1 Introduction

Cotton (Gossypium spp.) is a cornerstone of the global textile industry, providing natural fibers essential for fabric production. It holds significant economic value, with a raw material worth approximately $5.5 billion annually worldwide (Mirzaei et al., 2018). Major cotton-producing countries include China, the USA, India, and Pakistan, with Pakistan being the fourth-largest producer (Razzaq et al., 2021). The crop's economic importance extends beyond fiber production, contributing to the livelihoods of millions of farmers and workers in the textile industry.

Cotton cultivation faces numerous biotic stress challenges, including pests, diseases, and viruses, which significantly impact yield and quality. Common biotic stresses include infestations by cotton bollworm and Verticillium wilt, which can devastate crops if not managed effectively (Mirzaei et al., 2018). The cotton leaf curl virus (CLCuV) is another major threat, particularly in regions like Pakistan, where it has caused substantial yield losses (Razzaq et al., 2021). Despite advances in transgenic approaches, achieving permanent resistance to these biotic stresses remains a significant challenge.

Genetic diversity within cotton germplasm is crucial for developing biotic stress-resistant varieties. Conventional breeding programs have made strides in improving resistance, but the limited availability of germplasm with adequate resistance to biotic stresses has hindered progress (Mirzaei et al., 2018). Utilizing molecular markers, quantitative trait loci (QTLs), and genome-wide association studies (GWAS) has facilitated the identification and incorporation of resistance genes into commercial varieties (Razzaq et al., 2021; Zheng et al., 2021). The integration of genes such as cry1Ab and chitinase has shown promise in conferring resistance to pests and diseases. Additionally, wild cotton species, which possess inherent resistance traits, serve as valuable genetic reservoirs for breeding programs (Yu et al., 2021; Wu, 2024).

This study attempts to synthesize existing research on cotton germplasm to identify key genetic components and strategies for enhancing biotic stress resistance, discuss the genetic mechanisms underlying resistance and potential candidate genes for future breeding efforts, and provide an overview of how these findings can guide breeding programs and biotechnological interventions to develop more resilient cotton varieties for sustainable production and economic stability.

2 Biotic Stress Factors Affecting Cotton

2.1 Major pathogens: fungi, bacteria, and viruses

Cotton crops are significantly impacted by a variety of pathogens, including fungi, bacteria, and viruses. Fungal pathogens such as Fusarium and Verticillium wilt are particularly destructive, causing severe growth interruptions and yield losses (Billah et al., 2021). Bacterial pathogens also pose a significant threat, infecting various parts of the plant including leaves, stems, roots, and fruits (Tarazi et al., 2019). Viral infections, although less common, can lead to substantial crop damage and are often managed through chemical control methods, which have their own set of challenges including resistance development and environmental contamination (Wagemans et al., 2022).

2.2 Insect pests and their impact on cotton yield

Insect pests are another major biotic stress factor affecting cotton yield. The reduction in chemical insecticidal sprays has altered the biodiversity and dynamics of primary and secondary insects, leading to increased pest pressures (Figure 1) (Razzaq et al., 2023). Insects such as chewing and sucking pests are particularly problematic, causing significant damage to cotton crops. The impact of these pests is exacerbated by climate change, which influences their population dynamics and proliferation (Chaudhary et al., 2022). Effective management strategies include the use of synthetic pesticides, although these come with environmental and health risks, necessitating the integration of alternative measures such as resistant cultivars and biocontrol agents (Naeem-Ullah et al., 2020).

Figure 1 Changes in pest-community interactions due to Bt cotton and Bt toxins (Adopted from Razzaq et al., 2023) Image caption: * Plant debrises include defoliation, pollen falling, and sqare and boll shedding (Adopted from Razzaq et al., 2023)

2.3 Emerging biotic threats due to climate change and agricultural practices

Climate change is emerging as a significant factor that exacerbates biotic stress in cotton crops. Changes in temperature, humidity, and rainfall patterns are expected to increase the incidence of pests and diseases (Shahzad et al., 2021). For instance, global warming can extend the geographical range and developmental season of insect pests, leading to increased crop damage (Naeem-Ullah et al., 2020). Additionally, agricultural practices such as the unwise use of nutrients and the reduction in chemical controls contribute to the vulnerability of cotton crops to biotic stresses (Hassan et al., 2020). The integration of biotechnological solutions, including gene editing and the use of bioagents, is crucial for developing resilient cotton varieties that can withstand these emerging threats (Tarazi et al., 2019).

