Exploring the Solanaceaeous NB-LRR Gene Complement Using RenSeq (R gene enrichment and Sequencing)

RenSeq is a NB-LRR gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences (Jupe et al. 2013). We successfully applied RenSeq to several sequenced Solanaceae model and crop plants, including the reference genomes of potato (clone DM), tomato (S. lycopersicum Heinz 1706 and S. pimpinellifolium LA1598), and several Nicotiana spp. including N. benthamiana and N. tabacum. Analysis of the RenSeq data increased the number of NB-LRRs from 438 to 755 in DM, as well as corrected the number to 334 in Heinz 1706. The majority of these identified R gene loci reside in poorly- or previous un-annotated regions of the genome. Within the yet unannotated N. benthamiana genome we were able to annotate 340 NB-LRR loci. We further developed a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with disease resistance. We were able to apply this method to successfully identify markers co-segregating with resistance genes towards the late blight pathogen Phytophthora infestans in several Solanum species, including the tetraploid fresh market potato cultivar ‘Sarpo Mira’. RenSeq data was used to create two markers for two independently segregating major R genes that can be used in marker assisted selection of future breeding material. The RenSeq derived MiSeq reads are further being used to characterize the underlying Sarpo Mira R gene candidate sequences.