Early blight resistance in tomato: screening and genetic study

Tomato early blight (EB) caused by the fungus Alternaria solani is a field disease with a worldwide distribution, including Indonesia. The disease is currently controlled using frequent applications of fungicides. The use of resistant cultivar would be an attractive way to reduce fungicide application. The aims of the research are to support breeding of EB resistance cultivars for the Indonesian market, by identifying EB resistance genes effective in Indonesia and developing markers for MAS.In Chapter 1 the literature on A. solani, EB and resistance is reviewed. On the fungal side pathogenicity and genetic variation have been widely investigated. However, the existence of different physiological races has not been convincingly demonstrated or disproved. Reliable methods of screening are available for use in resistance breeding. Intensive screening of tomato accessions worldwide has shown that strong resistance is not available in the cultivated tomato but only in wild species. Resistance to A. solani is expressed quantitatively and is polygenically inherited. For that reason classical breeding has not been able to achieve high levels of resistance, and undesirable traits from the donors have been introgressed as well. Recently QTLs have been mapped in a few resistance sources, which could facilitate transferring such quantitative resistance genes and circumvent the problem of unfavourable linkage drag once markers tightly linked to the QTLs have been obtained.In Chapter 2 a resistance test method involving droplet inoculation is described, which is an adaptation of an existing but hardly-used technique. This method has advantages in comparison with the more widely used spray inoculation method, including a clear distinction between lesions caused by A. solani and necroses of 1eaf loss due to other causes, and an objective measurement of damage in contrast to subjective scoring. In the droplet inoculation method leaflets of intact plants are inoculated with droplets of an A. solani conidial suspension in water or an agar solution. Lesions are assessed quantitatively by measuring the length and the perpendicular width. In this way objective and accurate assessments, which are prerequisites for QTL analysis, can be achieved. This inoculation method was used to screen a collection of 54 tomato accessions for resistance to an Indonesian A. solani isolate,S. arcanum LA2157 is highly resistant to A. solani in the glasshouse screening tests. The genetics of the resistance in this wild relative of tomato was further studied using a QTL mapping approach (Chapter 3). The mapping population consisted of 176 F2 plants. A linkage map consisting of 12 linkage groups covering 1179 cM was based on 379 markers (33 SSR, 21 SNP and 316 AFLP markers). All linkage groups could be assigned to the 12 tomato chromosomes. About half of the markers showed deviation from the expected 1:2:1 segregation ratio. The F2 population was phenotyped in a glasshouse in Netherlands with an Indonesian isolate of A. solani. EB resistance was evaluated with respect to lesion size (LS) and related parameters (relative area under the lesion expansion curve [RAULEC] and percentage of small lesions [PSmL]). The derived F3 lines (156) were tested in a field in Indonesia. Percentage of EB index (PEBI) was assessed at six times and relative area under the disease progress curve (RAUDPC) was calculated. A total of six QTLs with a range of LOD scores 3.6 to 16.4 were mapped on chromosomes 1, 2, 5, 6, 7 and 9. Three of the QTLs showed effects in both tests despite differences in experimental method and observed traits. For the first time, three QTLs for resistance affecting the development of stem lesions, another disease symptom caused by the fungus on the main and secondary stems of the plant, were identified, which completely overlapped with QTL regions for early blight resistance. Two QTLs on chromosomes 2 and 9, which explained 7 to 16% of the phenotypic variation for EB resistance and 31% for stem lesion resistance, are recommended to be used in tomato breeding programs for resistance to A. solani.