Cotton crops face significant biotic stress from pathogens such as fungi, bacteria, and viruses, as well as from insect pests. Climate change and certain agricultural practices further exacerbate these challenges, making it essential to adopt integrated management strategies that include biotechnological solutions and sustainable agricultural practices.

3 Genetic Resources in Cotton

3.1 Importance of genetic diversity in biotic stress resistance

Genetic diversity is crucial for enhancing biotic stress resistance in cotton. The narrow genetic base of modern cultivars has become a significant bottleneck for crop improvement efforts. Utilizing crop wild relatives (CWRs) is a promising approach to enhance the genetic diversity of cultivated crops, providing a broader repertoire of resistance traits against various biotic stresses (Mammadov et al., 2018; Kapazoglou et al., 2023). The genetic diversity found in wild species and semi-domesticated races of cotton can be harnessed to develop varieties with improved resistance to pests and diseases, thereby ensuring agricultural sustainability and productivity (Figure 2) (Zhu et al., 2019).

Figure 2 Functional validation of two candidate genes related to Verticillium Wilt resistance (Adopted from Zhu et al., 2019) Image caption: (A). The spectrum of allele frequencies at the causal polymorphisms of two genes in each upland cotton group. (B). Relative expression levels of PR1 and WRKY20 were detected at six time point post inoculation in roots of TM-1 and Hai7124. Ghhis3 was used as an internal control. Error bars represent the standard deviation of three biological replicates. ** indicate a significant difference to 0 h at t-test with p value of 0.01. (C) Expression of two genes in normal plant, injected with TRV::00 plant and silencing plant, detected by qRT-PCR in leaves of Hai7124. Ghhis3 was used as an internal control. Error bars represent the standard deviation of three biological replicates. ** indicate a significant difference to normal plant and injected with TRV::00 plan at t-test with p value of 0.01. (D). Plant phenotypic of each treatment in 15 d, 20 d and 25 d after V991 inoculation. (E). The statistics of percentage of wilted leaves (PWL) in each treatment. Error bars represent the standard deviation of three replicates in each treatment (Adopted from Zhu et al., 2019)

3.2 Wild relatives of cotton as reservoirs of resistance traits

Wild relatives of cotton, such as Gossypium hirsutum and Gossypium davidsonii, serve as valuable reservoirs of resistance traits. These species have been exposed to natural environmental challenges for thousands of years, maintaining a higher level of genetic diversity compared to domesticated cultivars (Zhang et al., 2016; Peng et al., 2022). The genetic resources found in these wild species include genes involved in adaptation to environmental challenges, which can be introgressed into domesticated cotton to enhance resilience to biotic stresses. For instance, genes related to stress response, such as PR1 and WRKY20, have been identified in semi-domesticated races and shown to significantly contribute to biotic stress resistance (Zhu et al., 2019).

3.3 Role of traditional and modern breeding programs in developing resistant varieties

Traditional breeding programs have historically relied on phenotypic selection and cross-breeding to develop cotton varieties with improved resistance to biotic stresses. However, these methods are time-consuming and often limited by the genetic diversity available within cultivated species (Zhang et al., 2016). Modern breeding programs have increasingly incorporated advanced biotechnologies, such as next-generation sequencing and genome-wide association studies (GWAS), to accelerate the identification and transfer of resistance traits from wild relatives to cultivated varieties (Zheng et al., 2021). These technologies enable the precise manipulation of genomes and the efficient transfer of desirable traits, thereby enhancing the development of biotic stress-resistant cotton varieties (Mammadov et al., 2018). The integration of traditional and modern breeding approaches is essential for overcoming the challenges posed by biotic stresses and ensuring the continued improvement of cotton germplasm.

Genetic diversity is fundamental for developing biotic stress-resistant cotton varieties. Wild relatives of cotton provide a rich source of resistance traits that can be harnessed through both traditional and modern breeding programs. The use of advanced biotechnologies has significantly enhanced the efficiency of trait transfer, ensuring the development of resilient cotton varieties capable of withstanding biotic stresses.

