Recent Studies on Fusarium Wilt in Cotton

Abstract

Fusarium oxysporum has been a subject of intensive research since 1882, with over 200 studies published from key cotton-growing countries such as the United States, China, Uzbekistan, India, Pakistan, Australia, and Brazil. The present study has employed a diverse array of research methodologies and technological approaches, primarily emphasizing research publications disseminated within the past decade. It places specific emphasis on two key domains: Molecular Mapping and Genome-Wide Association Studies (GWAS), elucidating the evolutionary analysis transition from Simple Sequence Repeat (SSR) to Single Nucleotide Polymorphism (SNP) chip utilization. The creation of a comprehensive molecular map that incorporates Quantitative Trait Loci (QTLs) related to Fusarium and consolidates findings from several research groups, accompanied by figures and tables, serves to facilitate a more thorough understanding of the genetic architecture underlying Fusarium-related traits. An in-depth examination of recent advances in marker-assisted selection for traits conferring resistance to Fusarium oxysporum f. sp. vasinfectum (FOV), coupled with a comprehensive evaluation of the pertinent genes, offers valuable insights into the development of resistant cultivars and the underlying genetic mechanisms. This entails doing a critical review of recent relevant literature. Furthermore, this investigation examines the obstacles and potential associated with developing technologies.

1. Introduction

Fusarium wilt is a huge challenge in cotton (Gossypium spp.) farming, which causes a significant reduction in yield annually. This disease, first described by Atkinson in 1882, is caused by the soil-borne pathogen Fusarium oxysporum Schlechtend. f. sp. vasinfectum (Atk.) [1]. Environmental parameters like as temperature, pH, light, as well as substrates all influence Fusarium development [2]. For example, the optimal temperature for in vitro growth of F. oxysporum isolates is between 25 and 28°C, with limits when the temperature rises above 33°C or falls below 17°C [3]. Infected plants exhibit yellowing and subsequent shedding of leaves, followed by gradual wilting and eventual demise. A distinctive indicator of fusarium wilt manifests as a reddish-brown discoloration within the vascular tissues of stems and roots, visible upon sectioning these plant parts [4].

F. oxysporum exhibits distinct variations known as “races” within its taxonomy. In the global context of cotton farming, there are six primary nominal races (different from each other by virulence rate) of FOV recognized that include 1, 2, 3, 4, 6, and 8, as documented by various researchers [5, 6, 7, 8]. This classification was initially based on eight races but was refined through molecular characterization, revealing the merging of races 4 and 7, and races 3 and 5 [6, 9]. Geographic differences lead to distinct prevalence patterns, with race 4 causing significant losses in cotton-producing regions. In 2002, a highly virulent race 4 genotype of FOV was discovered in Californian cotton fields, marking its first appearance in the Western Hemisphere [10]. That FOV race 4 (FOV4) poses significant threats to the United States, potentially affecting the entire cotton belt, as highlighted by Zhu et al. [11].

Various studies have explored growth responses of F. oxysporum to metabolites of rhizospheric microflora in Egyptian cotton varieties [12]. The interaction between Belonolaimus longicaudatus (nematode) and FOV on cotton causes wilt development [13]. In the last few years, more cases of Fusarium wilt have been documented in Georgia, implying potential changes within the disease complex. During 2015 and 2016, an examination was conducted across 27 cotton fields in 10 Georgia counties. That survey involved collecting at least 10 soil and stem samples from each field from symptomatic plants to assess plant-parasitic nematode levels along with recognizing FOV races [14].

Recent years have seen a surge in scholarly articles on Fusarium oxysporum in cotton (Gossypium) species with this chapter on a comprehensive repository of relevant data on studies conducted between 2013 and 2023.

2. QTL mapping and marker-assisted selection for Fusarium wilt

A recent meta-analysis has examined the genetic factors associated with resistance to various stresses, both abiotic and biotic, in cotton plants. Zhang et al. in 2015 first studied a population of cotton plants known as “backcross inbred lines” (BIL) for their resistance to Verticillium wilt (VW) over 4 years. As a result, 10 genetic markers linked to VW resistance on cotton chromosomes, which were added to a map alongside markers, were identified. This comprehensive analysis identified 28 genetic regions, including 13 for VW, 8 for root-knot nematodes (Meloidogyne incognita) (RKN), and 3 for Fusarium wilt (FW) resistance [15].

