Identification and localisation of the NB-LRR gene family within the potato genome

Florian Jupe, Leighton Pritchard, Graham J Etherington, Katrin MacKenzie, Peter JA Cock, Frank Wright, Sanjeev Kumar Sharma, Dan Bolser, Glenn J Bryan, Jonathan DG Jones, Ingo Hein

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156 Citations (Scopus)

Abstract

Background: The potato genome sequence derived from the Solanum tuberosum Group Phureja clone DM1-3 516 R44 provides unparalleled insight into the genome composition and organisation of this important crop. A key class of genes that comprises the vast majority of plant resistance (R) genes contains a nucleotide-binding and leucine-rich repeat domain, and is collectively known as NB-LRRs.Results: As part of an effort to accelerate the process of functional R gene isolation, we performed an amino acid motif based search of the annotated potato genome and identified 438 NB-LRR type genes among the ~39,000 potato gene models. Of the predicted genes, 77 contain an N-terminal toll/interleukin 1 receptor (TIR)-like domain, and 107 of the remaining 361 non-TIR genes contain an N-terminal coiled-coil (CC) domain. Physical map positions were established for 370 predicted NB-LRR genes across all 12 potato chromosomes. The majority of NB-LRRs are physically organised within 63 identified clusters, of which 50 are homogeneous in that they contain NB-LRRs derived from a recent common ancestor.Conclusions: By establishing the phylogenetic and positional relationship of potato NB-LRRs, our analysis offers significant insight into the evolution of potato R genes. Furthermore, the data provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from Solanum species.

Original languageEnglish
Article number75
Number of pages14
JournalBMC Genomics
Volume13
DOIs
Publication statusPublished - 15 Feb 2012

Keywords

  • potato genome
  • genome composition
  • plant resistance
  • NB-LRRs

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    Jupe, F., Pritchard, L., Etherington, G. J., MacKenzie, K., Cock, P. JA., Wright, F., ... Hein, I. (2012). Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics, 13, [75]. https://doi.org/10.1186/1471-2164-13-75