Editorial – Three decades and beyond: Breeding, biotech breakthroughs andfuture of China’s GM insect-resistant cotton

Cotton (Gossypium spp.) is a pivotal crop in the global textile industry, providing essential natural fibers. Additionally, cottonseed offers significant value as a source of oil and as feed for livestock (Huang et al. 2021; Wen et al. 2023). The sector, dependent on cotton, features a comprehensive value chain extending from the processing of fibers to the production of finished textiles, and it employs tens of millions of individuals (Dorward et al. 1970). The vitality of the cotton industry is essential for the economic prosperity of a wide array of interconnected industries. It directly influences the livelihoods of millions of households (Chapman et al. 1972). Therefore, the cotton industry plays a pivotal role in accelerating agriculture modernization. The cotton bollworm, Helicoverpa armigera, represents a significant agricultural pest with a global distribution (Wu 2007a). During the 1990s, China experienced annual outbreaks of this pest, substantially threatening key crop production, including cotton, maize, and various vegetables (Wu 2007b). Statistical data from 1992 indicate that the cotton bollworm affected an aggregate area of about 21.9 million hectares across different crop types within China, resulting in direct economic losses exceeding 10 billion CNY (Wu 2007b). The widespread infestation of the cotton bollworm precipitated a multitude of economic, social, and environmental challenges. These encompassed diminished profitability of cotton cultivation, escalated pesticide pollution, and acute poisoning incidents among humans and livestock (Lu 2016). These challenges significantly impeded the advancement of cotton production and rural economic development in China. To mitigate the devastating impact of the cotton bollworm, the Chinese government initiated a crucial research project to develop transgenic insect-resistant cotton (Jia et al. 2001). Prof. Sandui Guo, along with his team, developed a novel insect-resistant gene through the fusion of two Bacillus thuringiensis (Bt) genes, Cry1Ab and Cry1Ac, utilizing DNA synthesis techniques (Jia et al. 2001; Guo et al. 2015). This innovation, GFM Cry1Ab/c, is characterized by its independent intellectual property rights. The team successfully developed a monogenic Bt insect-resistant cotton germplasm, demonstrating an insecticidal efficiency exceeding 80% (Cui and Guo 1996). This achievement positioned China as the second nation, following the United States, to hold independent intellectual property rights for insect-resistant cotton. In response to the observed decline in the resistance of monogenic insect-resistant cotton over time, the researchers advanced their work by creating digenic insect-resistant cotton, achieved by integrating the GFM Cry1Ab/c and CpTI genes. The breakthrough resulted in an about 35% increase in the corrected mortality rate of cotton bollworm during the later growth stages, thereby establishing China as a leader in insect-resistant cotton research globally (Guo et al. 1999). To concurrently enhance cotton’s insect resistance and yield, a three-line hybrid insect-resistant cotton breeding system was developed. This system improved seed production efficiency by about 20%, reduced costs by approximately 60%, and increased the yield of hybrid cotton by around 10% (Zhang et al. 2005). This development marked a significant breakthrough in cotton hybrid breeding. The opening and sharing of China’s insect-resistant cotton germplasm resources have expedited the industrial application of these cultivars within the Chinese market. Leveraging the comprehensive benefits of diverse varieties, superior adaptability, and competitive pricing, the market share of China’s insect-resistant cotton surged from 10% in 1999 to 50% in 2003, subsequently reaching over 99% (Guo et al. 2015). Researchers have developed over 200 new insect-resistant cotton varieties using this germplasm, cumulatively extending to an area exceeding about 35 million ha. This development has reduced pesticide usage by over 650,000 tons and generated an incremental output value of about 65 billion RMB (Guo et al. 2015). The adoption of insect-resistant cotton in China has effectively mitigated cotton bollworm damage, substantially increasing cotton yield potential. Consequently, China’s cotton yield has surpassed 1,000 kilograms