R Gene Enrichment Sequencing (RenSeq) – A Quick Method to Detect Polymorphisms Co-Segregating with Functional Resistance Gene Alleles in Solanum Species

Increasing availability of genome sequences, rapid evolution of next generation sequencing and other high-throughput mapping approaches led to development of numerous techniques for whole genome mapping, also in crop species. Most of these approaches, however, detect polymorphism in whole genome/transcriptome, not always resulting in development of closely linked markers. Here we present a technique for direct polymorphism detection in R gene alleles. Our approach, which takes advantage of Agilent Sureselect target enrichment of all potato NB-LRR R gene homologues in bulked DNA from resistant and susceptible populations, and Illumina sequencing, allows rapid and precise mapping of this class of R genes. This leads to quick identification of clusters of R genes conferring resistance; ideally, it would lead to development of markers directly in R gene of interest. As a proof of the concept, we have applied this technique to fine-map three Rpi (Resistance to Phytophthora infestans) genes from different diploid species of Solanum, for which the position in the Solanum genome was roughly known. Moreover, this approach can be used to fine-map any resistance gene of NB-LRR type in Solanumsp.  Furthermore, after redesigning one of the steps, our technique should be applicable to other crop species for which genome or closely related genome information is available.

Thanks to BBSRC grant BB/H019820/1 for funding this project.