Anders S, Pyl P T, Huber W. 2015. HTSeq - A Python framework to work with high-throughput sequencing data. Bioinformatics, 31, 166–169.

Ashburner M, Ball C A, Blake J A, Botstein D, Butler H, Cherry J M, Davis A P, Dolinski K, Dwight S S, Eppig J T, Harris M A, Hill D P, Issel-Tarver L, Kasarskis A, Lewis S, Matese J C, Richardson J E, Ringwald M, Rubin G M, Sherlock G. 2000. Gene ontology: Tool for the unification of biology. Nature Genetics, 25, 25–29.

Benedict C R, Liu J, Stipanovic R D. 2006. The peroxidative coupling of hemigossypol to (+)- and (–)-gossypol in cottonseed extracts. Phytochemistry, 67, 356–361.

Cai Y, Cai X, Wang Q, Wang P, Zhang Y, Cai C, Xu Y, Wang K, Zhou Z, Wang C. 2020. Genome sequencing of the Australian wild diploid species Gossypium australe highlights disease resistance and delayed gland morphogenesis. Plant Biotechnology Journal 18, 814–828.

Chen H, Nelson R, Sherwood J. 1994. Enhanced recovery of transformants of Agrobacterium tumefaciens after freeze-thaw transformation and drug selection. Biotechniques, 16, 664–668, 670.

Chen Y, Zhang R, Song Y, He J, Sun J, Bai J, An Z, Dong L, Zhan Q, Abliz Z. 2009. RRLC-MS/MS-based metabonomics combined with in-depth analysis of metabolic correlation network: Finding potential biomarkers for breast cancer. Analyst, 134, 2003–2011.

Desjardins P, Conklin D. 2010. NanoDrop microvolume quantitation of nucleic acids. Journal of Visualized Experiments, 22, 2565.

Eberwine J. 1996. Amplification of mRNA populations using aRNA generated from immobilized Oligo(dT)-T7 primed cDNA. BioTechniques, 20, 584–591.

Effenberger I, Harport M, Pfannstiel J, Klaiber I, Schaller A. 2017. Expression in Pichia pastoris and characterization of two novel dirigent proteins for atropselective formation of gossypol. Applied Microbiology and Biotechnology, 101, 2021–2032.

Feng S, Xu M, Liu F, Cui C, Zhou B. 2019. Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe. BMC Plant Biology, 19, 365.

Gao W, Xu F C, Long L, Li Y, Zhang J L, Chong L, Botella J R, Song C P. 2020. The gland localized CGP1 controls gland pigmentation and gossypol accumulation in cotton. Plant Biotechnol Journal, 18, 1573–1584.

Gao W, Zhu X, Ding L, Xu B, Gao Y, Cheng Y, Dai F, Liu B, Si Z, Fang L. 2022. Development of the engineered “glanded plant and glandless seed” cotton. Food Chemistry (Molecular Science), 9, 100130.

Gao X, Britt Jr R C, Shan L, He P. 2011. Agrobacterium-mediated virus-induced gene silencing assay in cotton. Journal of Visualized Experiments, 20, 2938.

Gomez K A, Gomez A A. 1984. Statistical Procedures for Agricultural Research. 2nd ed. John Wiley and Sons, New York.

Green M R, Sambrook J. 2019. Isolation of Poly(A)+ Messenger RNA Using Magnetic Oligo(dT) Beads. Cold Spring Harbor Protocols, 2019, doi: 10.1101/pdb.prot101733.

Huang G, Huang J Q, Chen X Y, Zhu Y X. 2021. Recent advances and future perspectives in cotton research. Annual Review of Plant Biology, 17, 437–462.

Janga M R, Pandeya D, Campbell L M, Konganti K, Villafuerte S T, Puckhaber L, Pepper A, Stipanovic R D, Scheffler J A, Rathore K S. 2019. Genes regulating gland development in the cotton plant. Plant Biotechnology Journal, 17, 1142–1153.

Juan H. 2012. Fine mapping of the dominant glandless gene Gl2e in cotton. MSc thesis, Henan University, Zhengzhou, China. (in Chinese)

Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28, 27–30.

