRNA by CRISPR/Cas9 during the cotton response to sapsucking insect infestation. Front Plant Sci 13, 784511.
Zhang, L., Liu, J., Cheng, J., Sun, Q., Zhang, Y., Liu, J., Li, H., Zhang, Z., Wang, P., Cai, C., et al. (2022e). Cotton long non-coding RNAs regulate cell wall defense genes and strengthen resistance to Verticillium wilt. Plant Physiol 189, 264–284.
Zhang, L., Lu, G., Huang, X., Guo, H., Su, X., Han, L., Zhang, Y., Qi, Z., **ao, Y., and Cheng, H. (2020). Overexpression of the caryophyllene synthase gene GhTPS1 in cotton negatively affects multiple pests while attracting parasitoids. Pest Manag Sci 76, 1722–1730.
Zhang, M., Han, L.B., Wang, W.Y., Wu, S.J., Jiao, G.L., Su, L., **a, G.X., and Wang, H.Y. (2017a). Overexpression of GhFIM2 propels cotton fiber development by enhancing actin bundle formation. J Integr Plant Biol 59, 531–534.
Zhang, M., Wang, X., Yang, J., Wang, Z., Chen, B., Zhang, X., Zhang, D., Sun, Z., Wu, J., Ke, H., et al. (2022f). GhENODL6 isoforms from the phytocyanin gene family regulated verticillium wilt resistance in cotton. Int J Mol Sci 23, 2913.
Zhang, M., Zheng, X., Song, S., Zeng, Q., Hou, L., Li, D., Zhao, J., Wei, Y., Li, X., Luo, M., et al. (2011). Spatiotemporal manipulation of auxin biosynthesis in cotton ovule epidermal cells enhances fiber yield and quality. Nat Biotechnol 29, 453–458.
Zhang, S., Jiang, Z., Chen, J., Han, Z., Chi, J., Li, X., Yu, J., **ng, C., Song, M., Wu, J., et al. (2021b). The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton. Mol Genet Genomics 296, 355–368.
Zhang, S., Lan, Q., Gao, X., Yang, B., Cai, C., Zhang, T., and Zhou, B. (2016a). Map** of genes for flower-related traits and QTLs for flowering time in an interspecific population of Gossypium hirsutum ×G. darwinii. J Genet 95, 197–201.
Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C.A., Scheffler, B.E., Stelly, D.M., et al. (2015). Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33, 531–537.
Zhang, T., **, Y., Zhao, J.H., Gao, F., Zhou, B.J., Fang, Y.Y., and Guo, H.S. (2016b). Host-induced gene silencing of the target gene in fungal cells confers effective resistance to the cotton wilt disease pathogen Verticillium dahliae. Mol Plant 9, 939–942.
Zhang, T., Zhao, Y.L., Zhao, J.H., Wang, S., **, Y., Chen, Z.Q., Fang, Y.Y., Hua, C.L., Ding, S.W., and Guo, H.S. (2016c). Cotton plants export microRNAs to inhibit virulence gene expression in a fungal pathogen. Nat Plants 2, 16153.
Zhang, X., Wei, J., Fan, S., Song, M., Pang, C., Wei, H., Wang, C., and Yu, S. (2016d). Functional characterization of GhSOC1 and GhMADS42 homologs from upland cotton (Gossypium hirsutum L.). Plant Sci 242, 178–186.
Zhang, X., Xue, Y., Guan, Z., Zhou, C., Nie, Y., Men, S., Wang, Q., Shen, C., Zhang, D., **, S., et al. (2021c). Structural insights into homotrimeric assembly of cellulose synthase CesA7 from Gossypium hirsutum. Plant Biotechnol J 19, 1579–1587.
Zhang, Y., Gao, Y., Wang, H.L., Kan, C., Li, Z., Yang, X., Yin, W., **a, X., Nam, H.G., Li, Z., et al. (2021d). Verticillium dahliae secretory effector PevD1 induces leaf senescence by promoting ORE1-mediated ethylene biosynthesis. Mol Plant 14, 1901–1917.
