Molecular, Genomic and Cellular Characterization of Emerging Fusarium Wilt of Cotton Race 4 in Texas

Fusarium wilt disease of cotton race 4(Fov4), poses a strategic threat to U.S upland cotton production by the recent expansion of Fov4 from California into Texas in 2017. Fov4 is  difficult to control as the hyphae resides in the woody vascular tissues protected from fungicides with chlamydospores that can survive in soils forever. Resistance in upland cotton has not been identified and commercial varieties are not available. There is a critical need to understand the disease mechanism and develop upland cotton with resistance to Fov4.  On the pathogen side, we need to understand the extent of the genetic diversity and parthenogenesis of different Fov isolates in the field and compare with existing Fov isolates. For this, we morphologically and molecularly characterized 54 Texas isolates from 2017 and 2018 and performed whole-genome sequencing of 30 Fov isolates using Oxford Nanopore MinION portable device and illumina sequencing.

Our study revealed unexpected genetic and virulence diversity of Texas Fov isolates. For example, some Texas Fov4 isolates are more virulent than classical California race 4 CA14, whereas some Texas Fov4 isolates are non-pathogenic on susceptible cotton varieties. To facilitate infection studies, we also established a fast, quantitative and highly reproducible seed soak disease assay to determine cotton response, such as high resistance, medium resistance or susceptibility to different isolates of Fov4. A survey of 20 cotton cultivars with this assay indicates a strong correlation with the large-scale field screens. To reveal the infection process at the cellular level, we tagged several Fov isolates with green fluorescent protein (GFP) to monitor the fungal attachment, penetration, colonization and establishment by live-cell imaging.  Our study reveals that Fov4 mainly colonizes the root surface of the tolerant cotton cultivars with a much-delayed multiplication rate while it rapidly multiplies in the vascular tissues on the susceptible cotton cultivars causing seedling death.