Identification of QTLs for early blight (Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum x L. hirsutum cross

Most commercial cultivars of tomato, Lycopersicon esculentum Mill., are susceptible to early blight (EB), a devastating fungal (Alternaria solani Sorauer) disease of tomato in the northern and eastern parts of the U.S. and elsewhere in the world. The disease causes plant defoliation, which reduces yield and fruit quality, and contributes to significant crop loss. Sources of resistance have been identified within related wild species of tomato. The purpose of this study was to identify and validate quantitative trait loci (QTLs) for EB resistance in backcross populations of a cross between a susceptible tomato breeding line (NC84173; maternal and recurrent parent) and a resistant Lycopersicon hirsutum Humb. and Bonpl. accession (PI126445). Sixteen hundred BC1 plants were grown to maturity in a field in 1998. Plants that were self-incompatible, indeterminant in growth habit, and/or extremely late in maturity, were discarded in order to eliminate confounding effects of these factors on disease evaluation, QTL mapping, and future breeding research. The remaining 145 plants (referred to as the BC1 population) were genotyped for 141 restriction fragment length polymorphism (RFLP) markers and 23 resistance gene analogs (RGAs), and a genetic linkage map was constructed. BC1 plants were evaluated for disease symptoms throughout the season, and the area under the disease progress curve (AUDPC) and the final percent defoliation (disease severity) were determined for each plant. BC1 plants were self-pollinated and produced BC1S1 seed. The BC1S1 population, consisting of 145 BC1S1 families, was grown and evaluated for disease symptoms in replicated field trials in two subsequent years (1999 and 2000) and AUDPC and/or final percent defoliation were determined for each family in each year. Two QTL mapping approaches, simple interval mapping (SIM) and composite interval mapping (CIM), were used to identify QTLs for EB resistance in the BC1 and BC1S1 populations. QTL results were highly consistent across generations, years and mapping approaches. Approximately ten significant QTLs (LOD ≥ 2.4, P ≤ 0.001) were identified (and validated) for EB resistance, with individual effects ranging from 8.4% to 25.9% and with combined effects of >57% of the total phenotypic variation. All QTLs had the positive alleles from the disease-resistant parent. The good agreement between results of the BC1 and 2 years of the BC1S1 generations indicated the stability of the identified QTLs and their potential usefulness for improving tomato EB resistance using marker-assisted selection (MAS). Further inspections using SIM and CIM indicated that six of the ten QTLs had independent additive effects and together could account for up to 56.4% of the total phenotypic variation. These complementary QTLs, which were identified in two generations and 3 years, should be the most useful QTLs for MAS and improvement of tomato EB resistance using PI126445 as a gene resource. Furthermore, the chromosomal locations of 10 of the 23 RGAs coincided with the locations of three QTLs, suggesting possible involvement of these RGAs with EB resistance and a potential for identifying and cloning genes which confer EB resistance in tomato.