Zhang, Y., He, P., Yang, Z., Huang, G., Wang, L., Pang, C., **ao, H., Zhao, P., Yu, J., and **ao, G. (2017b). A genome-scale analysis of the PIN gene family reveals its functions in cotton fiber development. Front Plant Sci 8.
Zhang, Z., Ge, X., Luo, X., Wang, P., Fan, Q., Hu, G., **ao, J., Li, F., and Wu, J. (2018c). Simultaneous editing of two copies of Gh14-3-3d confers enhanced transgene-clean plant defense against Verticillium dahliae in allotetraploid Upland cotton. Front Plant Sci 9, 842.
Zhang, Z., Wang, P., Luo, X., Yang, C., Tang, Y., Wang, Z., Hu, G., Ge, X., **a, G., and Wu, J. (2019b). Cotton plant defence against a fungal pathogen is enhanced by expanding BLADE-ON-PETIOLE1 expression beyond lateral-organ boundaries. Commun Biol 2, 238.
Zhang, Z., Chai, M., Yang, Z., Yang, Z., and Fan, L. (2022g). GRAND: an integrated genome, transcriptome resources, and gene network database for Gossypium. Front Plant Sci 13.
Zhang, Z., Ruan, Y.L., Zhou, N., Wang, F., Guan, X., Fang, L., Shang, X., Guo, W., Zhu, S., and Zhang, T. (2017c). Suppressing a putative sterol carrier gene reduces plasmodesmal permeability and activates sucrose transporter genes during cotton fiber elongation. Plant Cell 29, 2027–2046.
Zhao, B., Cao, J.F., Hu, G.J., Chen, Z.W., Wang, L.Y., Shangguan, X.X., Wang, L.J., Mao, Y.B., Zhang, T.Z., Wendel, J.F., et al. (2018a). Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. New Phytol 218, 1061–1075.
Zhao, N., Wang, W., Grover, C.E., Jiang, K., Pan, Z., Guo, B., Zhu, J., Su, Y., Wang, M., Nie, H., et al. (2022a). Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance. Plant Biotechnol J 20, 691–710.
Zhao, N., Wang, W., Jiang, K., Grover, C.E., Cheng, C., Pan, Z., Zhao, C., Zhu, J., Li, D., Wang, M., et al. (2022b). A calmodulin-like gene (GbCML7) for fiber strength and yield improvement identified by resequencing core accessions of a pedigree in Gossypium barbadense. Front Plant Sci 12.
Zhao, T., Tao, X., Feng, S., Wang, L., Hong, H., Ma, W., Shang, G., Guo, S., He, Y., Zhou, B., et al. (2018b). LncRNAs in polyploid cotton interspecific hybrids are derived from transposon neofunctionalization. Genome Biol 19, 195.
Zhao, W., Kong, X., Yang, Y., Nie, X., and Lin, Z. (2019). Association map** seed kernel oil content in Upland cotton using genome-wide SSRs and SNPs. Mol Breeding 39, 105.
Zhao, Y., Chen, W., Cui, Y., Sang, X., Lu, J., **g, H., Wang, W., Zhao, P., and Wang, H. (2021). Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton. Theor Appl Genet 134, 1063–1081.
Zhao, Y., Huang, Y., Wang, Y., Cui, Y., Liu, Z., and Hua, J. (2018c). RNA interference of GhPEPC2 enhanced seed oil accumulation and salt tolerance in Upland cotton. Plant Sci 271, 52–61.
Zhao, Y., Wang, Y., Huang, Y., Cui, Y., and Hua, J. (2018d). Gene network of oil accumulation reveals expression profiles in develo** embryos and fatty acid composition in Upland cotton. J Plant Physiol 228, 101–112.
Zheng, K., Ni, Z., Qu, Y., Cai, Y., Yang, Z., Sun, G., and Chen, Q. (2018). Genome-wide identification and expression analyses of TCP transcription factor genes in Gossypium barbadense. Sci Rep 8, 14526.
Zhou, J., Wu, Y., Zhang, X., Zhao, L., Feng, Z., Wei, F., Zhang, Y., Feng, H., Zhou, Y., and Zhu, H. (2022a). MPK homolog GhNTF6 was involved in cotton against Verticillium wilt by interacted with VdEPG1. Int J Biol Macromol 195, 456–465.
