Beyond an AFLP genome scan towards the identification of immune genes involved in plague resistance in Rattus rattus from Madagascar

• Published in: Molecular Ecology
• Main Authors: Tollenaere, C., Jacquet, Stéphane, Ivanova, Svilena, Loiseau, Anne, Duplantier, Jean-Marc, Streiff, Rejane, Brouat, Carine
• Other Authors: Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), IRD ('Institut de Recherche pour le Developpement'); IPM ('Institut Pasteur de Madagascar'); ANR-SEST ('Agence Nationale pour la Recherche, Sante-Environnement et Sante-Travail')
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2013
• Subjects: in silico AFLP analysis; pathogen-mediated selection; disease resistance; immune genes; population genomics; Rattus genome; analyse génomique; rattus rattus; rattus norvegicus; Yersinia pestis; phénotype; phénotype de résistance; madagascar; [SDV]Life Sciences [q-bio]; Rattus rattus
• Online Access: https://hal.archives-ouvertes.fr/hal-01506257; https://doi.org/10.1111/mec.12115

Genome scans using amplified fragment length polymorphism (AFLP) markers became popular in nonmodel species within the last 10 years, but few studies have tried to characterize the anonymous outliers identified. This study follows on from an AFLP genome scan in the black rat (Rattus rattus), the reservoir of plague (Yersinia pestis infection) in Madagascar. We successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. Searching these sequences in the genome of the closely related species Rattus norvegicus 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 in silico AFLP study of the R. norvegicus genome, which showed that outlier sequences could not have been inferred by this method in R. rattus (only four of the 15 sequences were predicted). However, in silico 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 kb 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 (Il1a and Il1b) that share homology with an antigen of Y. pestis, as the best candidates for genes subject to plague-mediated natural selection. At least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection.