title: Use of high-density SNP data to identify patterns of diversity and signatures of selection in broiler chickens.
abstract: The development of broiler chickens over the last 70 years has been accompanied by large phenotypic changes, so that the resulting genomic signatures of selection should be detectable by current statistical techniques with sufficiently dense genetic markers. Using two approaches, this study analysed high-density SNP data from a broiler chicken line to detect low-diversity genomic regions characteristic of past selection. Seven regions with zero diversity were identified across the genome. Most of these were very small and did not contain many genes. In addition, fifteen regions were identified with diversity increasing asymptotically from a low level. These regions were larger and thus generally included more genes. Several candidate genes for broiler traits were found within these 'regression regions', including IGF1, GPD2 and MTNR1AI. The results suggest that the identification of zero-diversity regions is too restrictive for characterizing regions under selection, but that regions showing patterns of diversity along the chromosome that are consistent with selective sweeps contain a number of genes that are functional candidates for involvement in broiler development. Many regions identified in this study overlap or are close to regions identified in layer chicken populations, possibly due to their shared precommercialization history or to shared selection pressures between broilers and layers.
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
authors.forename: J J
authors.initials: JJ
authors.lastname: Stainton
authors.affiliation: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
authors.forename: B
authors.initials: B
authors.lastname: Charlesworth
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.|MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, UK.
authors.forename: C S
authors.initials: CS
authors.lastname: Haley
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.|Aviagen Ltd, Edinburgh, UK.
authors.forename: A
authors.initials: A
authors.lastname: Kranis
authors.affiliation: Aviagen Ltd, Edinburgh, UK.
authors.forename: K
authors.initials: K
authors.lastname: Watson
authors.affiliation: The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK.
authors.forename: P
authors.initials: P
authors.lastname: Wiener
mesh_terms: D000818:Animals; D002645:Chickens / Q000145:classification / Q000235:genetics*; D004531:Eggs; D005260:Female; D015810:Linkage Disequilibrium; D008297:Male; D008460:Meat; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
keywords: Axiom chicken genotyping array; hitchhiking; poultry; regression method; selection mapping