Kong L, Li S, Qian Y, Cheng H, Zhang Y, Zuo D, Lv L, Wang Q, Li J, Song G. 2023. Comparative transcriptome analysis revealed key genes regulating gossypol synthesis in tetraploid cultivated cotton. Genes, 14, 1144.

Lai X, Stigliani A, Vachon G, Carles C, Smaczniak C, Zubieta C, Kaufmann K, Parcy F. 2019. Building transcription factor binding site models to understand gene regulation in plants. Molecular Plant, 12, 743–763.

Langfelder P, Horvath S. 2008. WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics, 29, 559.

Lieberman-Aiden E, van Berkum N L, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie B R, Sabo P J, Dorschner M O, Sandstrom R, Bernstein B, Bender M A, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny L A, Lander E S, Dekker J. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science, 326, 289–293.

Lin J L, Fang X, Li J X, Chen Z W, Wu W K, Guo X X, Liu N J, Huang J F, Chen F Y, Wang L J. 2023. Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds. Nature Plants, 9, 605–615.

Luo P, Wang Y H, Wang G D, Essenberg M, Chen X Y. 2001. Molecular cloning and functional identification of (+)-δ-cadinene–8-hydroxylase, a cytochrome P450 mono-oxygenase (CYP706B1) of cotton sesquiterpene biosynthesis. The Plant Journal, 28, 95–104.

Ma D, Hu Y, Yang C, Liu B, Fang L, Wan Q, Liang W, Mei G, Wang L, Wang H. 2016. Genetic basis for glandular trichome formation in cotton. Nature Communications, 22, 10456.

Ma Z, Zhang Y, Wu L, Zhang G, Sun Z, Li Z, Jiang Y, Ke H, Chen B, Liu Z. 2021. High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. Nature Genetics, 53, 1385–1391.

Mandel M A, Feldmann K A, Herrera-Estrella L, Rocha-Sosa M, León P. 1996. CLA1, a novel gene required for chloroplast development, is highly conserved in evolution. Plant Journal, 9, 649–658.

Maryam H, Ali Z, Saddique M A B, Nawaz F. 2022. GhCDNC and GhCYP706B1 genes mediate gossypol biosynthesis in upland cotton. Molecular Biology Reports, 49, 4919–4928.

Mehari T G, Fang H, Feng W, Zhang Y, Umer M J, Han J, Ditta A, Khan M K, Liu F, Wang B. 2023. Genome-wide identification and expression analysis of terpene synthases in Gossypium species in response to gossypol biosynthesis. Functional & Integrative Genomics, 23, 197.

Meyers J A, Sanchez D, Elwell L P, Falkow S. 1976. Simple agarose gel electrophoretic method for the identification and characterization of plasmid deoxyribonucleic acid. Journal of Bacteriology, 127, 1529–1537.

Pan Y, Meng F, Wang X. 2020. Sequencing multiple cotton genomes reveals complex structures and lays foundation for breeding. Frontiers in Plant Sciences, 16, 560096.

de la Paz Celorio-Mancera L, Ahn S J, Vogel H, Heckel D G. 2011. Transcriptional responses underlying the hormetic and detrimental effects of the plant secondary metabolite gossypol on the generalist herbivore Helicoverpa armigera. BMC Genomics, 23, 575.

Rathore K S, Pandeya D, Campbell L M, Wedegaertner T C, Puckhaber L, Stipanovic R D, Thenell J S, Hague S, Hake K. 2020. Ultra-low gossypol cottonseed: Selective gene silencing opens up a vast resource of plant-based protein to improve human nutrition. Critical Reviews in Plant Sciences, 39, 1–29.

SAS (Statistical Analysis System) Institute Inc. 2023. SAS/STAT® 15.3 User’s Guide. version 9.4. Statistical Analysis System Institute Inc, Cary, North Carolina, USA.

Schmittgen T D, Livak K J. 2008. Analyzing real-time PCR data by the comparative CT method. Nature Protocols, 3, 1101–1108.

Schwartz D C, Li X, Hernandez L I, Ramnarain S P, Huff E J, Wang Y K. 1993. Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping. Science, 262, 110–114.

