Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens.
A whole-genome scan for identifying selection acting on pairs of linked loci is proposed and implemented. The scan is based on , one of Ohta's 1982 measures of between-population linkage disequilibrium (LD). An approximate empirical null distribution for the statistic is suggested. Although the partitioning of LD into between-population components was originally used to investigate epistatic selection, we demonstrate that values of may also be influenced by single-locus selective sweeps with linkage but no epistasis. The proposed scan is implemented in a diverse panel of chickens including 72 distinct breeds genotyped at 538 298 single-nucleotide polymorphisms. In all, 1723 locus pairs are identified as putatively corresponding to a selective sweep or epistatic selection. These pairs of loci generally cluster to form overlapping or neighboring signals of selection. Known variants that were expected to have been under selection in the panel are identified, as well as an assortment of novel regions that have putatively been under selection in chickens. Notably, a promising pair of genes located 8 MB apart on chromosome 9 are identified based on as demonstrating strong evidence of dispersive epistatic selection between populations.
Department of Plant Sciences, University of California, Davis, CA, USA.|Department of Agronomy, University of Wisconsin, Madison, WI, USA.|Animal Sciences Department, University of Wisconsin, Madison, WI, USA.
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Beissinger
Animal Breeding and Genetics Group, Georg-August-University,Göttingen, Germany.
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Gholami
Animal Breeding and Genetics Group, Georg-August-University,Göttingen, Germany.|Institute of Animal Breeding, Bavarian State Research Centre for Agriculture, Grub, Germany.
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Erbe
Institute of Farm Animal Genetics, Friedrich Loeffler Institut, Neustadt-Mariensee, Germany.
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Weigend
Institute of Farm Animal Genetics, Friedrich Loeffler Institut, Neustadt-Mariensee, Germany.
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Weigend
Department of Agronomy, University of Wisconsin, Madison, WI, USA.|Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA.
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de Leon
Animal Sciences Department, University of Wisconsin, Madison, WI, USA.|Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA.|Department of Dairy Science, University of Wisconsin, Madison, WI, USA.
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Gianola
Animal Breeding and Genetics Group, Georg-August-University,Göttingen, Germany.
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Simianer
D000818:Animals; D002645:Chickens / Q000235:genetics*; D004843:Epistasis, Genetic; D008040:Genetic Linkage; D005828:Genetics, Population; D005838:Genotype; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic