A Genetic Analysis of Early blight (Alternaria spp.) Resistance and Fruit-Related Traits in Tomatoes (Solanum lycopersicum)

Abstract

Tomatoes (Solanum lycopersicum) are the second most important horticultural crop grown worldwide, with an estimated 192,317,973 tonnes of tomatoes produced globally in 2023 in 170 countries. Tomato plants are vulnerable to disease which is predominantly controlled with agrichemical applications. Pesticide use is both costly and environmentally damaging, so minimising these impacts through disease resistant crop varieties is more efficient and sustainable. Early blight is a fungal disease infecting solanaceous crops caused by multiple Ascomycete species of the genus Alternaria. These infect the leaves, stem and fruits of tomato plants, and can cause total defoliation and complete crop failure in severe outbreaks. There is a strong interest within the plant breeding industry to produce varieties which are resistant to Early blight, but little is known about the genetic mechanisms in place to induce this trait. There is also huge variability in types of tomato fruit brought to market, with different fruit shapes typically being associated with differing end uses. This may take the form of elongated “paste” tomatoes for use in canning, larger round “slicer” fruits for fresh usage, or smaller “cherry tomatoes. There are also fruit traits governed by ripening inhibitor genes which can extend shelf life and reduce damage in mechanical harvesting operations. These traits may be bred for using Marker-Assisted Selection (MAS) approaches.

In this thesis I aimed to identify Quantitative Trait Loci (QTLs) associated with early blight resistance and fruit shape, colour and ripening inhibition in one of the most highly regarded early blight resistant commercial varieties. I also used a growth trial to assess the early blight resistance level of currently available commercial cultivars and estimate their parentage with genotypic analysis. Finally, I evaluated wild tomato accessions (Solanum pimpinellifolium) for suitability for future early blight resistant tomato breeding programmes.
I produced a high-density linkage map containing 1,100 markers and identified QTLs for fruit traits. However, QTLs for early blight resistance were not found due to unreliable phenotypic data being produced using detached leaf assays. The currently available commercial cultivars assessed had at best moderate resistance, except for Matt’s Wild Cherry which had strong resistance in both polytunnel and outdoor trials. I also found evidence for the use of North Carolina State University’s breeding lines in some resistant cultivars, but resistance was limited. I identified genetic structure within the S. pimpinellifolium accessions trialled, which correlated with preferred fruit traits, however disease resistance was not reliably identified.

The results in this thesis show that the levels of early blight resistance in most domesticated S. lycopersicum varieties are generally poor, but that wild accessions do exist that have strong resistance. It may also be possible to guide the collection of new breeding material from the wild based on analysis of population structure. It also highlights that the use of quantitative genetics, including the generation of high-density linkage maps using a targeted genotyping approach, allows for the precise detection of QTLs and markers which can be used in marker-assisted selection. This will allow precise introgression of useful traits into future commercial tomato varieties.

Date of Award	14 Jan 2026
Original language	English
Supervisor	Katherine Steele (Supervisor), Alexander Papadopulos (Supervisor) & Owen Osborne (Supervisor)