per hectare, establishing the country as a global leader in this domain. The development of insect-resistant cotton in China represents a significant milestone in agricultural biotechnology. These insect-resistant cotton varieties have been successfully deployed and protected by stringent intellectual property rights, promoting an ecosystem conducive to innovation and exclusivity (Guo et al. 2015; Lu 2016). The strategic and methodical approach adopted in the research, development, and commercialization processes of these transgenic insect-resistant cotton varieties has substantially enhanced China’s proficiency in achieving autonomy in the innovation of transgenic cotton technologies. Recent progress in cotton research, encompassing areas such as multi-genome assembly, precise genome editing techniques, elucidation of fiber formation mechanisms, comprehensive metabolite profiling, and advanced genetic breeding strategies, has markedly propelled the field of cotton science forward (Yang et al. 2020; Huang et al. 2021; Long Y et al. 2023). These advancements underscore the substantial progress achieved and establish a solid theoretical foundation that will underpin future innovations in cotton research and development, thereby contributing to the sustainability and productivity of cotton agriculture. This special issue publishes 17 articles, organized into three thematic sections. The initial section presents research articles on cotton functional genomics, addressing areas such as developing fibers and seeds, resistance to Verticillium wilt (VW), and responses to abiotic stresses and nutritional factors. The subsequent section highlights progress in cotton biotechnology, specifically in transgenic methodologies and genome editing technologies. The final section concentrates on utilizing biotechnological strategies in the molecular design breeding of cotton. Section 1: Cotton functional genomics The quality of cotton fiber is a crucial factor in determining textile product quality precise quantification of critical fiber characteristics, such as maturity, fineness, and neps, using accurate instruments is vital for understanding the molecular determinants of fiber quality and guiding genetic enhancement efforts. Li H G et al. (2024) conducted a comprehensive study on 383 G. hirsutum accessions, utilizing the Advanced Fiber Information System (AFIS) for 12 single fiber quality traits and the High Volume Instrument (HVI) for eight conventional traits. Their genome-wide association study (GWAS) analyses revealed key genes linked to fiber quality. They identified the pleiotropic locus FL_D11 affecting fiber length, and novel loci FM_A03, FF_A05, and FN_A07 governing fiber maturity, fineness, and neps, respectively. Significant genes, including GhKRP6 (fiber length), GhMAP8 (maturity), and GhDFR (fineness), were pinpointed. Deng et al. (2024) performed a comparative analysis of the PEL gene family within 10 Malvaceae genomes, identifying 14 PEL genes in Gossypium barbadense linked to superior fiber length and strength. Additionally, six genes (GhPEL1-25, GhPEL4-09, GhPEL5b-01, GbPEL1-29, GbPEL5b-01, and GbPEL5b-02) were identified as key influencers of fiber characteristics, corroborated by SNP associations and expression analyses. These findings provide valuable insights for breeders who use molecular methods to improve agronomic traits. Lint percentage (LP) is a critical determinant of cotton fiber yield. Wang W W et al. (2024) identified the qLPA01.1 locus through map-based cloning in an F2 population derived from a cross between G. hirsutum cultivar CCRI35 and the chromosome segment substitution line HT_390. Further analysis revealed S-acyltransferase protein 24 (GoPAT24) as the candidate gene for qLPA01.1, providing a crucial genetic marker for marker-assisted selection in breeding programs targeting the LP trait. VW, caused by Verticillium dahliae Kleb., significantly reduces cotton yield and fiber quality, leading to losses of up to 80% (Wei et al. 2015). Termed “the cancer of cotton”, it affects 2.5 million hectares or 50% of China’s cotton areas annually, causing economic losses between 250–310 million USD (Li et al. 2015). Managing this disease is challenging due to V. dahliae’s soil persistence and the lack of effective treatments for G. hirsutum. Efforts to breed resistant cultivars are limited by the scarcity of genetic resources and target genes for genetic engineering (Cheng and