Bacterial canker resistance in tomato

Clavibacter michiganensis subsp. michiganensis (Cmm) is the pathogen causing bacterial canker in tomato. The disease was described for the first time in 1910 in Michigan, USA. Cmmis considered the most harmful bacteria threatening tomato. Disease transmission occurs via seed and symptoms become visible at least 20 days after infection. Due to its complex strategy and transmission, Cmm is under quarantine regulation in EU and other countries. There is no method to stop disease progress in plants after infection. Thus, disease management consists usually of chemical treatments as protection and by careful clean cultural practices. However, the use of resistant varieties is the most effective and environmentally friendly method. Unfortunately, there is no cultivar harboring effective resistance on the market although efforts to get resistant varieties already started in the 60s. Our aim in this thesis was to develop valuable genetic material for breeders in order to enable them to release resistant cultivars and provide comprehensive scientific knowledge for further detailed research about Cmm. Our scientific activity in this thesis started with the identification of new Cmm resistance sources and confirmation of existent ones. In Chapter 3 we have screened a collection of wild tomatoes for resistance to Cmm. We made use of Real Time TaqMan PCR for intensive phenotyping. Using wilting and bacterial concentration as parameters for evaluation of the sources, we have identified new sources and confirmed existent ones. We have decided to continue further with one new source, S. pimpinellifolium, and one existent source, S . arcanum. We continued our research in Chapter 4 with a genetic analysis of the new source coming from S. pimpinellifolium. A recombinant inbred line population between the resistant parent, S. pimpinellifolium, and the susceptible parent S. lycopersicum was evaluated in three different environments. Wilting, bacterial concentration, and stem discoloration were the scored parameters. Responses of resistance in different environments were determined and genomic regions responsible for different responses were mapped. In Chapter 5, we have continued our research by fine mapping of previously identified genomic regions and developing nearly isogenic lines containing those genomic regions. By doing fine mapping, we made use of old stock DNA and recently developed different types of SNP marker technology. Previously identified Quantitative Trait Loci(QTLs)could be more precisely delimited. During isogenic line development, embryo rescue was used in order to break the genetic barrier between our S. arcanum source and tomato. Marker assisted backcrossing was applied to obtain lines with a minimum of donor parent in a faster way. By using this method we gained two generations of backcrossing. In order to obtain comprehensive information about different Cmm isolates inTurkey, we have performed multi locus sequence analysis (MLST) analysis on a Cmm collection, which was collected in 20 years of time in different part of Turkey. In Chapter 6 a statistical analysis of this collection revealed that measurement of clonality of this collection was possible as well as it was possible to predict the virulence level of strainsusing a subset of housekeeping genes. All knowledge gained by our experiments and knowledge coming from literature about Cmm have led a Review paper, Chapter 2, by which comprehensive information about Cmm resistance sources, genetic analysis of these sources, detection methods of Cmm, infection strategies of Cmm and interaction with its host was discussed. In conclusion, two good Cmm resistance sources and several tools and methods are available for breeders. Genomic regions of these sources associated with resistance were determined. Wider knowledge about Cmm detection, Cmm infection and Cmm interaction with its host are available for further research.