Molecular characterisation of Phytophthora infestans resistance genes in Solanum caripense and development of molecular markers for genetic mapping

Genetic linkage maps were constructed for two parental genotypes of Solanum caripense. The maps consist of 240 molecular markers covering genetic distances of 1,080 cM (maternal) and 779 cM (paternal). These maps are a big milestone towards isolation of the Rpi-crp1 gene conferring unique resistance against virtually all strains of P. infestans affecting potato and tomato. Due to the sterility of potato x S. caripense crosses, isolation of the resistance (R) gene is an alternative to its eventual utilisation via selection for its syntenic counterparts within the potato genome or its direct transfer into potato. This gene could help build stable broad-spectrum resistance to the economically important late blight disease. The maps contain AFLP, SSR, RFLP-derived CAPS, RGA, COSII and the new SPD markers. Two RGA markers mapped to corresponding positions of known R genes but none was linked to the Rpi-crp1 locus. Two Pst1-based AFLP markers, P13M32-102 and P15M37-178 were genetically linked to the resistance locus, Rpi-crp1, at genetic distances of 4 and 5 cM, respectively. These fragments were isolated, cloned and sequenced, showing high levels of sequence similarity to a major R and a kinase gene. Subsequent development of a physical map and its screening with these markers will shed light on the actual physical distances. Sequence-Polymorphism-Derived markers were tailored for the S. caripense genome based on genetic sequences. Using these markers, it was possible for the first time to identify 11 of 12 Solanum chromosomes on S. caripense maps. Organisation of the S. caripense genome was highly similar to the potato and tomato genomes except one major inversion of a large fragment of chromosome XI and a translocation of a chromosome IX marker to chromosome XI. The late blight resistance locus Rpi-crp1 was mapped on chromosome IX. This opens up an avenue of synteny-based association mapping using other known candidate resistance genes from Solanum chromosome IX.