Jia 2001; Zhang et al. 2015). Liu J et al. (2024) identified GhMYB3D5, a novel R2R3-MYB transcription factor, as a specific responder to V. dahliae infection in cotton. This factor directly upregulates GhADH1 transcription, subsequently increasing the expression of genes involved in lignin biosynthesis, including PAL, C4H, 4CL, and POD/LAC. The resultant defense-induced lignin accumulation significantly improves cotton’s resistance to VW. Yu et al. (2024) found that overexpressing GhGRPL increases lignin production, thereby reinforcing the secondary cell wall and enhancing resistance to VW. Ethylene has been shown to bolster resistance against VW. Aini et al. (2024) identified GhERF91, an ethylene response factor, as a critical protein in combating V. dahliae, using transcriptomic analyses and weighted gene co-expression network analysis. GhERF91 plays a vital role in the ethylene signaling pathway, enhancing the plant’s defense against V. dahliae infection. Chai et al. (2024) discovered that GhPR6-5b, a key PR6 gene, enhances resistance to V. dahliae. This gene is positively regulated by GhWRKY75, a critical component of cotton’s defense against VW, through direct binding to the W-box TTGAC(T/C). The aforementioned study provides genetic resources for breeding cotton resistant to V. dahlia. Another strategy for VW control employs host-induced gene silencing (HIGS) to introduce dsRNA targeting V. dahliae pathogenic genes into host plants. Wang Q et al. (2024) engineered two transgenic cotton lines, VdThit-RNAi-1 and VdThit-RNAi-2, by introducing dsRNA against the VdThit, a thiamine transporter protein gene. These lines demonstrated enhanced resistance to VW and significantly improved yields in field trials. Recently, China’s cotton cultivation has increasingly concentrated in Xinjiang, a region where abiotic stresses, notably drought and salinity, substantially limit production. Identifying and cloning genes pivotal for stress adaptation, and integrating them into cotton breeding to enhance abiotic stress resilience, are key to ensuring stable yields. Yu et al. (2024) showed that the expression of GhGRPL positively affected both plant growth and elevated salt stress resilience in saline environments. Wang C X et al. (2024) observed that the expression of the atypical protein kinase genes, GhABC1K2-A05 and GhABC1K12-A07, was induced by various abiotic stress treatments in cotton. Furthermore, the knockdown of GhABC1K2-A05 and GhABC1K12-A07 resulted in increased sensitivity of cotton to salt and drought stress. It has long been established that the morphological traits and developmental dynamics of plant roots are crucial for water acquisition in plants, significantly contributing to adaptation under various environmental stresses. Zhu et al. (2024) showed that root drenching with exogenous melatonin significantly boosts cotton yield through enhanced root growth and reduced drought-related damage, establishing a basis for melatonin use in agriculture via this method. Wu et al. (2024) examined six root traits, including main root length (MRL), root fresh weight (RFW), total root length (TRL), root surface area (RSA), root volume (RV), and root average diameter (AvgD), across 242 upland cotton accessions, identifying 41 elite loci and 17 candidate genes associated with root development by GWAS. Furthermore, they provided experimental validation of GhWPP2’s positive effect on root development. Section 2: Cotton biotechnology Over the past three decades, insect-resistant cotton developed in China has emerged as one of the most successful applications of genetic engineering technology in plant breeding. The widespread adoption of Bt cotton in China has effectively reduced infestations of cotton bollworms. However, several studies have demonstrated that the expression of insecticidal proteins varies significantly among different cotton tissues, with the lowest expression observed in cotton bolls during their formation stage. Additionally, abiotic stressors, particularly high temperatures, have been shown to significantly reduce the levels of these proteins, thereby challenging the control of cotton bollworm populations. Liu Z Y et al. (2024) demonstrated that through the synergistic regulation of amino acids and ethylene diamine tetraacetic acid (EDTA), the Bt protein content was significantly enhanced in both cotton bolls and their subtending leaves, with increases of 67.5 and 