Detection and Characterization of Fusarium Wilt (Fusarium oxysporum f. sp. vasinfectum) Race 4 Causing Fusarium Wilt of Cotton Seedlings in New Mexico

Characterization of the High-Quality Genome Sequence and Virulence Factors of Fusarium oxysporum f. sp. vasinfectum Race 7

Fusarium oxysporum f. sp. vasinfectum (Fov) is a common soilborne fungal pathogen that causes Fusarium wilt (FW) disease in cotton. Although considerable progress has been made in cotton disease-resistance breeding against FW in China, and the R gene conferring resistance to Fov race 7 (FOV) in Upland cotton (Gossypium hirsutum) has been identified, knowledge regarding the evolution of fungal pathogenicity and virulence factors in Fov remains limited. In this study, we present a reference-scale genome assembly and annotation for FOV7, created through the integration of single-molecule real-time sequencing (PacBio) and high-throughput chromosome conformation capture (Hi-C) techniques. Comparative genomics analysis revealed the presence of six supernumerary scaffolds specific to FOV7. The genes or sequences within this region can potentially serve as reliable diagnostic markers for distinguishing Fov race 7. Furthermore, we conducted an analysis of the xylem sap proteome of FOV7-infected cotton plants, leading to the identification of 19 proteins that are secreted in xylem (FovSIX). Through a pathogenicity test involving knockout mutants, we demonstrated that FovSIX16 is crucial for the full virulence of FOV7. Overall, this study sheds light on the underlying mechanisms of Fov's pathogenicity and provides valuable insights into potential management strategies for controlling FW.

A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum

Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), is a devastating disease affecting cotton (Gossypium spp.) worldwide. Understanding the genetic basis of resistance in diploid cotton and successfully transferring the resistance to tetraploid Upland cotton (G. hirsutum) are crucial for developing resistant cotton cultivars. Although numerous studies have been conducted to investigate the genetic basis of Fusarium wilt in tetraploid cotton, little research has been conducted on diploid species. In this study, an association mapping panel consisting of 246 accessions of G. arboreum, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings in four greenhouse tests. Through a genome-wide association study (GWAS) based on 7,009 single nucleotide polymorphic (SNP) markers, 24 FOV4 resistance QTLs, including three major QTLs on chromosomes A04, A06, and A11, were detected. A validation panel consisting of 97 diploid cotton accessions was employed, confirming the presence of several QTLs. Evaluation of an introgressed BC2F7 population derived from G. hirsutum/G. aridum/G. arboreum showed significant differences in disease incidence and mortality rate, as compared to susceptible and resistant controls, suggesting that the resistance in G. arboreum and/or G. aridum was transferred into Upland cotton for the first time. The identification of novel major resistance QTLs, along with the transfer of resistance from the diploid species, expands our understanding of the genomic regions involved in conferring resistance to FOV4 and contributes to the development of resilient Upland cotton cultivars.

Development and validation of allele-specific PCR-based SNP typing in a gene on chromosome D03 conferring resistance to Fusarium wilt race 4 in Upland cotton (Gossypium hirsutum)

Upland cotton (Gossypium hirsutum) is the most important fiber crop for the global textile industry. Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive soil-borne fungal pathogens in cotton. Among eight pathogenic races and other strains, FOV race 4 (FOV4) is the most virulent race in US cotton production. A single nucleotide polymorphism (SNP) in a glutamate receptor-like gene (GhGLR4.8) on chromosome D03 was previously identified and validated to confer resistance to FOV race 7, and targeted genome sequencing demonstrated that it was also associated with resistance to FOV4. The objective of this study was to develop an easy and convenient PCR-based marker assay. To target the resistance SNP, a forward primer for the SNP with a mismatch in the 3rd position was designed for both the resistance (R) and susceptibility (S) alleles, respectively, with addition of 20-mer T7 promoter primer to the 5' end of the forward primer for the R allele. The two forward primers, in combination with each of five common reverse primers, were targeted to amplify amplicons of 50-260 bp in size with R and S alleles differing in 20 bp. Results showed that each of three common reverse primers in combination with the two forward primers produced polymorphic markers between R and S plants that were consistent with the targeted genome sequencing results. The polymorphism was distinctly resolved using both polyacrylamide and agarose gel electrophoreses. In addition, a sequence comparative analysis between the resistance gene and homologous sequences in sequenced tetraploid and diploid A and D genome species showed that none of the species possessed the resistance gene allele, suggesting its recent origin from a natural point mutation. The allele-specific PCR-based SNP typing method based on a three-primer combination provides a fast and convenient marker-assisted selection method to search and select for FOV4-resistant Upland cotton.

