Molecular Detection and Quantification of Fusarium oxysporum f. sp. vasinfectum Race 4 in Cotton Plants and Soils

The highly virulent soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) causes the inoculum density-dependent disease Fusarium wilt in cotton (Gossypium spp.), leading to vascular necrosis, plant death, and yield loss. Managing FOV4 relies on planting resistant cultivars, but no commercially available Upland (G. hirsutum L.) cultivars are resistant. Furthermore, detecting FOV4 in Upland cotton is more challenging due to fewer observable foliar symptoms than Pima (G. barbadense L.) cultivars. In two independent studies conducted over two years, Upland and Pima cultivars with varying responses to FOV4 were evaluated in naturally infested fields. In-season assessment of soil inoculum densities was performed by quantitative PCR (qPCR) at planting, first flower (midseason), and crop maturity (late season). Field measurements included plant mortality, visual root necrosis ratings, and yield. Highly susceptible Pima cultivars had the highest mortality rates, most severe necrosis, and the lowest yields. In contrast, publicly available resistant cultivars showed the lowest mortalities and necrosis, along with intermediate yields. Commercial Upland cultivars, assumed to have some degree of susceptibility, demonstrated intermediate levels of mortality and necrosis, but with greater yield potential, had the highest yields. Midseason soil inoculum densities significantly differed among cultivars, with highly susceptible Pima cultivars having the greatest densities, although most cultivars were not significantly different from each other. However, positive relationships were observed between at-plant and late season inoculum densities with mortality and necrosis in both Upland and Pima cultivars regardless of resistance. Despite being resistant, yield loss was observed in Pima PHY 881 RF with increasing inoculum density, but yield losses were not observed in Upland cultivars at the inoculum densities in this study. A separate effort aimed to develop a multiplex qPCR assay for the rapid race-specific identification of FOV in planta, simultaneously detecting races 1, 2, and 3 separately from FOV4. This assay was utilized in a limited survey of Fusarium in Texas cotton and demonstrated high specificity and reliable identification, enabling the identification of FOV4 directly from root tissue in one day. This molecular tool can also be used in future studies to quantify inoculum density within the plant, enhancing the understanding of FOV4 and other races of FOV in Upland cotton. Overall, this research highlights the importance of cultivar selection and effective diagnostic tools in managing FOV4.