Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan Maclean, Peter J. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D.G. Jones

Research output: Contribution to journalArticle

157 Citations (Scopus)
1 Downloads (Pure)

Abstract

RenSeq is a NB-LRR (nucleotide binding-site leucine-rich repeat) gene-targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB-LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB-LRRs and can be accessed through a genome browser that we provide. We compared these NB-LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum 'Heinz 1706' extended the NB-LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co-segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi-ber2) and S. ruiz-ceballosii (Rpi-rzc1), we were able to apply RenSeq successfully to identify markers that co-segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy-to-adapt Galaxy pipelines.

Original languageEnglish
Pages (from-to)530-544
Number of pages15
JournalPlant Journal
Volume76
Issue number3
Early online date8 Oct 2013
DOIs
Publication statusPublished - 30 Nov 2013

Keywords

  • NB-LRR
  • next-generation sequencing
  • pathogen resistance
  • solanaceae
  • Solanum berthaultii
  • Solanum lycopersicum
  • Solanum ruiz-ceballosii
  • Solanum tuberosum Group Phureja clone DM1-3 516 R44
  • target enrichment
  • technical advance

Cite this

Jupe, F., Witek, K., Verweij, W., Śliwka, J., Pritchard, L., Etherington, G. J., Maclean, D., Cock, P. J., Leggett, R. M., Bryan, G. J., Cardle, L., Hein, I., & Jones, J. D. G. (2013). Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. Plant Journal, 76(3), 530-544. https://doi.org/10.1111/tpj.12307