title: A practical approach to detect ancestral haplotypes in livestock populations.
abstract: The effects of different evolutionary forces are expected to lead to the conservation, over many generations, of particular genomic regions (haplotypes) due to the development of linkage disequilibrium (LD). The detection and identification of early (ancestral) haplotypes can be used to clarify the evolutionary dynamics of different populations as well as identify selection signatures and genomic regions of interest to be used both in conservation and breeding programs. The aims of this study were to develop a simple procedure to identify ancestral haplotypes segregating across several generations both within and between populations with genetic links based on whole-genome scanning. This procedure was tested with simulated and then applied to real data from different genotyped populations of Spanish, Fleckvieh, Simmental and Brown-Swiss cattle.
  
  
  
  The identification of ancestral haplotypes has shown coincident patterns of selection across different breeds, allowing the detection of common regions of interest on different bovine chromosomes and mirroring the evolutionary dynamics of the studied populations. These regions, mainly located on chromosomes BTA5, BTA6, BTA7 and BTA21 are related with certain animal traits such as coat colour and milk protein and fat content.
  
  
  
  In agreement with previous studies, the detection of ancestral haplotypes provides useful information for the development and comparison of breeding and conservation programs both through the identification of selection signatures and other regions of interest, and as indicator of the general genetic status of the populations.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK. Enrique.Sanchez-Molano@roslin.ed.ac.uk.
authors.forename: Enrique
authors.initials: E
authors.lastname: Sánchez-Molano
authors.affiliation: Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Tsiokos
authors.affiliation: Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agricultural Technology, School of Agricultural Technology, Food Technology and Nutrition, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki, Greece.
authors.forename: Dimitrios
authors.initials: D
authors.lastname: Chatziplis
authors.affiliation: Interbull Center, Uppsala, S-75007, Sweden.
authors.forename: Hossein
authors.initials: H
authors.lastname: Jorjani
authors.affiliation: Associazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Degano
authors.affiliation: Departamento de Mejora Genética Animal, INIA, Madrid, 28040, Spain.
authors.forename: Clara
authors.initials: C
authors.lastname: Diaz
authors.affiliation: Associazione Nazionale Allevatori Bovini della Razza Bruna, Verona, Italy.
authors.forename: Attilio
authors.initials: A
authors.lastname: Rossoni
authors.affiliation: ZuchtData EDV-Dienstleistungen GmbH, Wien, Austria.
authors.forename: Hermann
authors.initials: H
authors.lastname: Schwarzenbacher
authors.affiliation: Qualitas AG, Zug, Switzerland.
authors.forename: Franz
authors.initials: F
authors.lastname: Seefried
authors.affiliation: Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, Zaragoza, 50013, Spain.|Instituto Agroalimentario de Aragón (IA2), Zaragoza, 50013, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Varona
authors.affiliation: Associazione Nazionale Allevatori Bovini di razza Pezzata Rossa Italiana, Udine, Italy.
authors.forename: Daniele
authors.initials: D
authors.lastname: Vicario
authors.affiliation: Bioinformatics core facility, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. CascinaCodazza, Lodi, 26900, Italy.
authors.forename: Ezequiel L
authors.initials: EL
authors.lastname: Nicolazzi
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK.|SRUC,The Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, Edinburgh, UK.|School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
authors.forename: Georgios
authors.initials: G
authors.lastname: Banos
mesh_terms: D000818:Animals; D002417:Cattle; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D006239:Haplotypes; D058751:Livestock / Q000235:genetics*; D008297:Male; D008957:Models, Genetic
keywords: Ancestral haplotypes; Cattle; Population dynamics; Selection signatures