Ulloa et al. used special cotton plant lines to investigate genetic resistance to nematodes and fungal diseases, specifically RKN and FW, respectively [16]. They found that some lines, like CS-B16, showed strong resistance to Fusarium race 1 due to the presence of a key genetic marker. However, other lines, such as CS-B (17-11) and CS-B17, were more susceptible to Fusarium race 4, indicating the presence of genes making them vulnerable. That research highlights the need for nematode-resistant cotton varieties in disease management.

In the United States, some strains of the wilt pathogen (like race 1) interact with nematodes, such as the southern RKN, causing significant root damage. When exposed to both race 1 and nematodes, certain cotton varieties exhibited moderate wilt symptoms, while another variety showed milder symptoms. Interestingly, the more virulent race 4 caused severe wilt when nematodes were present. This study revealed that race 4 can cause disease on its own and worsens when combined with nematodes, emphasizing the importance of nematode-resistant cotton varieties [17]. The variations also were explored in disease aggressiveness at different stages of seedling development. Diaz and colleagues found complex interactions between different cotton cultivars and FOV isolates, highlighting various mechanisms of resistance [18]. Additionally, a study led by Wang and colleagues [19] focused on identifying genetic markers for resistance to FOV races 1 and 4 in an interspecific cotton population. They pinpointed several key genetic markers on different chromosomes that contributed to resistance against these specific races. Studies have revealed substantial genetic diversity among FOV strains in the United States. Different genetic markers were used to categorize these strains, with the discovery of multiple genetically distinct groups. That demonstrates the diversity of FOV, particularly within the widespread race 1 genotype [20]. Furthermore, extensive trials on various cotton cultivars were conducted to assess their susceptibility to both RKN and FOV. These trials highlighted the importance of developing cotton varieties resistant to both pathogens for effective disease control [21]. Bell et al. [22] examined the genetic diversity of FOV isolates responsible for causing cotton wilt in Georgia. Researchers identified distinct vegetative complementation groups (VCGs) linked to severe outbreaks. These VCGs were associated with a specific pathotype that caused severe wilt in cotton plants. Analysis of vegetative compatibility groups (VCGs) confirmed the prevalence of one specific group (VCG01111), underscoring the absence of an exotic FOV race 4 strain in the study areas. The disease incidence increased during the 2021/22 growing season due to favorable weather conditions. Genetic analysis showed the prevalence of Australian FOV isolates, distinct from overseas races [23].

Abdelraheem and colleagues [24] used a high-density genotyping approach to study resistance to VW and virulent FOV4 in diverse cotton population groups and identified significant genetic markers correlated with resistance to VW and FOV4, laying the groundwork for potential marker-assisted breeding programs. In a greenhouse setting, FOV4-resistant and susceptible cotton plants were tested. Several genetic markers associated with resistance and demonstrated the potential for marker-assisted selection to enhance FOV4 resistance were identified [25]. Zhang et al. [26] conducted an in-depth investigation into QTLs for FOV resistance in Upland cotton, revealing 42 distinct genetic markers associated with various disease parameters. Their findings shed light on the complex genetic architecture of FOV4 resistance, emphasizing the need for multistage evaluations. In a separate study, a unique genomic region on Chromosome D03 was closely linked to stem and root vascular discoloration [27]. As found, different cotton varieties exhibited varying levels of resistance, suggesting the presence of genes responsible for resistance in this region. That work holds promise for the use of genetic markers in selecting FOV4 resistance. These studies offer valuable insights into improving cotton crop disease resistance, with implications for future breeding programs and agricultural practices [28].

3. Genes associated with cotton disease resistance

Using varying methods, scientists have undertaken a quest to identify genes related to FOV, an important pathogen in cotton plants. One approach is genetic and physical mapping, which has led to the discovery of resistance genes on cotton chromosomes 11 and 21 [29]. The research underscores the significance of combining genetics and genomics to pinpoint genes involved in plant resistance. To unearth genes critical to FOV infectiousness, studies have employed diverse techniques such as virus-induced gene silencing (VIGS), overexpression studies, quantitative phosphoproteomics, and bioinformatics analyses to study the Enoyl-CoA reductase (GhECR) gene’s role in cotton’s defense against different pathogenic strains [30]. In the realm of plant defense mechanisms, recognizing chitin, a key component of fungal cell walls, is crucial. In cotton, a sophisticated chitin sensing and signaling system has been identified. It involves the dimerization and phosphorylation of GhLYK5-GhCERK1, along with the wall-associated kinase GhWAK7A, which plays a significant role in plant response to infections caused by V. dahliae and FOV [31].

The Mitogen-Activated Protein Kinase (MAPK) cascade serves as an essential conduit for transducing external signals into internal responses to biotic and abiotic stresses. GhMPK20, a key gene in this cascade, has been identified as a vital player in regulating cotton resistance to F. oxysporum. Researchers have employed VIGS to study GhMPK20’s function, revealing its importance. Silencing GhMPK20 enhanced cotton tolerance to F. oxysporum, while overexpression disrupted the salicylic acid (SA)-mediated defense pathway [32]. Transcriptome sequencing studies by the same researchers uncovered the essential role of group IIc WRKY transcription factors (TFs) in enhancing cotton resistance to FOV. That work also unveiled a novel MAPK cascade (GhMKK2, GhNTF6, and GhMYC2) that plays a profound role in boosting resistance by promoting the upregulation of genes involved in flavonoid biosynthesis. This, in turn, leads to flavonoid accumulation, contributing to enhanced resistance [33]. Phosphoproteomics has been used to reveal the role of GhMORG1, a scaffold protein, in enhancing cotton resistance to F. oxysporum. GhMORG1’s interaction with GhMKK6 and GhMPK4 significantly amplifies the activity of the GhMKK6-GhMPK4 cascade. The research highlights GhMORG1’s involvement in coordinating various aspects of disease resistance [34]. Furthermore, Guo et al. [35] explored the GhMKK6-GhMPK4 cascade, a critical axis in cotton resistance to FW. Silencing GhMPK4 reduced tolerance to the disease and led to decreased expression of resistance genes. These intricate cascade attributes are akin to GhMKK6, adding to the complex interactions in the cotton immune response. The regulation of the MAPK kinase-protein phosphatase framework has been enriched with the identification of GhAP2C1 as a negative regulator. The modulation of GhAP2C1’s expression revealed its dual role: silencing enhanced resistance to FW, while overexpression led to sensitivity to the disease. This highlights intricate interactions of GhAP2C1 with GhMPK4, adding another layer to the complex immune response. F. oxysporum extracellular superoxide dismutase FoSod5 plays a key role in pathogenicity. This protein is upregulated during infection of cotton and contributes to fungal virulence. Understanding its adaptive role in overcoming host defenses can aid in the development of effective disease management strategies [36]. These studies have illuminated the complex interplay of genes and cascades underlying defense against F. oxysporium in cotton, employing diverse methodologies and analytical approaches.

MicroRNAs (miRNAs) have a crucial role in regulating plant immunity and fitness. Various small RNA (sRNA) sequences, including microRNAs, during FOV pathogenesis have been identified. These sequences provide insights into plant response to the disease, with some miRNAs having roles in regulating immunity [37].

The intricate regulation of mitogen-activated protein kinase (MAPK) cascades in response to fungal stress remains enigmatic. Research has shed light on the collaborative role of MAPK kinase gene GhMKK6 and microRNA ghr-miR5272a in cotton resistance to FW [38]. Plant disease resistance is a complex trait, with long noncoding RNAs (lncRNAs) playing a significant role in modulating it. Sequencing the transcriptomes of sea-island cotton recombinant inbred lines (RILs) revealed a positive correlation between the expression of FOV infection-induced lncRNAs and plant susceptibility. These lncRNAs add some complexities to plant-pathogen interactions. Long noncoding RNAs (lncRNAs) have been investigated for their role in regulating disease resistance pathways in response to F. oxysporium infection [39].

