An ecological lens on the emergence of plant pathogencity: comparative studies of pathogenic and non-pathogenic Fusarium oxysporum
Open Access
- Author:
- Tesdall, Genna
- Graduate Program:
- Plant Pathology
- Degree:
- Master of Science
- Document Type:
- Master Thesis
- Date of Defense:
- August 29, 2018
- Committee Members:
- Maria del Mar Jimenez Gasco, Thesis Advisor/Co-Advisor
Beth Krueger Gugino, Committee Member
David Michael Geiser, Committee Member
Mary Ellen Barbercheck, Committee Member
Melanie Joy Miller Foster, Committee Member - Keywords:
- Fusarium oxysporum
Banana
International agriculture
Plant pathology
microbial ecology
soil-borne plant pathogens
fungal evolution
pathogen evolution - Abstract:
- Banana is a staple food crop in the developing world, where 85% of production is traded and consumed locally and exports generate $5 billion USD annually. Fusarium wilt of banana, caused by Tropical Race 4 (TR4) of Fusarium oxysporum (Fo) f. sp. cubense is threatening Cavendish cultivars that dominate the export industry. To design sustainable solutions to manage Fusarium wilt of banana caused by TR4, for which no marketable resistant cultivars or chemical controls exist, scientists must understand the mechanisms of pathogenicity and the ecology of this organism, including the role of the pathogenicity-associated genes known as Secreted In Xylem (SIX) genes. This project examines the differences between pathogenic and non-pathogenic Fo isolates isolated from banana, tomato, and chickpea by examining the role of SIX9, evaluating phylogenetic relationships between these isolates, and detecting SIX genes in these isolates. The role of SIX9 in pathogenic TR4 and Race 1 was examined by studying PEG-mediated knockout transformants in vitro and in planta. Mutants of TR4 displayed two in planta phenotypes: non-pathogenic and hypervirulent. Mutants of Race 1 isolates showed two in-planta phenotypes: non-pathogenic and pathogenic to Cavendish ‘Gran Naine’ and ‘Gros Michel’, or in other words, a TR4 in planta phenotype. The genetic underpinnings of these in planta phenotypes have yet to be determined. However, PCR and sequencing of insertion site amplicons indicated there may be more than one copy of SIX9 in the genome of TR4 O-2052. To understand evolutionary relationships between non-pathogenic isolates, phylogenetic relationships of Fo isolates from asymptomatic banana, tomato, and chickpea were inferred using TEF-1α and five novel genes, 04642, 06412, 10995, 15960, and 15695. This study designed primer pairs which showed high sequencing efficiency (>95%) and added 438 parsimony-informative characters to the 64 parsimony-informative characters from TEF1-α. Phylogenetic analysis indicated Fo isolates group together with isolates pathogenic and non-pathogenic to different hosts. No phylogenetic patterns were identified based on the detection of SIX genes, mating-type loci, geographic origin, or origin within the plant (i.e.: root, crown, or stem). This is the first study to report the presence of SIX genes in non-pathogenic isolates from tomato and chickpea. Twenty-nine endophytes of tomato, nineteen endophytes of chickpea, and eight Fo f. sp. ciceris were screened. There were eight PCR-based detections of SIX8; all eight detections were in Fo f. sp. ciceris isolates. SIX9 was detected in five isolates; all were endophytes of chickpea. SIX11 was detected in five isolates. Three of these detections were in three isolates characterized as Fo f. sp. ciceris. One detection was in an endophyte of tomato (2-1c1). One detection was in an endophyte of chickpea (cc44). SI X14 was detected in 9 isolates. Eight of these detections were in isolates characterized as Fo f. sp. ciceris (100% of all Fo f. sp. ciceris isolates screened). One detection was in an endophyte of chickpea (cc44). SIX1 was detected in one isolate, characterized as Fo f. sp. ciceris race 0 (Foc82108). These studies contribute knowledge to the field of Fo biology and ecology by providing new affordable molecular tools, in the form of five core genome regions, for understanding Fo phylogenetic relationships with may more parsimony-informative characters than the current phylogenetic standard, TEF1-α. Furthermore, this research provides a starting framework to study relationships between Fo isolates non-pathogenic and pathogenic to their hosts. We find endophytes do not show clear phylogenetic relationships based on the core genome to predict pathogenicity or make other conclusions, like on host specificity. Furthermore, this study reports the first sequence-confirmed presence of SIX genes in non-pathogenic isolates from chickpea and tomato, prompting further questions about the ecological role of SIX genes. Finally, transformants of Fo f. sp. cubense TR4 revealed in planta phenotypes that eliminate pathogenicity, and in one mutant, induced hypervirulence. These results prompt further investigation into the molecular underpinnings of these phenotypes. We seek to answer the question: why are some Fo isolates plant pathogenic while others are not?