Author ORCID Identifier
Semester
Fall
Date of Graduation
2025
Document Type
Dissertation
Supplementary Dataset 1
Dataset 2.xlsx (792 kB)
Supplementary Dataset 2
Dataset 3.xlsx (232 kB)
Supplementary Dataset 3
Degree Type
PhD
College
Davis College of Agriculture, Natural Resources and Design
Department
Division of Plant and Soil Sciences
Committee Chair
Vagner Benedito
Committee Co-Chair
Umesh K. Reddy
Committee Member
Mahfuz Rahman
Committee Member
Michael Gutensohn
Committee Member
Sven Verlinden
Abstract
Anthracnose, caused by species of the Colletotrichum complex, is one of the most destructive fungal diseases affecting tomato (Solanum lycopersicum L.), leading to significant pre- and postharvest losses worldwide. Despite its economic importance, no commercial tomato cultivars possess durable anthracnose resistance, mainly due to the polygenic nature of the trait and limited understanding of its molecular basis. This dissertation integrates quantitative genetics, genomics, and metabolomics to unravel the genetic architecture underlying anthracnose resistance and to identify key candidate genes and pathways that contribute to defense mechanisms in tomato. A recombinant inbred line population derived from a cross between the resistant wild-derived line 95L368 and the susceptible cultivar US28 was used to map resistance loci through genotyping-by-sequencing (GBS), genome-wide association study (GWAS), and whole-genome resequencing-based QTL-seq analysis. Twenty QTLs were identified across multiple chromosomes, and concordant signals revealed key candidate genes including AP2/ERF transcription factors, Nα-acetyltransferase (NatA), bHLH, cytochrome P450, and RGA2-like proteins. Functional enrichment analyses highlighted pathways related to plant hormone signal transduction, oxidative phosphorylation, and the biosynthesis of phenylpropanoids and terpenoids. High-throughput PCR Allelic Competitive Extension (PACE) markers were developed for major loci, enabling precise genotyping and marker-assisted selection of resistant alleles. Integration of metabolomic profiling further uncovered substantial biochemical differentiation between resistant and susceptible genotypes, with resistant fruit exhibiting elevated levels of steroidal glycoalkaloids, flavonoids, and phenolic acids that contribute to structural reinforcement and antifungal defense. These metabolic shifts aligned with enriched secondary-metabolite and diterpenoid biosynthetic pathways, establishing a link between genetic loci and metabolic phenotypes conferring resistance. Functional validation through CRISPR/Cas9 editing of AP2/ERF genes revealed their dual role in defense and development: knockout lines exhibited accelerated ripening and enhanced drought resilience, confirming AP2/ERF as a negative regulator of ripening and a modulator of stress-responsive signaling. Collectively, the integration of QTL discovery, metabolite profiling, and functional genomics provides a robust foundation for genomics-assisted breeding and precision genome editing to develop tomato cultivars with durable resistance and improved fruit quality.
Recommended Citation
Lopez Ortiz, Carlos Eloir, "Genetic Basis of Anthracnose Resistance in Tomato" (2025). Graduate Theses, Dissertations, and Problem Reports. 13094.
https://researchrepository.wvu.edu/etd/13094
Included in
Genetics Commons, Molecular Genetics Commons, Plant Biology Commons, Plant Breeding and Genetics Commons, Plant Pathology Commons