GBSOT4 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Flavonoid

Sulfotransferases (SOTs) (EC 2.8.2.-) are sulfate regulatory proteins in a variety of organisms that have been previously shown to be involved in regulating a variety of physiological and biological processes, such as growth, development, adaptation to land, stomatal closure, drought tolerance, and response to pathogen infection. However, there is a lack of comprehensive identification and systematic analysis of SOT in cotton, especially in G. barbadense. In this study, we used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structure, expression patterns, evolutionary relationships, selection pressure and stress response of SOT gene family members in G. barbadense. In this study, a total of 241 SOT genes were identified in four cotton species, among which 74 SOT gene members were found in G. barbadense. According to the phylogenetic tree, 241 SOT protein sequences were divided into five distinct subfamilies. We also mapped the physical locations of these genes on chromosomes and visualized the structural information of SOT genes in G. barbadense. We also predicted the cis-acting elements of the SOT gene in G. barbadense, and we identified the repetitive types and collinearity analysis of SOT genes in four cotton species. We calculated the Ka/Ks ratio between homologous gene pairs to elucidate the selective pressure between SOT genes. Transcriptome data were used to explore the expression patterns of SOT genes, and then qRT-PCR was used to detect the expression patterns of GBSOT4, GBSOT17 and GBSOT33 under FOV stress. WGCNA (weighted gene co-expression network analysis) showed that GB_A01G0479 (GBSOT4) belonged to the MEblue module, which may regulate the resistance mechanism of G. barbadense to FOV through plant hormones, signal transduction and glutathione metabolism. In addition, we conducted a VIGS (virus-induced gene silencing) experiment on GBSOT4, and the results showed that after FOV inoculation, the plants with a silenced target gene had more serious leaf wilting, drying and cracking than the control group, and the disease index of the plants with the silenced target gene was significantly higher than that of the control group. This suggests that GBSOT4 may be involved in protecting the production of G. barbadense from FOV infection. Subsequent metabolomics analysis showed that some flavonoid metabolites, such as Eupatorin-5-methylether (3'-hydroxy-5,6,7,4'-tetramethoxyflavone, were accumulated in cotton plants in response to FOV infection.

Pathogenic and Saprophytic Growth Rates of Fusarium oxysporum f. sp. vasinfectum Interact to Affect Variation in Inoculum Density and Interannual Infection Risk

Fusarium wilt of cotton caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) is a contemporary epidemic affecting cotton production in Far West Texas. The spatial distribution of soilborne FOV4 can be heterogeneous at small scales, and the factors that lead to this heterogeneity require investigation. Hypothetical causes include dissemination of spores through soils and variable saprophytic growth of the fungus. In the field, FOV4 DNA was quantified from soil during and after the cotton-growing season, and though the average amounts of DNA were not different between these time points, the variances of DNA across space were significantly different. Variability was higher when pathogenic growth of the fungus was expected owing to the presence of live cotton plants and lower when saprophytic growth was expected after cropping. In sterile-environment growth chamber experiments, the abundance of organic matter influenced the fungal vegetative growth rate and maximum amount as measured through quantitative PCR and the timing of the fungus' increasing its rate of spore production as measured through dilution plating. To investigate movement of spores in soils, spore mobility in experimental columns was quantified. Soil composition and organic matter abundance affected spore mobility, indicating that the timing of spore production relative to the availability of growth resources will affect the spatial spread of FOV4 and suggesting that soil properties affect the retention of conidia. The spatial spread of FOV4 through soil varies temporally and is affected by the shift between pathogenic and saprophytic growth modes of the fungus.

Targeted development of diagnostic SNP markers for resistance to Fusarium wilt race 4 in Upland cotton (Gossypium hirsutum)

Fusarium wilt caused by the soil-borne fungus Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) has become one of the most important emerging diseases in US cotton production. Numerous QTLs have been reported for resistance to FOV; however, no major FOV4-resistance QTL or gene has been identified and used in breeding Upland cotton (Gossypium hirsutum) for FOV4 resistance. In this study, a panel of 223 Chinese Upland cotton accessions was evaluated for FOV4 resistance based on seedling mortality rate (MR) and stem and root vascular discoloration (SVD and RVD). SNP markers were developed based on targeted genome sequencing using AgriPlex Genomics. The chromosome region at 2.130-2.292 Mb on D03 was significantly correlated with both SVD and RVD but not with MR. Based on the two most significant SNP markers, accessions homozygous for AA or TT SNP genotype averaged significantly lower SVD (0.88 vs. 2.54) and RVD (1.46 vs. 3.02) than those homozygous for CC or GG SNP genotype. The results suggested that a gene or genes within the region conferred resistance to vascular discoloration caused by FOV4. The Chinese Upland accessions had 37.22% homozygous AA or TT SNP genotype and 11.66% heterozygous AC or TG SNP genotype, while 32 US elite public breeding lines all had the CC or GG SNP genotype. Among 463 obsolete US Upland accessions, only 0.86% possessed the AA or TT SNP genotype. This study, for the first time, has developed diagnostic SNPs for marker-assisted selection and identified FOV4-resistant Upland germplasms with the SNPs.

Surveillance, Diversity and Vegetative Compatibility Groups of Fusarium oxysporum f. sp. vasinfectum Collected in Cotton Fields in Australia (2017 to 2022)

Cotton (Gossypium hirsutum) is a billion-dollar crop in regional New South Wales (NSW) and Queensland, Australia. Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. vasinfectum (Fov) is an economically important disease. Initial disease losses of up to 90% when the disease was first detected resulted in fields being taken out of cotton production. The disease is now well-managed due to the adoption of highly resistant varieties. However, annual disease surveys recently revealed that the disease dynamic has changed in the past few seasons. With relatively mild and wet weather conditions during the 2021/22 growing season, FW was detected in eight surveyed valleys in NSW and Queensland, with the disease incidence as high as 44.5% and 98.5% in individual fields in early and late seasons, respectively. Fov is genetically distinct and evolved from local Fusarium oxysporum strains. Additionally, the pathogen was reported to evolve rapidly under continuous cotton cropping pressure. However, our knowledge of the genetic composition of the prevailing population is limited. Sequences of the translation elongation factor alpha 1 (TEF1) revealed that 94% of Fusarium isolates recovered from FW-infected cotton were clustered together with known Australian Fov and relatively distant related to overseas Fov races. All these isolates, except for nine, were further confirmed positive with a specific marker based on the Secreted in Xylem 6 (SIX6) effector gene. Vegetative compatibility group (VCG) analyses of 166 arbitrarily selected isolates revealed a predominance of VCG01111. There was only one detection of VCG01112 in the Border Rivers valley where it was first described. In this study, the exotic Californian Fov race 4 strain was not detected using a specific marker based on the unique Tfo1 insertion in the phosphate (PHO) gene. This study indicated that the prevalence and abundance of Fov across NSW and Queensland in the past five seasons was probably independent of its genetic diversity.

Hypothetical protein FoDbp40 influences the growth and virulence of Fusarium oxysporum by regulating the expression of isocitrate lyase

Fungal growth is closely related to virulence. Finding the key genes and pathways that regulate growth can help elucidate the regulatory mechanisms of fungal growth and virulence in efforts to locate new drug targets. Fusarium oxysporum is an important plant pathogen and human opportunistic pathogen that has research value in agricultural and medicinal fields. A mutant of F. oxysporum with reduced growth was obtained by Agrobacterium tumefaciens-mediated transformation, the transferred DNA (T-DNA) interrupted gene in this mutant coded a hypothetical protein that we named FoDbp40. FoDbp40 has an unknown function, but we chose to explore its possible functions as it may play a role in fungal growth regulatory mechanisms. Results showed that F. oxysporum growth and virulence decreased after FoDbp40 deletion. FOXG_05529 (NCBI Gene ID, isocitrate lyase, ICL) was identified as a key gene that involved in the reduced growth of this mutant. Deletion of FoDbp40 results in a decrease of more than 80% in ICL expression and activity, succinate level, and energy level, plus a decrease in phosphorylated mammalian target of rapamycin level and an increase in phosphorylated 5′-adenosine monophosphate activated protein kinase level. In summary, our study found that the FoDbp40 regulates the expression of ICL at a transcriptional level and affects energy levels and downstream related pathways, thereby regulating the growth and virulence of F. oxysporum.

Quantitative Trait Locus Mapping for Fusarium Wilt Race 4 Resistance in a Recombinant Inbred Line Population of Pima Cotton (Gossypium Barbadense)

Fusarium oxysporum f. sp. vasinfectum (FOV) race 4 (FOV4) causes seedling death immediately after emergence, in addition to leaf chlorosis and necrosis, vascular discoloration, plant wilting, defoliation, and plant death at late stages. Breeding for FOV4 resistance is the most cost effective management method. In this study, 163 recombinant inbred lines (RILs) of FOV4-resistant Pima S-6 × susceptible 89590, together with the two parents (Gossypium barbadense), were artificially inoculated with FOV4 and assayed for resistance based on foliar disease severity ratings (DSR) at 30 days post inoculation (dpi) in two replicated tests in the greenhouse or controlled conditions. Significant genotypic variations were detected for FOV4 resistance in a combined analysis of variance. Although a significant genotype × test interaction was detected for DSR, the 10 most resistant RILs had significantly and consistently lower DSR than the susceptible parent in both tests. The heritability estimate for DSR was 0.65, indicating that two-thirds of the phenotypic variation for FOV4 resistance in this Pima RIL population was due to genetic factors. Based on 404 polymorphic SSR markers, five and four quantitative trait loci (QTL) on six chromosomes (c14, c17, c19, c21, c24, and c25) were detected in Tests 1 and 2, respectively, and each explained 15 to 29% of the phenotypic variation. Three QTL on c17, c24, and c25 were in common between the two tests, accounting for 60% and 75% of the QTL detected in Tests 1 and 2, respectively. The three QTL were also reported in previous studies and will be useful for marker-assisted selection for FOV4 resistance in Pima cotton.

Gb_ANR-47 Enhances the Resistance of Gossypium barbadense to Fusarium oxysporum f. sp. vasinfectum (FOV) by Regulating the Content of Proanthocyanidins

Anthocyanidin reductase (ANR) is an important regulator of flavonoid metabolism, and proanthocyanidins, the secondary metabolites of flavonoids, play an important role in the response of plants to pathogenic stress. Therefore, in this study, the expression analysis of the ANR gene family of Gossypium barbadense after inoculation with Fusarium oxysporum f. sp. vasinfectum (FOV) was performed at different time points. It was found that Gb_ANR-47 showed significant differences in the disease-resistant cultivar 06-146 and the susceptible cultivar Xinhai 14, as well as in the highest root expression. It was found that the expression of Gb_ANR-47 in the resistant cultivar was significantly higher than that in the susceptible cultivar by MeJA and SA, and different amounts of methyl jasmonate (MeJA) and salicylic acid (SA) response elements were found in the promoter region of Gb_ANR-47. After silencing GbANR-47 in 06-146 material by VIGS technology, its resistance to FOV decreased significantly. The disease severity index (DSI) was significantly increased, and the anthocyanin content was significantly decreased in silenced plants, compared to controls. Our findings suggest that GbANR-47 is a positive regulator of FOV resistance in Gossypium barbadense. The research results provide an important theoretical basis for in-depth analysis of the molecular mechanism of GbANR-47 and improving the anti-FOV of Gossypium barbadense.

A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance

A major QTL conferring resistance to Fusarium wilt race 4 in a narrow region of chromosome D02 was identified in a MAGIC population of 550 RILs of Upland cotton. Numerous studies have been conducted to investigate the genetic basis of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) resistance using bi-parental and association mapping populations in cotton. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs), together with their 11 Upland cotton (Gossypium hirsutum) parents, was used to identify QTLs for FOV race 4 (FOV4) resistance. Among the parents, Acala Ultima, M-240 RNR, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Twenty-two MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNPs, a major FOV4 resistance QTL within a narrow region on chromosomes D02 was detected, allowing identification of 14 candidate genes. Additionally, a meta-analysis of 133 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study represents the first GWAS study using a largest genetic population and the most comprehensive meta-analysis for FW resistance in cotton. The results illustrated that 550 lines were not enough for high resolution mapping to pinpoint a candidate gene, and experimental errors in phenotyping cotton for FW resistance further compromised the accuracy and precision in QTL localization and identification of candidate genes. This study identified FOV4-resistant parents and MAGIC lines, and the first major QTL for FOV4 resistance in Upland cotton, providing useful information for developing FOV4-resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in cotton.

