@article{fdi:010058225,
  title = {{B}eyond an {AFLP} genome scan towards the identification of immune genes involved in plague resistance in {R}attus rattus from {M}adagascar},
  author = {{T}ollenaere, {C}. and {J}acquet, {S}. and {I}vanova, {S}. and {L}oiseau, {A}. and {D}uplantier, {J}ean-{M}arc and {S}treiff, {R}. and {B}rouat, {C}arine},
  editor = {},
  language = {{ENG}},
  abstract = {{G}enome 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. {T}his study follows on from an {AFLP} genome scan in the black rat ({R}attus rattus), the reservoir of plague ({Y}ersinia pestis infection) in {M}adagascar. {W}e successfully sequenced 17 of the 22 markers previously shown to be potentially affected by plague-mediated selection and associated with a plague resistance phenotype. {S}earching these sequences in the genome of the closely related species {R}attus norvegicus assigned them to 14 genomic regions, revealing a random distribution of outliers in the genome (no clustering). {W}e 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). {H}owever, 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. {T}he 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. {W}e identified the two interleukin 1 genes ({I}l1a and {I}l1b) that share homology with an antigen of {Y}. pestis, as the best candidates for genes subject to plague-mediated natural selection. {A}t least six other genes known to be involved in proinflammatory pathways may also be affected by plague-mediated selection.},
  keywords = {disease resistance ; immune genes ; in silico {AFLP} analysis ; pathogen-mediated selection ; population genomics ; {R}attus genome ; {MADAGASCAR}},
  booktitle = {},
  journal = {{M}olecular {E}cology},
  volume = {22},
  numero = {2},
  pages = {354--367},
  ISSN = {0962-1083},
  year = {2013},
  DOI = {10.1111/mec.12115},
  URL = {https://www.documentation.ird.fr/hor/fdi:010058225},
}