Zhou, Y., Myat, A.A., Liang, C., Meng, Z., Guo, S., Wei, Y., Sun, G., Wang, Y., and Zhang, R. (2022b). Insights into microRNA-mediated regulation of flowering time in cotton through small RNA sequencing. Front Plant Sci 13.
Zhou, Y., Zhang, Z.T., Li, M., Wei, X.Z., Li, X.J., Li, B.Y., and Li, X.B. (2015). Cotton (Gossypium hirsutum) 14-3-3 proteins participate in regulation of fibre initiation and elongation by modulating brassinosteroid signalling. Plant Biotechnol J 13, 269–280.
Zhu, H., Tian, W., Zhu, X., Tang, X., Wu, L., Hu, X., and **, S. (2020). Ectopic expression of GhSAMDC1 improved plant vegetative growth and early flowering through conversion of spermidine to spermine in tobacco. Sci Rep 10, 14418.
Zhu, L., Jiang, B., Zhu, J., and **ao, G. (2022a). Auxin promotes fiber elongation by enhancing gibberellic acid biosynthesis in cotton. Plant Biotechnol J 20, 423–425.
Zhu, Q.H., **, S., Yuan, Y., Liu, Q., Zhang, X., and Wilson, I. (2022b). CRISPR/Cas9-mediated saturated mutagenesis of the cotton MIR482 family for dissecting the functionality of individual members in disease response. Plant Direct 6, e410.
Zhu, Q.H., Yuan, Y., Stiller, W., Jia, Y., Wang, P., Pan, Z., Du, X., Llewellyn, D., and Wilson, I. (2018a). Genetic dissection of the fuzzless seed trait in Gossypium barbadense. J Exp Bot 69, 997–1009.
Zhu, Q.H., Zhang, J., Liu, D., Stiller, W., Liu, D., Zhang, Z., Llewellyn, D., and Wilson, I. (2016). Integrated map** and characterization of the gene underlying the okra leaf trait in Gossypium hirsutum L. J Exp Bot 67, 763–774.
Zhu, S., Yu, X., Li, Y., Sun, Y., Zhu, Q., and Sun, J. (2018b). Highly efficient targeted gene editing in Upland cotton using the CRISPR/Cas9 system. Int J Mol Sci 19, 3000.
Zhu, T., Liang, C., Meng, Z., Sun, G., Meng, Z., Guo, S., and Zhang, R. (2017). CottonFGD: an integrated functional genomics database for cotton. BMC Plant Biol 17, 101.
Zhu, Y. (2016). The post-genomics era of cotton. Sci China Life Sci 59, 109–111.
Zhu, Y.Q., Xu, K.X., Luo, B., Wang, J.W., and Chen, X.Y. (2003). An ATP-binding cassette transporter GhWBC1 from elongating cotton fibers. Plant Physiol 133, 580–588.
Zhu, Y.X., and Li, F.G. (2013). The Gossypium raimondii genome, a huge leap forward in cotton genomics. J Integr Plant Biol 55, 570–571.
Zou, C., Lu, C., Shang, H., **g, X., Cheng, H., Zhang, Y., and Song, G. (2013). Genome-wide analysis of the Sus gene family in cotton. J Integr Plant Biol 55, 643–653.
Zou, X., Zhen, Z., Ge, Q., Fan, S., Liu, A., Gong, W., Li, J., Gong, J., Shi, Y., Wang, Y., et al. (2018). Genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species. Gene 646, 28–38.
Acknowledgements
This work was supported by the National Natural Science Foundation of China (32200286) and the China Postdoctoral Science Foundation (2022TQ0240, 2022M722470). We apologize to any authors whose work may not have been cited owing to length restrictions.
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Wen, X., Chen, Z., Yang, Z. et al. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. Sci. China Life Sci. 66, 2214–2256 (2023). https://doi.org/10.1007/s11427-022-2278-0
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DOI: https://doi.org/10.1007/s11427-022-2278-0