A novel approach to locate Phytophthora infestans resistance genes on the potato genetic map

Abstract

Mapping resistance genes is usually accomplished by phenotyping a segregating population for the resistance trait and genotyping it using a large number of markers. Most resistance genes are of the NBS-LRR type, of which an increasing number is sequenced. These genes and their analogs (RGAs) are often organized in clusters. Clusters tend to be rather homogenous, viz. containing genes that show high sequence similarity with each other. From many of these clusters the map position is known. In this study we present and test a novel method to quickly identify to which cluster a new resistance gene belongs and to produce markers that can be used for introgression breeding. We used NBS profiling to identify markers in bulked DNA samples prepared from resistant and susceptible genotypes of small segregating populations. Markers co-segregating with resistance can be tested on individual plants and directly used for breeding. To identify the resistance gene cluster a gene belongs to, the fragments were sequenced and the sequences analyzed using bioinformatics tools. Putative map positions arising from this analysis were validated using markers mapped in the segregating population. The versatility of the approach is demonstrated with a number of populations derived from wild Solanum species segregating for P. infestans resistance. Newly identified P. infestans resistance genes originating from S. verrucosum, S. schenckii, and S. capsicibaccatum could be mapped to potato chromosomes 6, 4, and 11, respectively.

Fig. 1

An example of a part of a NBS profiling gel. This figure shows part of the NBS profiling gel of population snk7458 using NBS2 and MseI. The arrows indicate the segregating NBS profiling bands. The upper arrow points at a band in coupling phase, the lower arrow points at a band in repulsion phase

Fig. 2

Marker CD67 shows co-segregation with P. infestans resistance in populations ver03-392 and ver03-394 after digestion with HpyCH4IV and digestion with SsiI