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

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

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    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 similar to 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
    Pages (from-to)-
    Number of pages14
    JournalBMC Genomics
    Volume13
    DOIs
    Publication statusPublished - 15 Feb 2012

    Cite this

    Jupe, F., Pritchard, L., Etherington, G. J., MacKenzie, K., Cock, P. J. A., Wright, F., Sharma, S. K., Bolser, D., Bryan, G. J., Jones, J. D. G., & 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