Comparative next-generation mapping of the Phytophthora infestans resistance gene Rpi-dlc2 in a European accession of Solanum dulcamara

Abstract

Phytophthora infestans, the causal agent of late blight, remains the main threat to potato production worldwide. Screening of 19 accessions of Solanum dulcamara with P. infestans isolate Ipo82001 in detached leaf assays revealed strong resistance in an individual belonging to accession A54750069-1. This plant was crossed with a susceptible genotype, and an F(1) population consisting of 63 individuals was obtained. This population segregated for resistance in 1:1 ratio, both in detached leaf assays and in an open-field experiment. Presence of the formerly mapped Rpi-dlc1 gene as the cause of the observed segregating resistance could be excluded. Subsequently, AFLP analyses using 128 primer combinations enabled identification of five markers linked to a novel resistance gene named Rpi-dlc2. AFLP markers did not show sequence similarity to the tomato and potato genomes, hampering comparative genetic positioning of the gene. For this reason we used next-generation mapping (NGM), an approach that exploits direct sequencing of DNA (in our case: cDNA) pools from bulked segregants to calculate the genetic distance between SNPs and the locus of interest. Plotting of these genetic distances on the tomato and potato genetic map and subsequent PCR-based marker analysis positioned the gene on chromosome 10, in a region overlapping with the Rpi-ber/ber1 and -ber2 loci from S. berthaultii. Pyramiding of Rpi-dlc2 and Rpi-dlc1 significantly increased resistance to P. infestans, compared with individuals containing only one of the genes, showing the usefulness of this strategy to enhance resistance against Phytophthora.

Genomic analysis of the native European Solanum species, S. dulcamara

“…We show that molecular markers derived from transcribed regions can be anchored to the genomes of related species for map comparison. Such information is very useful for gene mapping efforts, as we recently showed for mapping of the Rpi-dlc2 locus, which is located near the inversion breakpoint on chromosome 10, in comparison to tomato [10]. The observed chromosome inversions as deduced from the genetic map concur well with previously published data from other Solanaceae and support the position of S. dulcamara in the tomato/potato clade (“Clade I”) [2].…”

“…For map construction, we first identified sequence polymorphisms between accessions A54750069-1 and 944750001-2 for which an F 1 population was available [10] (Additional file 1: Table S1). By independently mapping the reads of the two parent genotypes to a subset of the contigs, 20,162 putative SNPs were identified (see methods for criteria).…”

“…Material used to test SSRs was provided by Dr Janny Peters (Radboud University Nijmegen, The Netherlands). The segregating population used for map construction (code 05-150) was derived from a cross between accession A54750069-1 and 944750001-2 [10]. All plants were cultivated in standard greenhouse conditions as described in [10], unless indicated otherwise.…”

“…On the other hand, as a host it can represent a European source of resistance genes for Solanum breeding, as alternative to the currently used American sources. We have recently reported on the identification of two resistance loci to Phytophthora infestans , Rpi-dlc1 and Rpi-dlc2 , which are located on chromosome 9 and 10, respectively [9,10]. …”

Resistance to Phytophthora Infestans in Three Solanum Nigrum F3 Families

“…Such approach has been applied in another distant Solanum relative -S. dulcamara that cannot be crossed with potato. Using intraspecific crosses two late blight resistance genes of this species have been mapped: Rpi-dlc1 to chromosome IX (Golas et al 2010) and Rpi-dlc2 to chromosome X (Golas et al 2012). What is interesting, mapping of Rpidlc2 has been difficult due to the fact that in the mapping population both Rpi-dlc1 and Rpi-dlc2 were segregating and their phenotypic effects have been overlapping which is similar to the situation in our population B.…”