A compendium of genome-wide sequence reads from NBS (nucleotide binding site) domains of resistance genes in the common potato

SolariX is a compendium of DNA sequence tags from the nucleotide binding site (NBS) domain of disease resistance genes of the common potato, Solanum tuberosum Group Tuberosum. The sequences, which we call NBS tags, for nearly all NBS domains from 91 genomes—representing a wide range of historical and contemporary potato cultivars, 24 breeding programs and 200 years—were generated using just 16 amplification primers and high-throughput sequencing. The NBS tags were mapped to 587 NBS domains on the draft potato genome DM, where we detected an average, over all the samples, of 26 nucleotide polymorphisms on each locus. The total number of NBS domains observed, differed between potato cultivars. However, both modern and old cultivars possessed comparable levels of variability, and neither the individual breeder or country nor the generation or time appeared to correlate with the NBS domain frequencies. Our attempts to detect haplotypes (i.e., sets of linked nucleotide polymorphisms) frequently yielded more than the possible 4 alleles per domain indicating potential locus intermixing during the mapping of NBS tags to the DM reference genome. Mapping inaccuracies were likely a consequence of the differences of each cultivar to the reference genome used, coupled with high levels of NBS domain sequence similarity. We illustrate that the SolariX database is useful to search for polymorphism linked with NBS-LRR R gene alleles conferring specific disease resistance and to develop molecular markers for selection

The Transcriptome of Compatible and Incompatible Interactions of Potato (Solanum tuberosum) with Phytophthora infestans Revealed by DeepSAGE Analysis

Late blight, caused by the oomycete Phytophthora infestans, is the most important disease of potato (Solanum tuberosum). Understanding the molecular basis of resistance and susceptibility to late blight is therefore highly relevant for developing resistant cultivars, either by marker-assissted selection or by transgenic approaches. Specific P. infestans races having the Avr1 effector gene trigger a hypersensitive resistance response in potato plants carrying the R1 resistance gene (incompatible interaction) and cause disease in plants lacking R1 (compatible interaction). The transcriptomes of the compatible and incompatible interaction were captured by DeepSAGE analysis of 44 biological samples comprising five genotypes, differing only by the presence or absence of the R1 transgene, three infection time points and three biological replicates. 30.859 unique 21 base pair sequence tags were obtained, one third of which did not match any known potato transcript sequence. Two third of the tags were expressed at low frequency (<10 tag counts/million). 20.470 unitags matched to approximately twelve thousand potato transcribed genes. Tag frequencies were compared between compatible and incompatible interactions over the infection time course and between compatible and incompatible genotypes. Transcriptional changes were more numerous in compatible than in incompatible interactions. In contrast to incompatible interactions, transcriptional changes in the compatible interaction were observed predominantly for multigene families encoding defense response genes and genes functional in photosynthesis and CO2 fixation. Numerous transcriptional differences were also observed between near isogenic genotypes prior to infection with P. infestans. Our DeepSAGE transcriptome analysis uncovered novel candidate genes for plant host pathogen interactions, examples of which are discussed with respect to possible function

Marker-assisted breeding for disease resistance in potato.

International audienceSub-project 5 of BIOEXPLOIT aims to design durable disease resistance through marker-assisted breeding by converting existing markers for high-throughput application, developing and validating high-throughput marker technologies and pyramiding major R genes and/or quantitative trait loci into elite material. Activities include (1) the fine mapping of the quantitative trait locus PiXspg which accounts for a large proportion of the variation in late blight resistance, (2) converting SNP-based markers and an AFLP marker to easy-to-use-markers, (3) testing of progenies with combined sources of late blight resistance for presence of R genes and agronomic features, (4) backcrossing new sources of resistance to S. tuberosum and molecular screening of breeding materials with marker GP94 linked with gene Rpi-phu1 conferring late blight resistance, (5) evaluating potato clones with enhanced resistance against Phytophthora infestans under field conditions of Toluca (México), and (6) developing populations and marker-assisted breeding for disease resistance

Two PR-1 loci detected in the native cultivated potato Solanum phureja appear differentially expressed upon challenge by late blight

Plant pathogenesis-related proteins are toxic to invading pathogens. Among them, the Subfamily PR-1 represents low-molecular weight proteins of unknown biochemical function. Here, we describe the cloning and isolation of two PR-1 genes (PR-1b1 (GenBank accession no. SPH493450) and PR-1b2 (SPH493451)) that encode predicted basic proteins. We isolated them from Solanum phureja, a native Andean potato with horizontal resistance to late blight, caused by the oomycete Phytoplithora infestans. We demonstrate that the PR-1 genes belong to a small multigene family with an estimated copy number of 4-6 with one of them located oil chromosome IX as determined by genetic mapping. The expression of PR-1 genes was different in late blight resistant and Susceptible genotypes. Therefore, we propose that both PR-1 genes may play a role in horizontal late blight resistance of S. phureja. (c) 2006 Elsevier Ltd. All rights reserved