Shannon P, Markiel A, Ozier O, Baliga N S, Wang J T, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498–2504.

Sheng K, Sun Y, Liu M, Cao Y, Han Y, Li C, Muhammad U, Daud M K, Wang W, Li H. 2023. A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol. Plant Communications, 4, 100421.

Sun Y, Han Y, Sheng K, Yang P, Cao Y, Li H, Zhu Q H, Chen J, Zhu S, Zhao T. 2023. Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of pigment glands in Gossypium bickii. Molecular Plant, 16, 694–708.

Sunilkumar G, Campbell L M, Puckhaber L, Stipanovic R D, Rathore K S. 2006. Engineering cottonseed for use in human nutrition by tissue-specific reduction of toxic gossypol. Proceedings of the National Academy of Sciences of the United States of America, 103, 18054–18059.

Tao T, Zhao L, Lv Y, Chen J, Hu Y, Zhang T, Zhou B. 2013. Transcriptome sequencing and differential gene expression analysis of delayed gland morphogenesis in Gossypium australe during seed germination. PLoS ONE, 8, 75323.

Tettelin H, Masignani V, Cieslewicz M J, Donati C, Medini D, Ward N L, Angiuoli S V, Crabtree J, Jones A L, Durkin A S, Deboy R T, Davidsen T M, Mora M, Scarselli M, Margarit y Ros I, Peterson J D, Hauser C R, Sundaram J P, Nelson W C, Madupu R, et al. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”. Proceedings of the National Academy of Sciences of the United States of America, 102, 13950–13955.

Tian X, Ruan J, Huang J, Fang X, Mao Y, Wang L, Chen X, Yang C. 2016. Gossypol: Phytoalexin of cotton. Science China (Life Science), 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. 2018. Characterization of gossypol biosynthetic pathway. Proceedings of the National Academy of Sciences of the United States of America, 115, E5410–E5418.

Trygg J, Wold S. 2002. Orthogonal projections to latent structures (O-PLS). Journal of Chemometrics, 16, 119–128.

Wen T, Xu X, Ren A, Zhao G, Wu J. 2023. Genome-wide identification of terpenoid synthase family genes in Gossypium hirsutum and functional dissection of its subfamily cadinene synthase A in gossypol synthesis. Frontiers in Plant Science, 26, 1162237.

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

Wu C, Cheng H, Li S, Zuo D, Lin Z, Zhang Y, Lv L, Wang Q, Song G. 2021. Molecular cloning and characterization of GhERF105, a gene contributing to the regulation of gland formation in upland cotton (Gossypium hirsutum L.). BMC Plant Biology, 21, 102.

WWF (World Wildlife Fund). 2022. Sustainable agriculture: Cotton. [2024-6-21]. https://www.worldwildlife.org/industries/cotton

Xu Y H, Wang J W, Wang S, Wang J Y, Chen X Y. 2004. Characterization of GaWRKY1, a cotton transcription factor that regulates the sesquiterpene synthase gene (+)-δ-cadinene synthase-A. Plant Physiology, 135, 507–515.

Ye K, Teng T, Yang T, Zhao D, Zhao Y. 2023. Transcriptome analysis reveals the effect of grafting on gossypol biosynthesis and gland formation in cotton. BMC Plant Biology, 23, 37.

Zang Y, Xu C, Xuan L, Ding L, Zhu J, Si Z, Zhang T, Hu Y. 2021. Identification and characteristics of a novel gland-forming gene in cotton. Plant Journal, 108, 781–792.

Zhang C, Liu X, Song Y, Sun Z, Zhang J, Wu H, Yang Y, Wang Z, He D. 2022. Comparative transcriptome analysis reveals genes associated with the gossypol synthesis and gland morphogenesis in Gossypium hirsutum. Genes (Basel), 13, 1452.

Zhao T, Xie Q, Li C, Li C, Mei L, Yu J Z, Chen J, Zhu S. 2020. Cotton roots are the major source of gossypol biosynthesis and accumulation. BMC Plant Biology, 20, 88.