Development of the gene-based SCARs for the Ph-3 locus, which confers late blight resistance in tomato

Late blight (LB) is a devastating disease in tomato (Solanum lycopersicum), which is caused by the oomycete Phytophthora infestans (Mont.) de Bary. In this study, the LB-resistance gene Ph-3 was evaluated using a pathogenic isolate of P. infestans from Korea. Molecular mapping of the TG328 and TG591 regions, which are tightly linked to the Ph-3 locus, was performed using F6 families derived by crossing the LB-resistant accession “L3708” (Solanum pimpinellifolium) with the LB-susceptible accession “AV107-4” (S. lycopersicum). The map indicated that the Ph-3 locus also conferred high resistance to the Korean isolate of P. infestans. To identify the putative Ph-3 gene, the ultracontig SL2.4ch09 of the S. pimpinellifolium draft-genome sequence, which contained the TG328 and TG591 clone sequences, was investigated. Four tandemly duplicated putative Ph-3 homologs (designated as Ph-3a, Ph-3b, Ph-3c, and Ph-3d in this study) belonging to the coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) class of pathogen resistance genes were identified in a flanking region of TG328 and TG591. TG591 sequences and partial sequences of Ph-3c and Ph-3d were tandemly repeated. Protein sequences of Ph-3 homologs showed high sequence homology with Rpi-vnt1.1 and Rpi-vnt1.3, the CC-NBS-LRR LB-resistance genes in potato. Ph-3c and Ph-3d showed the highest protein sequence homology (80%) to Rpi-vnt1.1 and Rpi-vnt1.3, whereas Ph-3a and Ph-3b showed 70% homology to these genes. A set of sequence characterized amplified region (SCAR) markers that could distinguish each copy of the Ph-3 gene homolog were developed, and allelic compositions of the Ph-3 locus were compared between “L3708” and a variety of LB-susceptible tomato accessions. These SCAR markers proved useful, not only for studying the organization of the Ph-3 homologs in an individual tomato plant, but also for selection of the LB-resistance allele.