Open Access
Genet. Sel. Evol.
Volume 40, Number 6, November-December 2008
Page(s) 639 - 661
Published online 24 October 2008
  1. Barton N.H., Genetic hitchhiking, Philos. Trans. R. Soc. Lond. B. Biol. Sci. 355 (2000) 1553–1562 [CrossRef] [PubMed].
  2. Bauer DuMont V., Aquadro C.F., Multiple signatures of positive selection downstream of Notch on the X chromosome in Drosophila melanogaster, Genetics 171 (2005) 639–653 [CrossRef] [PubMed].
  3. Buitenhuis A.J., Rodenburg T.B., van Hierden Y., Siwek M., Cornelissen S.J.B., Nieuwland M.G.B., Crooijmans R.P.M.A., Groenen M.A.M., Koene P., Korte S.M., Bovenhuis H., van der Poel J.J., Mapping quantitative trait loci affecting feather pecking behaviour and stress response in laying hens, Poult. Sci. 82 (2003) 1215–1222 [PubMed].
  4. Charlesworth B., Nordborg M., Charlesworth D., The effects of local selection, balanced polymorphism and background selection on equilibrium patterns of genetic diversity in subdivided populations, Genet. Res. 70 (1997) 155–174 [CrossRef] [PubMed].
  5. Crow J.F., Kimura M., An introduction to population genetics theory, Harper & Row, New York, USA, 1970.
  6. Degen W.G.J, van Daal N., Rothwell L., Kaiser P., Schijns V.E.J.C., Th1/Th2 polarization by viral and helminth infection in birds, Vet. Microbiol. 105 (2005) 163–167 [CrossRef] [PubMed].
  7. Erf G.F., Cell-mediated immunity in poultry, Poult. Sci. 83 (2004) 580–590 [PubMed].
  8. Falconer D.S., Mackay T.F.C., Introduction to quantitative genetics, Longman Scientific & Technical, Essex, UK, 1996.
  9. Gause W.C., Urban J.F. Jr., Stadecker M.J., The immune response to parasitic helminths: insights from murine models, Trends Immunol. 24 (2003) 269–277 [CrossRef] [PubMed].
  10. Goldringer I., Bataillon T., On the distribution of temporal variation in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection, Genetics 168 (2004) 563–568 [CrossRef] [PubMed].
  11. Goudet J. (2001), FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3),
  12. Groenen M.A.M., Cheng H.H., Bumstead N., Benkel B.F., Briles W.E., Burke T., Burt D.W., Crittenden L.B., Dodgson J., Hillel J., Lamont S., Ponce de Leon A., Soller M., Takahashi H., Vignal A., A consensus linkage map of the chicken genome, Genome Res. 10 (2000) 137–147 [PubMed].
  13. Hayes B.J., Lien S., Nilsen H., Olsen H.G., Berg P., Maceachern S., Potter S., Meuwissen T.H.E., The origin of selection signatures on bovine chromosome 6, Anim. Genet. 39 (2008) 105–111 [CrossRef] [PubMed].
  14. Hill W.G., Fixation probabilities of mutant genes with artificial selection, Genet. Sel. Evol. 17 (1985) 351–358 [CrossRef] [EDP Sciences].
  15. Hillel J., Groenen M.A.M., Tixier-Boichard M., Korol A.B., David L., Kirzhner V., Burke T., Barre-Dirie A., Crooijmans R.P.M.A., Elo K., Feldman M.W., Freidlin P.J., Mäki-Tanila A., Oosrtwijn M., Thompson P., Vignal A., Wimmers K., Weigend S., Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools, Genet. Sel. Evol. 35 (2003) 533–557 [CrossRef] [PubMed] [EDP Sciences].
  16. Iannucelli E., Woloszyn N., Arhainx J., Gellin J., Milan D., GEMMA: a database to automate microsatellite genotyping, in: Proceedings of the XXVth International Conference on Animal Genetics, 21–25 July 1996, Tours, France, Anim. Genet., Suppl., pp. 2–55.
