title: Relative extended haplotype homozygosity signals across breeds reveal dairy and beef specific signatures of selection.
abstract: BACKGROUND
  A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds.
  
  
  RESULTS
  A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production.
  
  
  CONCLUSIONS
  Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production.
authors.affiliation: Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy. lorenzo.bomba@unicatt.it.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Bomba
authors.affiliation: Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy. ezequiel.nicolazzi@tecnoparco.org.
authors.forename: Ezequiel L
authors.initials: EL
authors.lastname: Nicolazzi
authors.affiliation: Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy. marco.milanesi@unicatt.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Milanesi
authors.affiliation: Associazione Italiana Allevatori (AIA), Via Tomassetti 9, Rome, 00161, Italy. riccardo.negrini@unicatt.it.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Negrini
authors.affiliation: Center for Computational Chemistry and Cosmology, Scuola Normale Superiore, Via Consoli del Mare 2, Pisa, 56126, Italy. giordano.mancini@sns.it.
authors.forename: Giordano
authors.initials: G
authors.lastname: Mancini
authors.affiliation: Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy. filippo.biscarini@tecnoparco.org.
authors.forename: Filippo
authors.initials: F
authors.lastname: Biscarini
authors.affiliation: Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900, Italy. alessandra.stella@tecnoparco.org.|Istituto di biologia e biotecnologia Agraria (IBBA-CNR), Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi, 26900, Italy. alessandra.stella@tecnoparco.org.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Stella
authors.affiliation: Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), via de Lellis, Viterbo, 01100, Italy. alessio@unitus.it.
authors.forename: Alessio
authors.initials: A
authors.lastname: Valentini
authors.affiliation: Istituto di Zootecnica, UCSC, via Emilia Parmense 84, Piacenza, 29122, Italy. paolo.ajmone@unicatt.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ajmone-Marsan
mesh_terms: D000818:Animals; D001947:Breeding; D002417:Cattle / Q000235:genetics*; D003612:Dairying; D023281:Genomics; D006239:Haplotypes; D006720:Homozygote; D008297:Male; D008460:Meat; D058977:Molecular Sequence Annotation; D012641:Selection, Genetic