[en] Selection for new favorable variants can lead to selective sweeps. However, such sweeps might be rare in the evolution of different species for which polygenic adaptation or selection on standing variation might be more common. Still, strong selective sweeps have been described in domestic species such as chicken lines or dog breeds. The goal of our study was to use a panel of individuals from 12 different cattle breeds genotyped at high density (800K SNPs) to perform a whole-genome scan for selective sweeps defined as unexpectedly long stretches of reduced heterozygosity. To that end, we developed a hidden Markov model in which one of the hidden states corresponds to regions of reduced heterozygosity. Some unexpectedly long regions were identified. Among those, six contained genes known to affect traits with simple genetic architecture such as coat color or horn development. However, there was little evidence for sweeps associated with genes underlying production traits.
Disciplines :
Veterinary medicine & animal health Agriculture & agronomy Genetics & genetic processes
Author, co-author :
Druet, Tom ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Perez-Pardal, L.
Charlier, Carole ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Gautier, M.
Language :
English
Title :
Identification of large selective sweeps associated with major genes in cattle.
Publication date :
2013
Journal title :
Animal Genetics
ISSN :
0268-9146
eISSN :
1365-2052
Publisher :
Blackwell, Oxford, United Kingdom
Volume :
44
Issue :
6
Pages :
758-62
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
(c) 2013 The Authors, Animal Genetics (c) 2013 Stichting International Foundation for Animal Genetics.
Barendse W., Harrison B.E., Bunch R.J., Thomas M.B., &, Turner L.B., (2009) Genome wide signatures of positive selection: the comparison of independent samples and the identification of regions associated to traits. BMC Genomics 10, 178.
Boitard S., Schlotterer C., &, Futschik A., (2009) Detecting selective sweeps: a new approach based on hidden Markov models. Genetics 181, 1567-78.
Boitard S., Schlotterer C., Nolte V., Pandey R.V., &, Futschik A., (2012) Detecting selective sweeps from pooled next-generation sequencing samples. Molecular Biology and Evolution 29, 2177-86.
Chevin L.M., &, Hospital F., (2008) Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics 180, 1645-60.
Flori L., Fritz S., Jaffrezic F., Boussaha M., Gut I., Heath S., Foulley J.L., &, Gautier M., (2009) The genome response to artificial selection: a case study in dairy cattle. PLoS ONE 4, e6595.
Fontanesi L., Tazzoli M., Russo V., &, Beever J., (2009) Genetic heterogeneity at the bovine KIT gene in cattle breeds carrying different putative alleles at the spotting locus. Animal Genetics 41, 295-303.
Gautier M., Faraut T., Moazami-Goudarzi K., et al,. (2007) Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 177, 1059-70.
Gautier M., Flori L., Riebler A., Jaffrezic F., Laloe D., Gut I., Moazami-Goudarzi K., &, Foulley J.L., (2009) A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics 10, 550.
Grobet L., Martin L.J., Poncelet D., et al,. (1997) A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nature Genetics 17, 71-4.
Gutierrez-Gil B., Wiener P., &, Williams J.L., (2007) Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-backcross Charolais x Holstein population. BMC Genetics 8, 56.
Hermisson J., &, Pennings P.S., (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169, 2335-52.
Hernandez R.D., Kelley J.L., Elyashiv E., Melton S.C., Auton A., McVean G., Sella G., &, Przeworski M., (2011) Classic selective sweeps were rare in recent human evolution. Science 331, 920-4.
Kambadur R., Sharma M., Smith T.P., &, Bass J.J., (1997) Mutations in myostatin (GDF8) in double-muscled Belgian Blue and Piedmontese cattle. Genome Research 7, 910-16.
Karim L., Takeda H., Lin L., et al,. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics 43, 405-13.
Klungland H., Vage D.I., Gomez-Raya L., Adalsteinsson S., &, Lien S., (1995) The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination. Mammalian Genome 6, 636-9.
Lango Allen H., Estrada K., Lettre G., et al,. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467, 832-8.
Lindholm-Perry A.K., Sexten A.K., Kuehn L.A., et al,. (2011) Association, effects and validation of polymorphisms within the NCAPG-LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BMC Genetics 12, 103.
Maynard Smith J., &, Haigh J., (1974) The hitch-hiking effect of a favourable gene. Genetical Research 23, 23-35.
Peter B.M., Huerta-Sanchez E., &, Nielsen R., (2012) Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genetics 8, e1003011.
Pritchard J.K., Pickrell J.K., &, Coop G., (2010) The genetics of human adaptation: hard sweeps, soft sweeps, and polygenic adaptation. Current Biology 20, R208-15.
Pryce J.E., Hayes B.J., Bolormaa S., &, Goddard M.E., (2011) Polymorphic regions affecting human height also control stature in cattle. Genetics 187, 981-4.
Rabiner L.R., (1989) A tutorial on Hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77, 257-86.
Rubin C.J., Zody M.C., Eriksson J., et al,. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464, 587-91.
Seichter D., Russ I., Rothammer S., Eder J., Forster M., &, Medugorac I., (2012) SNP-based association mapping of the polled gene in divergent cattle breeds. Animal Genetics 43, 595-8.
Setoguchi K., Furuta M., Hirano T., Nagao T., Watanabe T., Sugimoto Y., &, Takasuga A., (2009) Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate. BMC Genetics 10, 43.
Signer-Hasler H., Flury C., Haase B., Burger D., Simianer H., Leeb T., &, Rieder S., (2012) A genome-wide association study reveals loci influencing height and other conformation traits in horses. PLoS ONE 7, e37282.
Stella A., Ajmone-Marsan P., Lazzari B., &, Boettcher P., (2010) Identification of selection signatures in cattle breeds selected for dairy production. Genetics 185, 1451-61.