  17. Jankovic D., Liu Z., Gause W.C., Th1- and Th2-cell commitment during infectious disease: asymmetry in divergent pathways, Trends Immunol. 22 (2001) 481–482 [CrossRef] [PubMed].
  18. Keightley P.D., Bulfield G., Detection of quantitative trait loci from frequency changes of marker alleles under selection, Genet. Res. 62 (1993) 195–203 [PubMed].
  19. Langella O., Populations 1.2.28, logiciel de ge'ne'tique des populations, Laboratoire Populations, Ge'ne'tique et E' volution, CNRS UPR9304, Gif-sur- Yvette, France, 2002.
  20. Laval G., San Cristobal M., Chevalet C., Measuring genetic distances between breeds: use of some distances in various short term evolution models, Genet. Sel. Evol. 34 (2002) 481–507 [CrossRef] [PubMed] [EDP Sciences].
  21. Loywyck V., Bijma P., Pinard-van der Laan M.-H., van Arendonk J., Verrier E., A comparison of two methods for prediction of response and rates of inbreeding in selected populations with the results obtained in two selection experiments, Genet. Sel. Evol. 37 (2005) 273–289 [CrossRef] [PubMed] [EDP Sciences].
  22. Loywyck V., Pinard-van der Laan M-H., Goldringer I., Verrier E., On the need of combining complementary analyses to assess the effect of a candidate gene and the evolution of its polymorphism: the example of the Major Histocompatibility Complex in chicken, Genet. Res. 87 (2006) 125–131 [CrossRef] [PubMed]. Erratum in: Genet. Res. 87 (2006) 223.
  23. Mc Rae A.F., McEwan J.C., Dodds K.G., Wilson T., Crawford A.M., Slate J., Linkage disequilibrium in domestic sheep, Genetics 160 (2002) 1113–1122 [PubMed].
  24. Minozzi G., Antibody responses to KLH, LPS and Newcastle disease virus vaccine in F2 and backcrosses of White Leghorn lines selected for two different immune traits, SABRE – EADGENE Conference on Genomics for Animal Health, Utrecht, The Netherlands, 2007.
  25. Minozzi G., Parmentier H.K., Nieuwland M.G.B., Bed'Hom B., Minvielle F., Gourichon D., Pinard-van der Laan M.-H., Antibody responses to keyhole limpet hemocyanin, lipopolysaccharide and Newcastle disease virus in F2 and backcrosses of White Leghorn lines selected for two different immune response traits, Poult. Sci. 86 (2007) 1316–1322 [PubMed].
  26. Minozzi G., Parmentier H.K., Mignon-Gastreau S., Nieuwland M.G.B., Bed'Hom B., Gourichon D., Minvielle F., Pinard-van der Laan M.-H., Correlated effects of selection for immunity in White Leghorn chicken lines on natural antibodies and specific antibody responses to KLH and M. butyricum, BMC Genet. 9 (2008) 5 [CrossRef] [PubMed].
  27. Morisson M., Leroux S., Jiguet-Jiglaire C., Assaf S., Pitel F., Lagarrigue S., Bardes S., Feve K., Faraut T., Milan D., Vignal A., A gene-based radiation hybrid map of chicken chromosome 14: comparison to human and alignment to the assembled chicken sequence, Genet. Sel. Evol. 37 (2005) 229–251 [CrossRef] [PubMed] [EDP Sciences].
  28. Nair S., Williams J.T., Brockman A., Paiphun L., Mayxay M., Newton P.N., Guthman J.-P., Smithuis F.M., Hien T.T., White N.J., Nosten F., Anderson T.J.C., A selective sweep driven by pyrimethamine treatment in southeast malaria parasites, Mol. Biol. Evol. 20 (2003) 1526–1536 [CrossRef] [PubMed].
  29. Nei M., Molecular evolutionary genetics, Columbia University Press, New York, USA, 1987.
  30. Nei M., Tajima F., Genetic drift and estimation of effective population size, Genetics 98 (1981) 625–640 [PubMed] [MathSciNet].
  31. Pinard-van der Laan M.-H., Immune modulation: the genetic approach, Vet. Immunol. Immunopathol. 87 (2002) 199–205 [CrossRef] [PubMed].