4 Case Study: Evaluating Fusarium Wilt Resistance in Cotton Germplasm

4.1 Overview of fusarium wilt as a major biotic stress in cotton

Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. vasinfectum (FOV), is a significant threat to cotton production globally. The disease manifests through symptoms such as root rot, seedling wilt, vascular discoloration, plant wilting, defoliation, and ultimately plant death (Abdelraheem et al., 2022; Zhang et al., 2022). Among the various races of FOV, race 4 (FOV4) is particularly destructive, causing severe damage in regions like California's San Joaquin Valley and recently identified in New Mexico and Texas (Ulloa et al., 2020). The pathogen's ability to persist in soil and infect plants at various growth stages makes it a persistent challenge for cotton growers ((Zhang et al., 2020; Zhu et al., 2022).

4.2 Advances in identifying and utilizing resistant germplasm

Significant progress has been made in identifying and utilizing cotton germplasm resistant to Fusarium wilt. Studies have employed various methods, including genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping, to pinpoint genetic regions associated with resistance. For instance, a major QTL for FOV4 resistance was identified on chromosome D02 in a multi-parent advanced generation inter-cross (MAGIC) population of Upland cotton (Zhu et al., 2022). Additionally, screening of over 3000 germplasm lines under controlled conditions has revealed significant genetic variation in resistance, with some lines showing complete resistance to FOV4 (Zhang et al., 2020). The development of rapid and reliable evaluation methods, such as taproot rot-based assessments during seed germination, has further facilitated the identification of resistant cultivars (Zhu et al., 2023).

4.3 Success stories and challenges in fusarium wilt resistance breeding

Breeding for Fusarium wilt resistance has seen several success stories, particularly in the development of resistant Pima cotton lines. For example, the Pima S-6 germplasm has shown high levels of resistance and has been used to develop improved resistant lines. Similarly, pedigree selection within Acala 1517-08 and its derivatives has led to the identification of progenies with resistance levels comparable to resistant controls (Zhang et al., 2020). However, challenges remain, such as the complex inheritance patterns of resistance in Upland cotton, which range from recessive to intermediate, making breeding efforts more complicated (Ulloa et al., 2020). Additionally, environmental factors and the presence of endophytes can affect the accuracy of resistance evaluations, necessitating the use of controlled conditions for reliable screening (Figure 3) (Parris et al., 2021).

Figure 3 Plants of three cultivars of Gossypium species growing in tissue culture 35 days after transfer to Oasis Horticubes (Adopted form Parris et al., 2021) Image caption: Showing healthy growth of foliage, A, Gossypium bar- badense 'DP348RF; B, G. barbadense 'GB1031'; and C, G. hirsutum 'TM-1' (Adopted form Parris et al., 2021)

Fusarium wilt, particularly race 4, poses a significant threat to cotton production. Advances in genetic mapping and screening methods have facilitated the identification of resistant germplasm, leading to the development of resistant cultivars. Despite these successes, challenges such as complex inheritance patterns and environmental variability continue to complicate breeding efforts.

5 Advances in Genomic and Breeding Tools

5.1 Role of molecular markers in identifying resistance genes

Molecular markers have revolutionized the identification of resistance genes in cotton by enabling precise mapping and selection. Techniques such as Quantitative Trait Loci (QTL) mapping and marker-assisted selection (MAS) have been instrumental in identifying genes associated with resistance to various biotic stresses. For instance, the development of Kompetitive Allele Specific PCR (KASP) markers has facilitated the identification of genes related to Verticillium wilt resistance in cotton, allowing for more efficient breeding programs (Zhao et al., 2021). Additionally, the use of high-density SNP arrays has enabled the detection of significant SNPs associated with disease resistance, further enhancing the precision of resistance breeding (Yasir et al., 2022).

5.2 Application of genome-wide association studies (GWAS) in resistance trait discovery

Genome-Wide Association Studies (GWAS) have become a powerful tool for uncovering the genetic basis of resistance traits in cotton. By analyzing the genetic variation across diverse populations, GWAS can identify SNPs linked to resistance traits. For example, GWAS has been used to identify QTLs associated with resistance to Fusarium wilt in Upland cotton, providing valuable insights into the genetic architecture of this trait (Zhu et al,, 2022). Moreover, GWAS has facilitated the identification of candidate genes involved in basal defense mechanisms, which are crucial for developing resistant cotton varieties. The integration of GWAS with other genomic tools, such as QTL-seq and transcriptome sequencing, has further enhanced the resolution and accuracy of resistance gene identification (Zhao et al., 2021; Pang et al., 2021).

5.3 Integration of CRISPR and other gene-editing technologies in resistance breeding

CRISPR/Cas-mediated genome editing has emerged as a game-changing tool in resistance breeding, offering a rapid and precise method for creating genetic variations associated with biotic stress resistance. This technology allows for the targeted modification of genes involved in resistance to pathogens such as fungi, viruses, and bacteria, thereby accelerating the development of resistant cotton varieties. The application of CRISPR/Cas has been demonstrated to improve resistance traits efficiently and cost-effectively, making it a valuable addition to traditional breeding methods. Furthermore, the integration of CRISPR with other genomic tools, such as GWAS and molecular markers, holds great promise for enhancing the precision and efficiency of resistance breeding programs (Wang et al., 2022; Yasir et al., 2022).

The integration of advanced genomic and breeding tools, including molecular markers, GWAS, and CRISPR/Cas-mediated genome editing, has significantly advanced the identification and development of resistance traits in cotton. These tools have enabled precise mapping and selection of resistance genes, facilitated the discovery of genetic variations associated with resistance traits, and provided rapid and efficient methods for creating resistant cotton varieties. Together, these advancements are paving the way for more resilient and productive cotton crops.

6 Compilation and Meta-Analysis of Germplasm Studies

6.1 Key traits associated with biotic stress resistance

Biotic stress resistance in cotton is primarily associated with several key traits, including resistance to various pathogens and pests. Notable traits include resistance to Verticillium wilt, Fusarium wilt, root-knot nematodes, and reniform nematodes. Quantitative trait loci (QTL) mapping has identified numerous loci associated with these resistances. For instance, 201 QTLs have been identified for Verticillium wilt resistance, 47 for Fusarium wilt, and 85 for root-knot and reniform nematodes resistance (Abdelraheem et al., 2017). Additionally, resistance to Aspergillus leaf spot involves the accumulation of specific metabolites such as flavonoids, phenylpropanoids, and terpenoids, which play crucial roles in the plant's defense mechanisms (Khizar et al., 2020).

6.2 Overview of datasets and germplasm repositories analyzed

The datasets analyzed in this meta-analysis include a wide range of genetic and phenotypic data from various cotton germplasm repositories. For example, a study involving 149 elite Gossypium hirsutum cultivar accessions used genome-wide SNP data to evaluate salt tolerance traits (Zheng et al., 2021). Another study utilized a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines to identify QTLs for Fusarium wilt resistance (Zhu et al., 2022). Additionally, six upland cotton germplasm lines with resistance to root-knot and reniform nematodes were registered and analyzed for their resistance traits (McCarty et al., 2017). These datasets provide a comprehensive overview of the genetic diversity and resistance traits present in cotton germplasm.

6.3 Trends and patterns in resistance trait distribution

The distribution of resistance traits in cotton germplasm is not uniform across the genome. Certain chromosomes carry a disproportionate number of QTLs, indicating hotspots for specific resistance traits. For instance, 23 QTL clusters were found on 15 chromosomes, with notable hotspots on chromosomes c4, c19, and c24 for various resistance traits (Abdelraheem et al., 2017). Similarly, a genome-wide association study identified significant QTLs for drought and salt tolerance, as well as thrips resistance, distributed across multiple chromosomes (Abdelraheem et al., 2021). The integration of multiple QTLs, such as combining Renbarb1 and Renbarb2 with Renlon, has shown potential for improving resistance to reniform nematodes while also enhancing plant growth under nematode pressure (Gaudin et al., 2020).

This meta-analysis highlights the significant progress made in identifying and mapping key traits associated with biotic stress resistance in cotton. The datasets analyzed provide a rich source of genetic and phenotypic information, revealing trends and patterns in the distribution of resistance traits. These findings are crucial for developing marker-assisted selection strategies and breeding programs aimed at enhancing biotic stress resistance in cotton.

7 Practical Applications and Future Perspectives

7.1 Strategies for incorporating resistant germplasm into breeding programs

Incorporating resistant germplasm into cotton breeding programs is essential for developing cultivars that can withstand biotic stresses such as pests and diseases. One effective strategy is the identification and utilization of quantitative trait loci (QTL) associated with resistance traits. For instance, a meta-analysis identified 661 QTLs for various biotic and abiotic stress resistances, including resistance to Verticillium wilt, Fusarium wilt, and root-knot nematodes (Abdelraheem et al., 2017). Marker-assisted selection (MAS) can be employed to integrate these QTLs into high-yielding cultivars, enhancing their resistance profiles (Abdelraheem et al., 2019). Additionally, interspecific introgression, such as transferring tolerance traits from Gossypium barbadense to Gossypium hirsutum, can be a viable approach to incorporate resistance traits. Advanced genomic tools like genome-wide association studies (GWAS) and transcriptomic analyses can further aid in identifying and utilizing resistance genes effectively (Zheng et al., 2021; Bano et al., 2022).