Comparative Analysis of Infection Process in Pima Cotton Differing in Resistance to Fusarium Wilt Caused by Fusarium oxysporum f. sp. vasinfectum Race 4

Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) causes an early season cotton disease including seedling deaths. This study compared two Pima cottons (Gossypium barbadense) in the infection process of FOV4 using a confocal and a scanning electron microscope. Seedlings were grown in a hydroponic system and inoculated with a virulent local FOV4 isolate. As compared with the susceptible Pima S-7, the resistant Pima PHY 841 RF had significantly fewer conidia attached and germinated on the root surface. FOV4 penetration into the root epidermis of PHY 841 RF was delayed until 24 h postinoculation (hpi) as compared with 8 hpi in Pima S-7. In Pima S-7, hyphae progressed to the xylem through the cortex between 5 and 7 days postinoculation. However, hyphae grew much slower in the cortex with no apparent hyphae observed in the xylem of PHY 841 RF. At plant maturity, no FOV4 was detected through fungal isolation and PCR in the stem of PHY 841 RF and its resistance donor parents PHY 800 and Pima S-6, as compared with Pima S-7 and DP 744 with positive results. The results demonstrate that PHY 841 RF is resistant to FOV4, due to delayed infection, reduced fungal growth and reproduction, and prevention of the fungus from invading the xylem.

Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population of Gossypium barbadense

Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive diseases in cotton (Gossypium spp.) production, and use of resistant cultivars is the most cost-effective method managing the disease. To understand the genetic basis of cotton resistance to FOV race 7 (FOV7), this study evaluated a recombinant inbred line (RIL) population of 110 lines of G. barbadense from a cross between susceptible Xinhai 14 and resistant 06-146 in eight tests and constructed a high-density genetic linkage map with resequencing-based 933,845 single-nucleotide polymorphism (SNP) markers covering a total genetic distance of 2483.17 cM. Nine quantitative trait loci (QTLs) for FOV7 resistance were identified, including qFOV7-D03-1 on chromosome D03 in two tests. Through a comparative analysis of gene expression and DNA sequence for predicted genes within the QTL region between the two parents and selected lines inoculated with FOV7, GB_D03G0217 encoding for a calmodulin (CaM)-like (CML) protein was identified as a candidate gene. A further analysis confirmed that the expression of GB_D03G0217 was suppressed, leading to increased disease severity in plants of the resistant parent with virus induced gene silencing (VIGS).

Studies of Evaluation Methods for Resistance to Fusarium Wilt Race 4 (Fusarium oxysporum f. sp. vasinfectum) in Cotton: Effects of Cultivar, Planting Date, and Inoculum Density on Disease Progression

Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) is an early season disease causing root rot, seedling wilt, and death. To develop an appropriate field evaluation method for resistance to FOV4 in cotton breeding, the objectives of this study were to investigate the effects of cultivar, planting date, and inoculum density on disease progression in 2020-2021. Results showed that the usual local mid-April planting had the lowest disease severity (DSR) or mortality rate (MR) in 2020 and 2021. DSR or MR increased at the late April and early May plantings in both years and reached the highest at the early May planting in 2020, while MR in 2021 was followed by a decrease in the late May planting and reached the highest in the mid-June planting. Local daily low temperatures between mid-April and mid-June were favorable for FOV4 infections, whereas daily high temperatures at 35°C or higher suppressed wilt severity. When seedlings at the 2-true leaf stage were inoculated with 10⁴, 10⁵, 10⁶, and 10⁷ conidia ml^-1 per plant in 2020, DSR was low but a linear relationship between inoculum density and DSR was observed. When a FOV4-infested soil supplemented with artificial inoculation was used, disease progression in three moderately susceptible or moderately resistant cultivars followed a linear model, while it followed a quadratic model in the highly susceptible Pima S-7 cultivar only. Among the other three cultivars, FM 2334GLT had the lowest DSR or MR except for one planting date in both years, followed by PHY 725 RF and Pima PHY 881 RF in ascending order, which were consistent with the difference in regression coefficients of the linear models. This study demonstrates that disease progression curves due to FOV4 can be used to compare responses to FOV4 infections among cotton genotypes in cotton breeding and genetic studies, regardless of planting date and inoculation method.