21.7%, respectively. Furthermore, the discrepancy in Bt protein levels between cotton bolls and their subtending leaves was reduced by 31.2%. This effect is attributed to the elevation of soluble protein content and transaminase activity, coupled with a reduction in catabolic enzyme activity, thereby facilitating an increase in Bt protein content. The advent of transgenic insect-resistant cotton has provided critical insights into overcoming cotton production challenges. Weed infestations, a significant threat, compete for vital resources and exacerbate disease and pest issues, negatively impacting cotton yield and quality. Herbicide-resistant crops now account for about 80% of the global genetically modified (GM) crop area, with these cotton varieties representing 90% in the United States. China has made notable progress in developing herbicide-resistant cotton germplasms (Liang et al. 2017), particularly with the certification of the highly herbicide-resistant cotton strain GGK2 by the Ministry of Agriculture and Rural Affairs of China. This certification marks a significant step forward in expanding the available germplasm resources for the swift development and application of herbicide-resistant cotton varieties. Interestingly, Yan et al. (2024) discovered a stable dwarf phenotype, DHR1, in EPSPS-overexpressing cotton, attributing DHR1 dwarfism to the EPSPS gene. This inheritable phenotype exhibited elevated flavonoid metabolites and reduced lignin metabolites in DHR1 lines, modifying auxin signaling gene expression, thereby influencing auxin response and cell elongation. This study advances understanding of the biological functions of EPSPS in cotton. Beyond expressing exogenous genes like Bt and EPSPS for insect resistance or herbicide tolerance, researchers are leveraging transgenic technology to precisely control the expression of several endogenous genes in cotton, aiming to attain specific trait enhancements. Chong et al. (2024) showed that overexpressing the G. barbadense LMI1 gene (GbLMI1) significantly boosts vegetative growth in cotton, leading to increased leaf size and dry weight and, consequently, enhanced biomass. Gene editing, an advanced biotechnological method, enables precise genetic modifications by inserting, deleting, or replacing DNA sequences, facilitating targeted phenotypic improvements in organisms (Manghwar et al. 2019). In cotton research, the rapid advancement of gene editing technologies, particularly the development of various CRISPR/Cas systems by Chinese scientists, has been notable (Yang et al. 2024). These systems, including CRISPR/Cas9, Cas12a, Cas12b, cytosine base editors (CBE), adenine base editors (ABE), ABE8e, Cas13a/13b/13d, CasRX, dCas9-TV, and targeted RNA methylation/demethylation editors (TME/TDE), offer high editing efficiency, specificity, and reduced off-target effects (Gao et al. 2017; Long et al. 2018; Wang et al. 2018, 2020, 2022; Zhu et al. 2018; Li B et al. 2019; Qin et al. 2020; Li et al. 2022; Yu et al. 2023). They enable various genetic interventions, from gene knockouts and knock-ins to base editing, point mutations, RNA editing, transcriptional activation, and epigenetic modifications. A rigorous framework for evaluating the off-target effects of these CRISPR/Cas systems in cotton has been established, utilizing whole-genome high-throughput resequencing (Li J et al. 2019). Utilizing these gene editing tools, Li T W et al. (2024) generated the ghpdct mutant in cotton, which disrupts GhPDCT1/2 and influences the conversion of phosphatidylcholine to diacylglycerol in cottonseeds, resulting in changes to oleic acid, linoleic acid, palmitic acid, and stearic acid levels. This new germplasm with elevated oleic acid content in cottonseed oil could enhance the economic and nutritional value of cotton as an oil crop, promoting the industrial progress of cotton. In addition, a mutant library of over 5,000 genes has been created, addressing traits such as fiber and seed quality, anther development, plant architecture, disease and pest resistance, drought tolerance, and haploid induction. This has led to the development of novel cotton germplasms with enhanced traits, including increased oleic acid in seeds, gossypol elimination, herbicide resistance, heat tolerance, desirable plant architecture, early maturity, and efficient haploid induction (Gao et al. 2020; Chen et al. 2021; Li et al. 2021; Long L et al. 2023; Yu et al. 2023; Wang G et al. 2024). The