Identification of late blight resistance QTLs in an interspecific RIL population of tomato via genotyping-by-sequencing

Late blight (LB), caused by Phytophthora infestans, is a destructive disease of the cultivated tomato, Solanum lycopersicum. Environmental concerns and pathogen resistance have propelled research towards developing host resistance. The current LB-resistant cultivars of tomato exhibit susceptibility under severe disease pressure, necessitating the identification, characterization, and incorporation of additional resistance genes into new tomato cultivars. Recently, we identified Solanum pimpinellifolium accession PI 270443 with strong resistance to LB and developed a RIL population from its cross with an LB-susceptible tomato breeding line. In the present study, we constructed a high-density genetic map of the RIL population, using 8,470 SNP markers set into 1,195 genomic bins, with a total genetic distance of 1232 cM and an average bin size of 1 cM. We identified 2 major adjoining LB-resistance QTLs on chromosome 10 and a few minor QTLs on chromosomes 1 and 12 of PI 270443. While one of the QTLs on chromosome 10 colocalized with the known LB-resistance gene Ph- 2 and a LB-resistance QTL previously identified in an F2 population of the same cross, the present study allowed marker saturation of the region, fine mapping of the QTL, and identification of candidate resistance genes in the region. One of the 2 major QTLs on chromosome 10 and the 3 QTLs on chromosomes 1 and 12 were not previously reported in S. pimpinellifolium for LB resistance. These results will expedite transferring of LB resistance from PI 270443 into the tomato cultigen via MAS and discovering the underpinning LB-resistance genes in PI 270443.