Mapping novel quantitative trait loci (QTL) associated with resistance to Pseudoidium neolycopersici in tomato

Abstract

The cultivated tomato (Solanum lycopersicum) is grown for both processing and fresh markets and is ranked as one of the most important vegetable crops globally. Its economic contribution to agriculture has permitted tomato to be the most studied species within the Solanaceae family as a model organism for fruit ripening, development and resistance to multiple biotic and abiotic stresses. Throughout their short life cycle, tomatoes can be challenged with more than 200 diseases. Enhancing host defence by breeding for disease resistance has become a priority globally. Powdery Mildew (PM) is a disease that challenges tomato production in both greenhouse and field. Three species of PM are able to infect tomatoes, namely Leveillula taurica, Oidium lycopersici and Pseudoiudium neolycopersici. Most historical epidemics are caused by P. neolycopersici which is also the main PM pathogen responsible for increased infections in South Africa. As with a lot of diseases affecting tomatoes, wild tomato relatives have been the source of resistant loci against PM infections. These loci include five dominant Ol-genes (Ol-1, Ol-3 and Ol-4 to Ol-6 mapped to chromosome 6), one recessive ol-gene (ol-2, mapped to chromosome 4) and three Ol-QTLs (mapped to chromosome 6 and 12). The aim of this study was to identify a region on the tomato genome conferring possible novel resistance against PM infections caused by P. neolycopersici. Starke Ayres breeding lines, observed to be free of PM infection, did not contain any of the known resistance loci previously mapped. An F2 population, created by the tomato breeder that observed the resistant breeding lines, was used as an initial mapping population. A QTL mapping study was conducted using polymorphic KASP assays designed from the SolCAP SNP array to genotype the F2 segregating population produced through crossing TF 3936 (an observed resistant parent line) and TF 3346 (an observed susceptible line). Initial mapping results indicated a significant association on chromosome 3. Significance on chromosome 3 was confirmed during a seedling trial conducted on an F3 mapping population. Additionally, 15 Starke Ayres breeding lines were re-sequenced and aligned to the reference genome for SNP detection on chromosome 3. Sequence analysis revealed an approximate 1 Mbp region of DNA with thousands of SNPs unique to the resistant parent, TF 3936. Furthermore, 24.7 % of the sequence data within this region did not map back to the reference genome. These findings are consistent with that of an introgression from a wild species. Genotyping with the newly designed SNP markers revealed a rare crossing over event for two individuals that occurred between 2 markers at 5.3 Mbp and 5.7 Mbp located within the possible introgression region. A genotype first approach was conducted to screen for further recombinants within this region. Selected seedlings were transplanted and phenotyped at the 8-week developmental stage (adult plants). A total of 0.58 % of individuals screened underwent a recombination event indicating severe suppression of recombination thus further supporting the presence of an introgression. The results of this study clearly indicate the presence of novel tomato resistance against PM infections located within a 400 000 bp region on chromosome 3. In addition, this research has allowed for two markers to be added to the Starke Ayres MAS marker panel in the tomato breeding program. Lastly, this study has shown that resequencing various breeding lines and aligning them to an available reference genome aid in SNP detection for marker development or discovering a new source of resistance.