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

• Published in: Molecular ecology Vol. 22; no. 2; pp. 354 - 367
• Main Authors: Tollenaere, C., Jacquet, S., Ivanova, S., Loiseau, A., Duplantier, J.-M., Streiff, R., Brouat, C.
• Format: Journal Article
• Language: English
• Published: Oxford Blackwell Publishing Ltd 01.01.2013; Blackwell; Wiley
• Subjects: Amplified Fragment Length Polymorphism Analysis; Animals; Biological and medical sciences; Biomarkers; Classical genetics, quantitative genetics, hybrids; disease resistance; Disease Resistance - genetics; Disease Resistance - immunology; Fundamental and applied biological sciences. Psychology; Genetic Loci; Genetics of eukaryotes. Biological and molecular evolution; Genomics - methods; immune genes; Immune response; Immunity (Disease); in silico AFLP analysis; Life Sciences; Madagascar; pathogen-mediated selection; Plague; Plague - genetics; Plague - immunology; Polymorphism; population genomics; Rats - genetics; Rats - microbiology; Rattus; Rattus genome; Rattus norvegicus; Rattus rattus; Rodents; Selection, Genetic; Yersinia pestis; Malagasy Republic; Africa; Madagascar; in silico AFLP analysis; Rattus genome; Disease; Tropical zone; Genomics; Rodentia; population genomics; Infection; Plague; Vertebrata; pathogen-mediated selection; Mammalia; Sensitivity resistance; Gene; disease resistance; immune genes; Pathogenic; Bacteriosis; Rattus rattus; Genome; Amplified fragment length polymorphism marker; Yersiniosis; rattus norvegicus; phénotype de résistance; Yersinia pestis; phénotype; analyse génomique; madagascar; rattus rattus
• ISSN: 0962-1083; 1365-294X; 1365-294X
• DOI: 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.