Author ORCID Identifier
Semester
Fall
Date of Graduation
2025
Document Type
Dissertation
Degree Type
PhD
College
Davis College of Agriculture, Natural Resources and Design
Department
Not Listed
Committee Chair
Vagner Benedito
Committee Member
Mahfuz Rahman
Committee Member
Michael Gutensohn
Committee Member
Sven Verlinden
Committee Member
Umesh Reddy
Abstract
Septoria leaf spot, caused by Septoria lycopersici, represents a re-emerging disease threat in North American tomato cultivation, particularly impacting organic production systems. We developed a comprehensive methodology to introgress Septoria leaf spot resistance from wild Solanum accessions into cultivated tomato backgrounds. To generate interspecific F1 hybrids, we optimized ovule culture protocols, successfully yielding five acclimatized plants from 34,475 cultured ovules. Hybridity was rigorously confirmed through diagnostic morphological traits and a 24-marker genome-wide CAPS markers panel. While self-compatibility segregated, allowing one arcanum-derived F1 to self-pollinate, most F1 hybrids exhibited post-zygotic incompatibility barriers that precluded direct backcrossing to elite 'WV-63'/'WV-17B' lines. The use of 'Micro-Tom' as a bridging recurrent parent successfully overcame this barrier, facilitating the production of viable BC1 populations. Composite interval mapping identified a compact quantitative trait locus on chromosome 8 in the arcanum-derived BC1 population and a significant signal on chromosome 6 in the peruvianum-derived pseudo-F2, along with a minor, reproducible effect on chromosome 2. This integrated workflow encompassing wild donor discovery, precisely timed ovule rescue, bridging backcrossing strategies, CAPS-anchored quality control, and early-stage QTL identification offers a reproducible and low-infrastructure pathway for transferring valuable wild SLS resistance into elite tomato germplasm while minimizing undesirable linkage drag.
The identified genetic materials and chromosomal intervals are composed to facilitate marker-assisted introgression and multi-isolate validation efforts, crucial for developing and deploying durable resistance. While wild relatives such as Solanum arcanum and S. peruvianum offer robust resistance, integrating this resistance into cultivated tomatoes is challenging due to difficulties in crossing, the unintentional transfer of undesirable traits, and the imprecise identification of these wild genetic segments within improved varieties. This study utilized advanced genetic sequencing techniques to map segments of DNA from wild relatives. This was done in a specific breeding line (BC₄) derived from S. arcanum and in another line that combined genetic material from both S. arcanum and S. peruvianum. Unique genetic markers from these wild donors (variants present in the resistant lines but absent in the cultivated parents “WV-63”, “WV-17B”, and “Cherokee Purple”) were then used to precisely locate these introgressed DNA segments on the tomato genome, specifically within 1-Mb regions of the SL4.0 reference genome. By comparing these mapped blocks with known gene information (ITAG4.0 gene models and descriptions), we identified concentrated “defense hotspots.” These hotspots are rich in genes known to be crucial for plant immunity, such as NLR-like genes, receptor-like kinases/proteins, WRKY/ERF transcription factors, MAP kinases, PR proteins, and enzymes involved in hormone and redox pathways. Collectively, these findings support a model where resistance is provided by a few key genes (oligogenic) arranged in functional units (modular). The framework of using donor-private variants and the identified defense hotspots offer practical markers and candidategenes for detailed genetic mapping, functional validation, and the use of marker-assisted selection to deploy wild Septoria leaf spot resistance into cultivated tomato varieties.
To dissect the genetic basis of SLS resistance introgressed from S. arcanum into cultivated tomato, the study combined high-density genotyping and time-resolved transcriptomics in near-isogenic backgrounds. Genotyping-by-sequencing of advanced backcross and introgressed lines defined S. arcanum introgression blocks, refining previously detected QTL and enriching for defense-annotated genes. Alongside, this study profiled the transcriptional response of a highly resistant introgression line and its susceptible recurrent parent at 36- and 72-hours post-inoculation with S. lycopersici. Both genotypes displayed a broad early response, but only the resistant line exhibited sustained and amplified defense activation at 72 hours. Comparative analysis identified 180 genes specifically up-regulated in the resistant line at both time points. Intersecting this resistance-specific module with S. arcanum-unique variants yielded 31 candidate genes within introgressed regions. Functional annotation highlighted nine genes with clear roles in plant immunity: three receptor-like kinases, a WRKY transcription factor, a pathogenesis-related protein, two pleiotropic drug-resistance transporters, and two canonical R proteins, including the known late blight gene Ph-3. These loci, collectively spanning pathogen perception, signal transduction, transcriptional reprogramming, and defense execution, represent the most plausible causal genes for SLS resistance. Overall, this chapter establishes an integrated framework linking wild-species introgression mapping, variant discovery, and RNA-seq to pinpoint mechanistic resistance candidates, thereby offering concrete targets for fine mapping, functional validation, and deployment in tomato breeding programs.
Recommended Citation
Hernandez De Lira, Inty Omar, "Wild Introgression and Comparative Genomics for Breeding Septoria Leaf Spot Resistant Tomato" (2025). Graduate Theses, Dissertations, and Problem Reports. 13140.
https://researchrepository.wvu.edu/etd/13140