title: Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information.
abstract: An increasing interest is being placed in the detection of genes, or genomic regions, that have been targeted by selection because identifying signatures of selection can lead to a better understanding of genotype-phenotype relationships. A common strategy for the detection of selection signatures is to compare samples from distinct populations and to search for genomic regions with outstanding genetic differentiation. The aim of this study was to detect selective signatures in layer chicken populations using a recently proposed approach, hapFLK, which exploits linkage disequilibrium information while accounting appropriately for the hierarchical structure of populations. We performed the analysis on 70 individuals from three commercial layer breeds (White Leghorn, White Rock and Rhode Island Red), genotyped for approximately 1 million SNPs. We found a total of 41 and 107 regions with outstanding differentiation or similarity using hapFLK and its single SNP counterpart FLK respectively. Annotation of selection signature regions revealed various genes and QTL corresponding to productions traits, for which layer breeds were selected. A number of the detected genes were associated with growth and carcass traits, including IGF-1R, AGRP and STAT5B. We also annotated an interesting gene associated with the dark brown feather color mutational phenotype in chickens (SOX10). We compared FST, FLK and hapFLK and demonstrated that exploiting linkage disequilibrium information and accounting for hierarchical population structure decreased the false detection rate.
authors.affiliation: Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany.
authors.forename: Mahmood
authors.initials: M
authors.lastname: Gholami
authors.affiliation: Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Reimer
authors.affiliation: Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany.
authors.forename: Malena
authors.initials: M
authors.lastname: Erbe
authors.affiliation: LOHMANN Tierzucht GMBH, Cuxhaven, Germany.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Preisinger
authors.affiliation: Institute of Farm Animal Genetics (ING), Friedrich-Loeffler-Institut (FLI), Neustadt, Germany.
authors.forename: Annett
authors.initials: A
authors.lastname: Weigend
authors.affiliation: Institute of Farm Animal Genetics (ING), Friedrich-Loeffler-Institut (FLI), Neustadt, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Weigend
authors.affiliation: Laboratoire Génétique, Physiologie et Systèmes d'Elevage, Institut National de la Recherche Agronomique, Castanet-Tolosan, France.
authors.forename: Bertrand
authors.initials: B
authors.lastname: Servin
authors.affiliation: Animal Breeding and Genetics Group, Department of Animal Sciences, Georg-August-University Göttingen, Göttingen, Germany.
authors.forename: Henner
authors.initials: H
authors.lastname: Simianer
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics; D002645:Chickens / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D005260:Female; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D055757:SOXE Transcription Factors / Q000235:genetics; D012641:Selection, Genetic
chemical_list: D030161:Avian Proteins; D055757:SOXE Transcription Factors