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This study follows on from an AFLP genome scan in the black rat (<jats:italic>Rattus rattus<\/jats:italic>), the reservoir of plague (<jats:italic>Yersinia pestis<\/jats:italic> infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague\u2010mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species <jats:italic>Rattus norvegicus<\/jats:italic> assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). We compared these results with those of an <jats:italic>in silico<\/jats:italic> AFLP study of the <jats:italic>R. norvegicus<\/jats:italic> genome, which showed that outlier sequences could not have been inferred by this method in <jats:italic>R. rattus<\/jats:italic> (only four of the 15 sequences were predicted). However, <jats:italic>in silico<\/jats:italic> analysis allowed the prediction of AFLP markers distribution and the estimation of homoplasy rates, confirming its potential utility for designing AFLP studies in nonmodel species. The 14 genomic regions surrounding AFLP outliers (less than 300\u00a0kb from the marker) contained 75 genes encoding proteins of known function, including nine involved in immune function and pathogen defence. We identified the two interleukin 1 genes (<jats:italic>Il1a<\/jats:italic> and <jats:italic>Il1b<\/jats:italic>) that share homology with an antigen of <jats:italic>Y. pestis<\/jats:italic>, as the best candidates for genes subject to plague\u2010mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague\u2010mediated selection.<\/jats:p>","DOI":"10.1111\/mec.12115","type":"journal-article","created":{"date-parts":[[2012,12,13]],"date-time":"2012-12-13T20:33:44Z","timestamp":1355430824000},"page":"354-367","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Beyond an <scp>AFLP<\/scp> genome scan towards the identification of immune genes involved in plague resistance in <i>Rattus rattus<\/i> from Madagascar"],"prefix":"10.1111","volume":"22","author":[{"given":"C.","family":"Tollenaere","sequence":"first","affiliation":[{"name":"IRD UMR CBGP (INRA \/ IRD \/ Cirad \/ Montpellier SupAgro) Campus International Baillarguet CS 30016 34988 Montferrier sur Lez cedex France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S.","family":"Jacquet","sequence":"additional","affiliation":[{"name":"IRD UMR CBGP 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