7.2 Implications for sustainable cotton production under biotic stress pressures

The integration of resistant germplasm into cotton breeding programs has significant implications for sustainable cotton production. By developing cultivars with enhanced resistance to biotic stresses, the reliance on chemical pesticides can be reduced, leading to more environmentally friendly farming practices (Egan and Stiller, 2022). For example, the successful incorporation of genes like cry1Ab and chitinase into commercial cotton varieties has shown promising results in conferring resistance to cotton bollworm and Verticillium wilt, respectively (Mirzaei et al., 2018). This not only improves crop resilience but also ensures stable yields under biotic stress conditions. Moreover, the development of multiple stress-tolerant germplasms can help cotton adapt to varying environmental conditions, thereby supporting long-term agricultural sustainability (Farooq et al., 2023).

7.3 Recommendations for future research and resource development

Future research should focus on expanding the genetic base of cotton germplasm by exploring and utilizing diverse genetic resources. Developing larger and more diverse mapping populations will be crucial for high-resolution QTL mapping and the identification of novel resistance genes (Abdelraheem et al., 2019). Additionally, there is a need for high-throughput and reliable phenotyping methods to accurately assess resistance traits in large populations. Integrative approaches combining genomics, transcriptomics, and metabolomics can provide deeper insights into the molecular mechanisms underlying stress resistance (Tahmasebi et al., 2019; Shami et al., 2023). Furthermore, the application of advanced breeding techniques such as gene editing and genomic selection should be explored to accelerate the development of resistant cultivars (Egan and Stiller, 2022). Collaborative efforts between research institutions and breeding programs will be essential to translate these findings into practical applications.

Incorporating resistant germplasm into cotton breeding programs is vital for developing cultivars that can withstand biotic stresses, thereby promoting sustainable cotton production. Strategies such as marker-assisted selection, interspecific introgression, and advanced genomic tools can enhance the effectiveness of breeding programs. Future research should focus on expanding genetic resources, developing reliable phenotyping methods, and utilizing integrative approaches to understand the molecular mechanisms of resistance. These efforts will contribute to the development of resilient cotton cultivars, ensuring stable yields and environmental sustainability.

8 Concluding Remarks

The meta-analysis of cotton germplasm for biotic stress resistance has revealed significant insights into the genetic and molecular mechanisms underlying resistance traits. A comprehensive analysis of quantitative trait loci (QTL) identified numerous chromosomal regions associated with resistance to various biotic stresses, including Verticillium wilt, Fusarium wilt, and nematodes. Additionally, integrative transcriptomic studies highlighted differentially expressed genes (DEGs) and key transcription factors involved in stress responses, further elucidating the complex regulatory networks in cotton. Metabolomic profiling also identified critical metabolites and pathways that contribute to resistance against pathogens like Aspergillus tubingensis and insect pests.

The findings from this meta-analysis underscore the critical role of diverse cotton germplasm in developing biotic stress-resistant varieties. The identification of specific QTL clusters and hotspots provides valuable targets for marker-assisted selection, facilitating the breeding of resistant cotton lines. The successful transfer and stacking of resistance genes, such as cry1Ab and chitinase, into commercial cotton varieties demonstrate the potential of genetic engineering in enhancing biotic stress resistance. Moreover, the development of germplasm lines with resistance to root-knot and reniform nematodes highlights the practical applications of these genetic resources in breeding programs.

Advancing cotton research requires a multidisciplinary approach that integrates genomics, transcriptomics, metabolomics, and advanced breeding techniques. Collaborative efforts between academic researchers, industry stakeholders, and breeding programs are essential to translate these scientific findings into practical solutions for cotton production. The development of resistant cotton varieties not only ensures sustainable crop yields but also reduces the reliance on chemical pesticides, promoting environmental sustainability. Future research should focus on exploring novel resistance genes, understanding their regulatory mechanisms, and leveraging biotechnological advancements to enhance the resilience of cotton against biotic stresses.

Acknowledgments

We are grateful to Dr. Wang for critically reading the manuscript and providing valuable feedback that improved the clarity of the text. We express our heartfelt gratitude to the two anonymous reviewers for their valuable comments on the manuscript.

Conflict of Interest Disclosure

The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.

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