Characterization of Early Blight Resistance in a Recombinant Inbred Line Population of Tomato: II. Identification of QTLs and Their Co-localization with Candidate Resistance Genes

Early blight (EB), caused by fungi Alternaria solani and A. tomatophila, is a major foliar disease of the tomato in many growing regions. Sources of resistance have been identified within the related wild species of tomato, including S. habrochaites, S. peruvianum and S. pimpinellifolium. Breeding for EB resistance via traditional protocols has been difficult due to the complexity of resistance and influence of several plant physiological and morphological characteristics on tomato response to EB. Identification of genetic markers associated with EB resistance and application of marker-assisted selection (MAS) would facilitate development of elite tomato breeding lines and hybrid cultivars with EB resistance. The goals of this study were to identify quantitative trait loci (QTLs) conferring resistance to EB in a resistant accession (LA 2093) of the tomato wild 150 Hamid Ashrafi and Majid R. Foolad species S. pimpinellifolium, and discover putative candidate resistance genes and expressed sequence tags (ESTs) that co-localize with the QTLs. Previously, a recombinant inbred line (RIL) population of tomato was developed from a cross between LA 2093 and S. lycopersicum breeding line NCEBR-1 and a genetic linkage map with 294 molecular markers spanning the 12 tomato chromosomes constructed. In the present study, the RIL population was grown and evaluated for EB resistance under field conditions in four successive years and generations (F7, F8, F9 and F10). Early blight disease severity, measured as the final % defoliation as well as the area under disease progress curve (AUDPC), was subjected to QTL analysis using simple interval mapping (SIM) and composite interval mapping (CIM). The SIM and CIM analyses resulted in identification of the same QTLs, though CIM detected QTLs with substantially more accuracy. Across the four generations, 5 major QTLs (LOD ≥ 2.4, P ≤ 0.001) were identified for EB resistance on tomato chromosomes 2 (2 QTLs), 5, 6 and 9. Three QTLs on chromosomes 2 and 6 were contributed from LA 2093 with individual phenotypic effects ranging from 8% to 16%, and two QTLs on chromosomes 5 and 9 were contributed from NCEBR-1 with individual phenotypic effects ranging from 7% to 18%. The QTLs on chromosomes 5 and 6 exhibited largest effects (10% to 18%) among all QTLs and were identified in three of the four generations. These two QTLs should be most useful for MAS and improvement of tomato EB resistance using LA 2093 and NCEBR-1 as resistant resources. The identified QTLs showed co-localization with several resistance genes and candidate ESTs, including Mi-1, ethylene response factor-5, lipoxygenase B, wound-induced protein-1, and phosphoenolpyruvate carboxylase kinase-2. With the genome sequence of tomato available, further investigation of these QTLs may lead to the identification of candidate genes underlying EB resistance in tomato.