Exploring the Solanaceaeous NB-LRRome using RenSeq (R gene enrichment sequencing)

Plant pathogens can evolve to overcome new resistance (R) genes introduced into crop varieties by plant breeders. This makes resistance breeding a challenging task involving constant recruitment of new R genes.  Most R genes encode nucleotide-binding, leucine-rich repeat (NB-LRR) proteins. Typically, plants carry 120- 800 NB-LRR-encoding genes, comprising 0.2- 0.5% of the genome.

Although whole genome shotgun sequencing has become affordable, it remains challenging to identify the full NB-LRR gene repertoire, and we therefore established a method for R gene enrichment sequencing (RenSeq). Because we study diseases of tomato and potato, we designed Agilent Sureselect baits against the annotated NB-LRR complement from the reference genomes of these crops. Target enrichment of tomato and potato NB-LRR R gene homologs followed by Illumina or PacBio sequencing of gDNA and cDNA from bulked resistant or susceptible populations allows rapid mapping of NB-LRR gene alleles linked to a trait of interest. We applied this technique to fine-map three Rpi (Resistance to Phytophthora infestans) genes from different diploid and one tetraploid species of Solanum. We also have used the method to reannotate the NB-LRR repertoire of potato, tomato and various Nicotianas, discovering 100s of new NB-LRR genes and correcting errors in previous annotations.

Jupe et al (2013) Plant Journal 76:530-544  doi: 10.1111/tpj.12307