  32. Pollinger J.P., Bustanante C.D., Fledel-Alon A., Schmutz S., Gray M.M., Wayne R.K., Selective sweep mapping of genes with large phenotypic effects, Genome Res. 15 (2006) 1809–1819 [CrossRef].
  33. Pudovkin A.I., Zaykin D.V., Hedgecock D., On the potential for estimating the effective number of breeders from heterozygote-excess in progeny, Genetics 144 (1996) 383–387 [PubMed].
  34. Reynolds J.,Weir B.S., Cockerham C.C., Estimation of the coancestry coefficient basis for short-term genetic distance, Genetics 105 (1983) 767–779 [PubMed].
  35. Schlö tterer C., A microsatellite-based multilocus screen for the identification of local selective sweeps, Genetics 160 (2002) 753–763 [PubMed].
  36. Siwek M., Cornelissen S.J.B., Nieuwland M.G.B., Buitenhuis A.J., Crooijmans R.P.M.A., Groenen M.A.M., de Vries-Reilingh G., Parmentier H.K., van der Poel J.J., Detection of QTL for immune response to Sheep Red Blood Cells in laying hens, Anim. Genet. 34 (2003) 422–428 [CrossRef] [PubMed].
  37. Siwek M., Buitenhuis A.J., Cornelissen S.J.B., Nieuwland M.G.B., Bovenhuis H., Crooijmans R.P.M.A., Groenen M.A.M., de Vries-Reilingh G., Parmentier H.K., van der Poel J.J., Detection of different QTL for antibody response to keyhole lympet hemocyanin and Mycobacterium butyricum in two unrelated populations of laying hens, Poult. Sci. 82 (2003) 1845–1852 [PubMed]. Erratum in: Poult. Sci. 85 (2006) 1118–1119.
  38. Siwek M., Buitenhuis A.J., Cornelissen S.J.B., Nieuwland M.G.B., Knol E.F., Bovenhuis H., Crooijmans R.P.M.A., Groenen M.A.M., de Vries-Reilingh G., Parmentier H.K., van der Poel J.J., Detection of QTL for innate: non-specific antibody levels binding LPS and LTA in two independent populations of laying hens, Dev. Comp. Immunol. 30 (2006) 659–666 [CrossRef] [PubMed].
  39. Storey J.D., A direct approach to false discovery rates, J. R. Stat. Soc., Series B 64 (2002) 479–498.
  40. Tajima F., Nei M., Note on genetic drift and estimation of effective population size, Genetics 106 (1984) 569–574 [PubMed].
  41. Takahashi H., Tsudzuki M., Sasaki O., Niikura J., Inoue-Murayama M., Minezawa M., A chicken linkage map based on microsatellite markers genotyped on a Japanese Large Game and White Leghorn cross, Anim. Genet. 36 (2005) 463–467 [PubMed].
  42. van der Zijp A.J., Nieuwland M.G.B., Immunological characterization of lines selected for high and low antibody production, 7th European Poultry Conference, 1986, Paris, France, vol. 1, pp. 211–215.
  43. Vigouroux Y., McMullen M., Hittinger C.T., Houchins K., Schulz L., Kresovich S., Matsuoka Y., Doebley J., Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication, in: Proceeding of the National Academy of Sciences, 2002, vol. 9, pp. 9650–9655.
  44. Waples R.S., A generalized approach for estimating effective population size from temporal changes in allele frequency, Genetics 121 (1989) 379–391 [PubMed].
  45. Weir B.S., Cockerham C.C., Estimating F-statistics for the analysis of population structure, Evolution 38 (1984) 1358–1370 [CrossRef].
  46. Wiener P., Burton D., Ajmone-Marsan P., Dunner S., Mommens G., Nijman I.J., Rodellar C., Valentini A., Williams J.L., Signatures of selection? Patterns of microsatellite diversity on a chromosome containing a selected locus, Heredity 90 (2003) 350–358 [CrossRef] [PubMed].
  47. Wright S., On the roles of directed and random changes in gene frequency in the genetics of populations, Evolution 2 (1948) 279–294 [CrossRef].