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

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Jupe, Florian, Pritchard, Leighton, Etherington, Graham J., Mackenzie, Katrin, Cock, Peter J. A., Wright, Frank, Sharma, Sanjeev Kumar, Bolser, Dan, Bryan, Glenn J., Jones, Jonathan D. G. and Hein, Ingo (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics, 13. ISSN 1471-2164

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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 ~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.

Item Type: Article
Faculty \ School: Faculty of Science > The Sainsbury Laboratory
Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science > School of Biological Sciences
UEA Research Groups: Faculty of Science > Research Groups > Plant Sciences
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Depositing User: Pure Connector
Date Deposited: 05 Aug 2013 13:52
Last Modified: 15 Dec 2022 18:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/43112
DOI: 10.1186/1471-2164-13-75

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