4. Enhancing cotton resistance to FOV and V. Dahliae

The introduction of transgenic insect-resistant cotton has raised questions about its interactions with pathogens. Gaspar and his team [40] focused on enhancing cotton resistance to FOV and V. dahliae by introducing the plant defensin NaD1. They created transgenic cotton plants expressing NaD1, which displayed robust field resistance to both pathogens. These genetically modified cotton plants exhibited increased survival rates, improved tolerance, and higher lint yield when compared to non-transgenic control counterparts. In the pursuit of boosting plant resistance against Fusarium wilt, Zhang et al. [24] explored innovative approaches involving the introduction of novel antimicrobial proteins like Hcm1. This approach is promising in conferring resistance to both Verticillium and Fusarium wilts in cotton by triggering innate immunity and inhibiting pathogen growth. Transgenic cotton lines expressing Hcm1 consistently exhibited higher resistance to these wilts in both greenhouse and field trials when compared to non-transgenic counterparts. Additionally, Hcm1 protein hindered the growth of V. dahliae and F. oxysporum under laboratory settings. The spread of fungal biomass was notably reduced in transgenic cotton plants as well, as the biomass of V. dahliae decreased significantly after inoculation with V. dahliae [41]. Researchers delved into the role of polygalacturonases (PGs) in the pathogenicity of V. dahliae and FOV. They cloned VDPG1 and FOVPG1 genes and studied their expression in different G. hirsutum cotton cultivars and conditions. The study revealed that VDPG1 and FOVPG1 were significantly elevated during infection. These findings highlight the importance of PGs in symptom development and disease progression, shedding light on the role of these enzymes in fungal pathogenicity [42]. Molecular evidence also supports the involvement of polygalacturonase-inhibiting proteins (PGIPs) in enhancing resistance to both Verticillium and Fusarium wilts. Purified GhPGIP1, a key defense protein, inhibits pathogenic endopolygalacturonases secreted by these fungal pathogens. Overexpressing GhPGIP1 in transgenic Arabidopsis enhances resistance and triggers the expression of pathogenesis-related proteins (PRs) and defense-related genes [43].

Li et al. [44] investigated the physiological differences between transgenic and conventional cotton when infected by F. oxysporum. Their findings emphasize the impact of genetic backgrounds and modifications on the plant response to pathogens and environmental stressors. Germin-like proteins (GLPs) play a pivotal role in plant responses to various stresses. A novel GLP, GhABP19, from G. hirsutum has been identified and characterized. GhABP19 is implicated in modulating resistance against both Verticillium and Fusarium wilt pathogens through its superoxide dismutase activity and regulation of jasmonic acid pathways [45]. GLPs are versatile glycoproteins involved in plant responses to various stresses. Another study by Pei et al. [46] emphasizes the role of GhGLP2 in cotton’s defense against V. dahliae, F. oxysporum, and oxidative stress. GhGLP2 exhibits superoxide dismutase (SOD) activity and inhibits pathogen spore germination. Transgenic Arabidopsis overexpressing GhGLP2 displays enhanced resistance to pathogens and oxidative stress, confirming its role in defense responses. Future research endeavors should focus on identifying additional factors that enhance resistance, deciphering GLP functions in various plant–fungal interactions, exploring ecological implications of horizontal gene transfer, and translating genomic insights into practical disease management practices. Furthermore, studies suggest that stink bugs may act as potential vectors for FOV4 transmission. These insects can acquire and transmit the pathogen, emphasizing the importance of managing stink bugs as part of disease control strategies. That research has deepened our understanding of Fusarium wilt pathogenesis, including the role of specific proteins, hormonal interactions, and vector-mediated transmission. These insights provide opportunities for developing targeted strategies to manage and mitigate the impact of this devastating disease on crops [47].

5. Enhancing plant defense mechanisms

Shafique and colleagues [48] emphasize the positive impact of combining antagonistic microorganisms with organic amendments to boost plant defense mechanisms. They conducted research involving Pseudomonas aeruginosa and Paecilomyces lilacinus, combined with cotton cake, which effectively suppressed root rot fungi. This combination also stimulated the synthesis of polyphenols and antioxidants in okra plant, showcasing its potential benefits. The application of nanotechnology has enabled the creation of functionalized silver nanoparticles (AgNPs) using cellular extracts of endophytic F. oxysporum-NFW16. These AgNPs exhibit potent antibacterial activity against multidrug-resistant bacteria and hold promise for use in antimicrobial textile finishes [49]. Furthermore, biogenic nanoparticles, including biogenic AgNPs synthesized from extract of F. oxysporum, show potential for antimicrobial applications in textile and agriculture industries. Impregnating cotton fibers with these nanoparticles demonstrates their ability to prevent microbial spread, suggesting their use in antiseptic clothing and agrochemicals [50]. Cheng and colleagues [51] characterized an endochitinase (VDECH) from V. dahliae. Their research revealed that VDECH triggered plant defense responses and inhibited fungal spore germination, indicating its potential for disease control. The resurgence of FOV in the USA necessitates a thorough understanding of pathogenicity and host responses for effective disease prevention and management. Researchers including Cox et al. [52] explored factors contributing to disease recurrence and potential applications of existing technologies for the biological control of these pathogens. While Fusarium wilt is a global issue, its expansion can be managed through various approaches, including chemical and biological controls. Biological control methods have gained attention due to the adverse effects of chemical options. One study investigated the potential of the biological control agent Saccharothrix algeriensis NRRL B-24137 (SA) in combination with the chemical fungicide carbendazim against FOV-induced cotton wilt. The results showed significant disease control under in vivo conditions, highlighting the promise of integrated strategies [53]. Subsequently, the potential of the actinomycete SA as a biological control against FOV was explored. Their research included in vitro tests and greenhouse pot experiments, which demonstrated substantial anti-Fusarium activity and a reduction in disease incidence, suggesting the effectiveness of SA NRRL B-24137 in disease management [54]. Li and colleagues [55] investigated the role of salicylic acid (SA) as a biofungicide against Fusarium wilt. They found that SA could inhibit the pathogen by targeting the TOR (target of rapamycin) signaling pathway, offering a natural and environmentally friendly approach to disease management. Zhu et al. [56] conducted a comprehensive survey to identify and characterize FOV race 4 in New Mexico. Their research provided insights into the occurrence and virulence of FOV4 in western and southwestern regions.

The antimicrobial activities of endophytic bacteria from Glycyrrhiza uralensis (licorice) were examined by Mohamad et al. [57]. Bacillus spp., particularly B. atrophaeus, displayed broad-spectrum antifungal and antibacterial activity, showing promise as biocontrol agents [56]. Plant Growth-Promoting Rhizobacteria (PGPR) have gained attention for their potential to enhance plant growth and suppress fungal pathogens. Zain and colleagues [58] isolated and characterized antagonistic bacteria from cotton and sugarcane plants, highlighting their potential as biocontrol agents. B. altitudinis MS16 demonstrated its capability to promote mustard plant growth, while inhibiting phytopathogens like Sclerotinia sclerotiorum were isolated [59]. Endophytic actinobacteria associated with the medicinal plant Thymus roseus were found to exhibit plant growth-promoting traits, contributing to sustainable bio-fertilizer use. The antifungal activity of a cold-adapted Pseudomonas strain from Antarctica that produces chitinase at low temperatures was explored, potentially serving as a biocontrol agent for plant pathogens in cold environments [60]. The interactions between microbial communities in the rhizosphere and the pathobiome, as well as the role of biocontrol agents, were studied to resist pathogenic stress [61]. Streptomyces alfalfae was identified as a potential biocontrol agent against Fusarium wilt of cotton by Chen and colleagues (2021), emphasizing the multifunctionality of biocontrol agents [62]. B. velezensis was explored by Mohamad et al. [57] for its antimicrobial properties against viral and fungal pathogens, with potential applications in sustainable agriculture. Sahayaraj and colleagues [63] demonstrated the bioefficacy of silver nanoparticles (AgNPs) synthesized using seaweed extracts against cotton pathogenic fungi.

To overcome challenges in pathogenicity assays, an in vitro co-culture system was designed to study FOV infection. This foam-based system allowed controlled interaction between domesticated cotton species and FOV. The system was used to assess disease severity in different cotton cultivars, demonstrating varying responses to FOV infection. Parris and colleagues 2022, developed an in vitro co-culture system for studying FOV infection, providing a controlled environment for assessing disease severity in different cotton cultivars [64]. The fermentation medium for Streptomyces alfalfae XN-04, enhancing the production of antifungal metabolites for combatting Fusarium wilt in cotton, was optimized. The result showed the potential of adjusting medium components to enhance the production of antifungal metabolites that can effectively combat Fusarium wilt in cotton [65].

Field evaluation methods were explored for resistance to FOV race 4 in cotton breeding. The study investigated the effects of cultivar, planting date, and inoculum density on disease progression. Results revealed the impact of planting date and temperature on disease severity and the potential use of disease progression curves to assess resistance [66].

These studies collectively illustrate the potential of microbial strategies for crop protection and disease management. Utilizing antagonistic microorganisms, optimizing fermentation mediums, exploring antimicrobial metabolites, and understanding microbiota’s role contribute to the advancement of sustainable agricultural practices.

6. Extracellular vesicles (EVs) in fungal systems

Extracellular vesicles (EVs) have gained considerable attention for their role in facilitating intercellular communication and macromolecule transport, especially in mammalian systems. Bleackley and colleagues [67] investigated the role of EVs in FOV infection and their involvement in the infection process. According to them, EVs isolated from the FOV culture medium contained unique proteins, including pigments, proteases, and polyketide synthesis-related proteins. Infiltration of FOV EVs into cotton and N. benthamiana leaves induced a phytotoxic response, suggesting their involvement in the infection process.

While primarily studied in human yeast pathogens, recent investigations have shed light on the involvement of fungal EVs in transporting virulence-related cargo and modulating host immune responses. Nevertheless, our understanding of EVs in filamentous fungi has been limited due to challenges such as the absence of protein markers and efficient isolation techniques. Addressing this knowledge gap, a comprehensive study has focused on the filamentous cotton pathogen FOV, providing valuable insights. The study involved isolating and characterizing the proteome of EVs derived from FOV.

To accomplish this, EVs were successfully isolated and purified by Garcia-Ceron and colleagues [68] through size-exclusion chromatography from two different growth media, Czapek Dox and Saboraud’s dextrose broth. The EV proteome exhibited significant variations depending on the growth medium, while EV production remained consistent. Notably, the EVs contained proteins associated with diverse processes, including polyketide synthesis, cell wall modifications, proteases, and potential effector molecules. These findings collectively suggest the possible involvement of FOV EVs in influencing the complex interactions between the pathogen and its host, shedding light on a previously understudied aspect of host–pathogen dynamics.

In a detailed examination, the infection process of FOV4 in Pima cotton (G. barbadense) was dissected. Using techniques like confocal and scanning electron microscopy, the dynamics of infection by the virulent FOV4 isolate were meticulously traced in two Pima cotton varieties that included the resistant PHY 841 RF and the susceptible Pima S-7. The differences in infection were evident. PHY 841 RF displayed significantly fewer germinated conidia on its root surface, and FOV4’s penetration into the root epidermis was notably delayed. Subsequent infection stages highlighted PHY 841 RF’s resilience, with reduced hyphal growth and reproduction, effectively restricting the fungal ability to infiltrate the xylem. These contrasting infection dynamics provide insights into PHY 841 RF’s resistance to FOV4, attributed to a series of defense mechanisms including delayed infection, inhibited fungal growth, and prevention of xylem invasion. These findings hold significance not only for comprehending cotton defense mechanisms but also for envisioning strategies to enhance crop resilience against Fusarium wilt [69].

7. Plant treatment in disease resistance

The application of silicon treatment has demonstrated its capacity to bolster plant resistance against various pathogens. A study delved into the influence of silicon treatment on the cellular defense responses in cotton root tissues following infection with FOV [70]. The investigation revealed that silicon treatment had a discernible impact on defense responses, especially in cotton cultivars naturally more resistant to the pathogen. Fusaric acid, a phytotoxic secondary metabolite produced by Fusarium spp., holds a pivotal role in pathogenicity. Another study unveiled the detoxification capabilities of the soil microbe Mucor rouxii, which effectively converts fusaric acid into a less harmful compound. That research highlighted the potential of microbial interactions to alleviate the adverse effects of Fusarium toxins on susceptible cotton plants (G. hirsutum and G. barbadense) [71].

Recent studies have explored the potential of Talaromyces flavus in inhibiting the growth of crucial plant pathogens, including V. dahliae, Fusarium oxysporum f. sp. lycopersici, and Fusarium oxysporum f. sp. Cucumerinum [72]. In response to contemporary challenges, researchers in Iran [73] have developed nano-capsules containing T. flavus in powder and suspension forms. Evaluations of these formulations in greenhouse conditions demonstrated their effectiveness in reducing the incidence of cotton VW.

In the context of carnation crops, Fusarium wilt remains a significant concern, necessitating the exploration of alternative disease management strategies. The feasibility of using near-infrared spectroscopy (NIRS) as a rapid and nondestructive method for assessing the suppressive potential of different plant growth media against carnation Fusarium wilt was investigated. The results indicate that NIRS holds promise for identifying suppressants, providing an efficient tool for sustainable disease management [74].

8. The complexities of Fusarium: host interactions and disease management strategies

Cotton cultivation faces substantial challenges due to attacks by pathogens like FOV and V. dahliae, which result in significant yield losses. Recent research endeavors have focused on innovative strategies for disease management. CDRAt01 is an Aspergillus tubingensis strain isolated from soil, known for its high tolerance to fusaric acid (FA). HPLC analysis of culture filtrates obtained from the growth of A. tubingensis isolate CDRAt01 in the presence of FA revealed the gradual formation of a metabolite, coinciding with a decrease in FA concentration. Subsequent spectral analysis and chemical synthesis confirmed the identity of the compound as 5-butyl-2-pyridinemethanol, commonly referred to as fusarinol. The comparative phytotoxicity assessment between fusarinol and FA was conducted by evaluating the necrotic response induced in cotyledons of cotton (G. hirsutum L. cv. Coker 312). Notably, fusarinol exhibited significantly lower phytotoxicity compared to FA. Consequently, the detoxification mechanism offered by the A. tubingensis strain presents a novel approach for mitigating Fusarium wilt [75]. The emergence of new FOV genotypes in China was characterized in terms of their interactions with cotton cultivars [76]. These findings underscore the necessity for ongoing surveillance to detect shifts in pathogen populations.

Research has also explored FOV race 3 resistances in Uzbek cotton germplasm, and genetic analyses indicated that FOV resistance is primarily influenced by a recessive single-gene action under high inoculum levels or disease pressure [77]. These complexities were evident in differing segregation distributions of susceptible and resistant phenotypes among Uzbek populations.

Plant–pathogen interactions are significantly shaped by phytohormones, with salicylic acid (SA) generally reducing plant susceptibility, while hormones like jasmonic acid (JA), ethylene (ET), abscisic acid (ABA), and auxins exhibit complex effects [78]. Bernardino et al. [79] showcased the antiviral activity of glucosylceramides (GlcCer) isolated from F. oxysporum against tobacco mosaic virus (TMV), offering a potential eco-friendly approach to enhance plant immunity. Another study by Puckhaber et al. [80] elucidated differences in active defense responses of two G. barbadense L. cultivars resistant to FOV race 4. The accumulation of antimicrobial terpenoids and novel compounds contributed to these resistance mechanisms [78]. Further research may explore the efficacy of AgNPs in field trials, investigate the core microbiome interactions with other pathogens, and delve deeper into noncanonical resistance genes in cotton–FOV interactions [81].

Understanding the molecular, genetic, and physiological aspects of plant–fungal interactions in cotton has paved the way for novel strategies to enhance disease resistance. The studies emphasize the importance of integrated approaches involving genetic studies, molecular analyses, and the utilization of beneficial microbes. These insights hold promise for the development of disease-resistant cotton cultivars, ultimately contributing to sustainable cotton production and global food security.

9. Detection and genotyping for disease management

A recent study by Zambounis and his colleagues [82] has delved into the evolutionary aspects of cotton resistance gene analogs (RGAs), unveiling signs of positive selection and potential functional implications. RGAs show great promise as functional markers in breeding programs aimed at bolstering cotton’s resistance to Fusarium wilt. Furthermore, a specific PCR method was developed to detect FOV California race 4 by targeting a unique Tfo1 insertion event. This technique enables the timely identification of infected fields and seed lots, which is crucial for effective disease management [83]. To safeguard agricultural productivity, a comprehensive understanding of the mechanisms underlying Fusarium–host interactions and the development of effective disease management strategies is vital. G. hirsutum, susceptible to Fusarium wilt, often proves resilient to conventional disease management practices. Zhang et al. in 2019 delved into the population genomics of V. dahliae, shedding light on the defoliation phenotype and the mechanisms driving its development [84]. That study exemplifies the complexity of host–pathogen interactions and the role of horizontal gene transfer in shaping disease outcomes. Additionally, the identification and characterization of a highly virulent cotton wilt pathogen, FOV VCG0114 (race 4), from diverse geographical origins has provided a deep understanding on its pathogenicity and genetic diversity. The utilization of PCR-based methods for genotype determination enables effective monitoring and tracking of these devastating pathogens [85]. The sequencing of genomes of FOV isolates by Seo et al. [86] has provided an essential resource for identifying genes involved in pathogenicity and developing improved disease management strategies [84]. By using a combination of Nanopore and Illumina sequencing technology, Srivastava et al. [87] generated genome resources for distinct FOV races, leading to concepts into their genetic makeup and unique genes. These findings hold promise for developing diagnostic markers and methods to distinguish FOV subgroups. Furthermore, G. barbadense, a close relative of G. hirsutum, faces Fusarium wilt challenges. Su et al. [88] uncovered the role of the anthocyanidin reductase gene (Gb_ANR-47) in enhancing resistance to FOV by regulating the content of proanthocyanidins. Such information highlights the intricate molecular mechanisms that contribute to plant defense responses against fungal pathogens.

