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Breeding for Broad-Host Resistance of Fusarium Wilt in Cotton
Date
2023-05-04Metadata
Show full item recordAbstract
Fusarium oxysporum is a cross-kingdom pathogen that causes notorious diseases with the most diverse host range, including plants, animals, and humans. Different isolates in F. oxysporum species complex (FOSC) were defined as formae speciales based on their host specificity. F. oxysporum f. sp. vasinfectum (Fov) causes Fusarium wilt (FW) in cotton, which could lead to up to 80% yield loss. FOSC possesses complex genome structures with a set of core chromosomes and diverse small accessory chromosomes that are assumed to associate with virulence and host specificity. It remains unknown the genetic diversity and evolution of different isolates within a formae speciales. We sequenced and assembled high-quality genomes of two classical Fov races and two newly evolved isolates in a naturally infected field in Texas, USA. Comparative genomic analysis revealed that Fov isolates share 11 core chromosomes with other FOSC isolates that infect both plants and humans, and a group of unique accessory chromosomes. Surprisingly, although the core chromosomes are highly conserved, the accessory chromosomes are extremely divergent within Fov isolates, with the same degree of divergence among different formae speciales. Consistently, phylogenetic analysis indicates the independent evolution of different Fov races within FOSC, and different Fov isolates could infect multiple hosts. Extensive microsynteny was observed among accessory chromosomes within the same or different FOSC isolates, suggesting the existence of a shared ancestral accessory chromosome in FOSC. Genome sequencing of Texas Fov field isolates differing in virulence further revealed the rapid genome structure and sequence changes of accessory chromosomes within the Fov race. The increased pathogenicity of some newly evolved Fov isolates is associated with the increased copy number of putative effector genes in the accessory chromosomes. Together, our data reveal that different isolates in the same formae speciales of F. oxysporum could have evolved independently, and the accessory chromosomes in FOSC might have a common ancestor of evolution. Our analysis also suggests that massive whole accessory chromosome duplications, intrachromosomal segmental duplications, chromosome rearrangements, gene losses and gains, and transposable element expansion in different FOSC isolates drive pathogen aggressiveness and host adaptation. This study also reports the identification of promising Upland cotton lines that exhibit a wide range of resistance and susceptibility to Fov4 through field screen, a vital aspect of breeding for resistance, as well as a valuable resource for genome-wide association studies. Furthermore, the generation of a high-density genome-wide SNPs dataset from 362 Upland cotton lines from whole-genome sequencing is described, which provides a powerful tool for the identification of multi-loci traits in Upland cotton. These findings hold great potential for advancing our understanding of Upland cotton resistance to Fov4 and have significant implications for accelerating the development of improved cotton varieties with enhanced disease resistance, and for the advancement of genomic research in the field of Upland cotton.
Citation
Danmaigona Clement, Catherine (2023). Breeding for Broad-Host Resistance of Fusarium Wilt in Cotton. Doctoral dissertation, Texas A&M University. Available electronically from https : / /hdl .handle .net /1969 .1 /199167.