deployment and broad application of gene editing in cotton have significantly advanced cotton functional genomics and biological breeding, promising to play a crucial role in future research and development efforts. Section 3: Cotton molecular design breeding Introducing Chinese transgenic insect-resistant cotton marks a new phase in biotechnological breeding. The completion and release of the cotton genome sequence have significantly accelerated advancements in cotton molecular design breeding. Enhanced by the proliferation of multi-omics data, such as genomics, phenomics, and transcriptomics, the process of identifying gene loci linked to essential traits has been expedited. Moreover, this data richness has enabled the identification of loci controlling complex cotton traits, which were difficult to detect using conventional approaches. In this special issue, Li H G et al. (2024) combined AFIS and HVI fiber phenotyping with GWAS to identify the pleiotropic locus FL_D11, regulating fiber length, and three novel loci (FM_A03, FF_A05, and FN_A07) influencing fiber maturity, fineness, and neps, offering key markers for breeding improved fiber quality. Similarly, Wu et al. (2024) utilized the CottonSNP80K array to analyze 56,010 SNPs for GWAS on six root traits, identifying 41 QTLs: MRL (9), RFW (6), TRL (9), RSA (12), RV (12), and AvgD (2), offering critical markers for enhancing root traits in cotton breeding. Focusing on key breeding objectives beyond yield, quality, and stress tolerance, developing early-maturing cotton varieties aims to shorten growth duration, enhance cropping efficiency, and alleviate the competition between grain and cotton cultivation in China. Ma et al. (2024) investigated five early maturity traits in cotton: whole growth period, flowering timing, node of the first fruiting branch, height of the first fruiting branch, and plant height, utilizing BSA-seq and QTL mapping. They identified a significant gene on chromosome D03 associated with these traits, providing essential markers for breeding early-maturing cotton varieties. Improving seed germination rates is essential for uniform cotton seedling emergence, directly impacting yield and profitability. Pei et al. (2024) showed that GhPMEI53 and related genes modify cell wall mechanical properties, affecting the endosperm or testa’s mechanical resistance. Additionally, they regulate phytohormone pathways, notably ABA and GA, essential for seed germination. This study lays a crucial theoretical basis for breeding cotton seeds with increased vigor. Over the preceding three decades, advancements in the domains of cotton functional genomics, biotechnology, molecular breeding, and the deployment of insect-resistant cotton varieties, have exerted substantial direct and indirect influences across diverse agricultural sectors. Specifically, in crop genomics, the generation of high-resolution reference genomes for various Gossypium species has facilitated a deeper understanding of the evolutionary trajectories of cotton germplasm (Yang et al. 2020; Long Y et al. 2023). From an agroecological perspective, empirical investigations into the modulatory effects of insect-resistant cotton on the evolutionary dynamics of pest populations have underscored that the extensive adoption of Bt cotton, in conjunction with reduced pesticide application, augments the efficacy of biological pest management strategies within agroecosystems (Wu et al. 2008; Lu et al. 2012). Unfortunately, due to space constraints, this special issue could not cover all relevant agricultural research areas or include many noteworthy cotton studies. Nonetheless, we aim to enhance our understanding of transgenic Bt cotton’s development and contributions in China through this publication, hoping it offers valuable insights to our readers. We thank Dr. Fuguang Li (Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS)), Dr. Hezhong Dong (Institute of Industrial Crops, Shandong Academy of Agricultural Sciences), Dr. Yongjun Zhang (Institute of Plant Protection of CAAS), and Dr. Quanjia Chen (College of Agronomy, Xinjiang Agricultural University) for serving as co-guest editors and organizing this special issue. We thank the Editorial Department and Editor-in-Chief of the Journal of Integrative Agriculture (JIA) for their collaboration in organizing this special issue, inviting the peer reviewers and eventually assembling the accepted manuscripts into this work.