Molecular mapping of the Ph-3 gene for late blight resistance in tomato

Late blight, caused by Phytophthora infestans (Mont.) deBary, is a major disease of tomato (Lycopersicon esculentum Mill.) in cool, wet environments. In this study we report on the mapping of a gene in L. pimpinellifolium (Jusi.) Mill. accession L3708 conditioning race-specific resistance to P. infestans. F-2 tomato plants from the cross CLN657 (susceptible) X L3708 (resistant) and segregating for late blight resistance were evaluated for resistance to P. infestans isolate Pi-16 that overcomes host resistance genes Ph and Ph-2. Resistant and susceptible DNA pools, created by bulking equal amounts of DNA from nine resistant F2 plants (for R-pool) and eight susceptible F2 plants (for S-pool), and the DNA pools were used to screen amplified fragment length polymorphic (AFLP) primers. Polymerase chain reaction (PCR) using 120 combinations of three-base selective nucleotide primer pairs revealed five DNA bands from five primer pairs unique to the resistant parent and R-pool, and a DNA band from one primer pair associated with the susceptible parent and S-pool. After DNA band isolation and cloning, two single-copied DNA clones associated with resistance were hybridized with 50 introgression lines (IL) derived from L. esculentum X L. pennellii; IL9-3, containing an introgression from the long arm of chromosome 9, was the only polymorphic IL. Restriction fragment length polymorphism (RFLP) markers mapped to chromosome 9 and two AFLP-derived RFLP markers were used to probe a second F2 population. A major quantitative trait locus (QTL) with an LOD score of 18.41 was found at RFLP marker TG591; it accounted for 71.4% of the variance. This gene, Ph-3, is non-allelic to tomato late blight resistance genes Ph (previously mapped to chromosome 7 or Ph-2 (mapped to chromosome 10)).