To support effective disease management strategies, early detection and accurate genotyping of the pathogen are crucial. Molecular techniques, such as multiplex and singleplex PCR diagnostics, enable the identification and classification of different FOV genotypes, aiding in the prevention of further disease spread [89]. Additionally, environmental factors play a significant role in disease dynamics. DNA-based quantification and droplet digital PCR methods were used to analyze spatial variation in FOV inoculum density in soil. Their findings highlight the need to account for spatial variability in disease assessment, particularly in cultivar trials, to accurately interpret results [90].

10. The role of climate change spreading of Fusarium infections

Climate change profoundly impacts the distribution and severity of Fusarium infections. Alkhalifah et al. [91] employed geographic information system data and predictive modeling to project the future global distribution of F. oxysporum. The study illuminates how shifting environmental conditions under different climate scenarios could influence the prevalence of this pathogen and its associated diseases. Deletion mutants of seven genes within a single LSR (G-LSR2) were obtained from FOV using horizontal gene transfer. The findings provided compelling evidence that horizontal gene transfer from Fusarium to Vd991 played an important role in its adaptation to cotton, potentially indicating a significant mechanism in the evolutionary trajectory of this asexual plant pathogen. This dynamic adaptation mechanism makes a significant contribution to V. dahliae virulence in cotton [92].

Lastly, susceptibility of cotton to different races of Fusarium wilt calls for innovative approaches to disease resistance evaluation. Zhu et al. introduced a taproot rot-based method for assessing cotton resistance to Fusarium wilt race 4, with findings indicating congruence between responses at the seed germination stage and subsequent stages, presenting a potential alternative for efficient and reliable resistance assessment [93]. Resequencing-based high-density genetic mapping was employed to identify QTLs for resistance to Fusarium wilt race 7 in G. barbadense, emphasizing the importance of understanding the genetic factors underlying disease resistance in cotton [94].

11. Conclusion

In summary, the comprehensive review presents a broad spectrum of research endeavors aimed at bolstering disease resistance and effectively managing the impact of pathogens, notably FOV in cotton. The key findings and themes encompass a range of insights. For instance, researchers have identified genetic markers associated with disease resistance in cotton, paving the way for the development of resilient cotton varieties. These markers span various chromosomes. Disease interactions can be intricate, with RKNs exacerbating Fusarium wilt symptoms, underscoring the multifaceted nature of plant–pathogen relationships. The importance of developing nematode-resistant cotton varieties is reviewed, particularly when nematodes and FOV jointly affect cotton plants. High-density genotyping and genetic markers have the potential to enhance disease resistance in cotton crops. Specific genomic regions closely linked to disease resistance offer the promise of selecting cotton varieties with enhanced disease resistance. Research into the molecular mechanisms of disease resistance through various techniques has provided valuable insights into the ability of cotton to fend off FOV and other pathogens. MAPK cascade has been identified as a key player in regulating resistance of cotton to FOV. Various proteins have been identified as key contributors to defense mechanisms against FOV and related pathogens in cotton.

Environmental factors, including climate change, significantly impact disease dynamics, affecting the distribution and prevalence of pathogens. Novel approaches for assessing resistance in cotton to diseases, such as the taproot rot-based method and high-density genetic mapping, offer efficient and reliable tools for resistance assessment. Various strategies, including silicon treatment, detoxification of phytotoxins, nanotechnology-based formulations, and early detection methods, have been explored. In conclusion, this collective body of research contributes to the ongoing mission of enhancing cotton disease resistance and mitigating the impact of devastating pathogens on cotton cultivation. These findings serve as a cornerstone for the development of sustainable agricultural practices, ultimately bolstering global food security through the cultivation of more resilient cotton varieties.

Acknowledgments

The work was done as part of the project 58-0210-9-228F “Combating Fusarium wilt disease, a serious economic threat for sustainable cotton production in the USA and Uzbekistan” supported by USDA-ARS. We acknowledge the Center of Genomics and Bioinformatics, Academy Sciences of the Republic of Uzbekistan research team for supporting the interpretation of the research data used in this manuscript.

Author contributions

MA, IY – coordinated, wrote, and revised the manuscript; AM, BM, AY, NO, ZB, AM, MD, KU, SS, ZB, US, and NA – collected and analyzed literature and drafted the manuscript; IA – critically read and edited the manuscript.

Ethical issues

Not applicable.