title: Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip.
abstract: BACKGROUND
  Among the European countries, Italy counts the largest number of local goat breeds. Thanks to the recent availability of a medium-density SNP (single nucleotide polymorphism) chip for goat, the genetic diversity of Italian goat populations was characterized by genotyping samples from 14 Italian goat breeds that originate from different geographical areas with more than 50 000 SNPs evenly distributed on the genome.
  
  
  RESULTS
  Analysis of the genotyping data revealed high levels of genetic polymorphism and an underlying North-south geographic pattern of genetic diversity that was highlighted by both the first dimension of the multi-dimensional scaling plot and the Neighbour network reconstruction. We observed a moderate and weak population structure in Northern and Central-Southern breeds, respectively, with pairwise FST values between breeds ranging from 0.013 to 0.164 and 7.49 % of the total variance assigned to the between-breed level. Only 2.11 % of the variance explained the clustering of breeds into geographical groups (Northern, Central and Southern Italy and Islands).
  
  
  CONCLUSIONS
  Our results indicate that the present-day genetic diversity of Italian goat populations was shaped by the combined effects of drift, presence or lack of gene flow and, to some extent, by the consequences of traditional management systems and recent demographic history. Our findings may constitute the starting point for the development of marker-assisted approaches, to better address future breeding and management policies in a species that is particularly relevant for the medium- and long-term sustainability of marginal regions.
authors.affiliation: DIVET, Università degli Studi di Milano, via Celoria 10, 20133, Milan, Italy. letizia.nicoloso@unimi.it.
authors.forename: Letizia
authors.initials: L
authors.lastname: Nicoloso
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy. lorenzo.bomba@unicatt.it.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Bomba
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy. licia.colli@unicatt.it.
authors.forename: Licia
authors.initials: L
authors.lastname: Colli
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy. riccardo.negrini@unicatt.it.|Associazione Nazionale della Pastorizia, via Palmiro Togliatti 1587, 00155, Rome, Italy. riccardo.negrini@unicatt.it.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Negrini
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy. marco.milanesi@unicatt.it.
authors.forename: Marco
authors.initials: M
authors.lastname: Milanesi
authors.affiliation: Laboratorio Genetica e Servizi (LGS) - Associazione Italiana Allevatori (AIA), via Bergamo, 292, 26100, Cremona, Italy. mazza.r@aia.it.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Mazza
authors.affiliation: Agris Sardegna, Unità di Ricerca di Genetica e Biotecnologie, Sassari, Italy. tsechi@agrisricerca.it.
authors.forename: Tiziana
authors.initials: T
authors.lastname: Sechi
authors.affiliation: DIVET, Università degli Studi di Milano, via Celoria 10, 20133, Milan, Italy. stefano.frattini@unimi.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Frattini
authors.affiliation: DIVET, Università degli Studi di Milano, via Celoria 10, 20133, Milan, Italy. andrea.talenti@unimi.it.
authors.forename: Andrea
authors.initials: A
authors.lastname: Talenti
authors.affiliation: DIVET, Università degli Studi di Milano, via Celoria 10, 20133, Milan, Italy. beatrice.coizet@unimi.it.
authors.forename: Beatrice
authors.initials: B
authors.lastname: Coizet
authors.affiliation: CNR - IBBA, UOS di Lodi, via Einstein, Località Cascina Codazza, 26900, Lodi, Italy. chessa@ibba.cnr.it.
authors.forename: Stefania
authors.initials: S
authors.lastname: Chessa
authors.affiliation: Dipartimento di Agricoltura, Alimentazione e Ambiente Di3A, Università degli Studi di Catania, via Valdisavoia 5, 95123, Catania, Italy. d.marletta@unict.it.
authors.forename: Donata
authors.initials: D
authors.lastname: Marletta
authors.affiliation: Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, via Francesco De Sanctis s.n.c., 86100, Campobasso, Italy. dandrea@unimol.it.
authors.forename: Mariasilvia
authors.initials: M
authors.lastname: D'Andrea
authors.affiliation: Dipartimento di Agricoltura, Alimentazione e Ambiente Di3A, Università degli Studi di Catania, via Valdisavoia 5, 95123, Catania, Italy. s.bordonaro@unict.it.
authors.forename: Salvatore
authors.initials: S
authors.lastname: Bordonaro
authors.affiliation: Dipartimento Scienze Biomediche Comparate, Università di Teramo, Piazza Aldo Moro 45, Teramo, Italy. gptak@unite.it.
authors.forename: Grazyna
authors.initials: G
authors.lastname: Ptak
authors.affiliation: Agris Sardegna, Unità di Ricerca di Genetica e Biotecnologie, Sassari, Italy. acarta@agrisricerca.it.
authors.forename: Antonello
authors.initials: A
authors.lastname: Carta
authors.affiliation: DIVET, Università degli Studi di Milano, via Celoria 10, 20133, Milan, Italy. giulio.pagnacco@unimi.it.
authors.forename: Giulio
authors.initials: G
authors.lastname: Pagnacco
authors.affiliation: Dipartimento per l'Innovazione nei sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, via de Lellis, 01100, Viterbo, Italy. alessio@unitus.it.
authors.forename: Alessio
authors.initials: A
authors.lastname: Valentini
authors.affiliation: Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, via Francesco De Sanctis s.n.c., 86100, Campobasso, Italy. pilla@unimol.it.
authors.forename: Fabio
authors.initials: F
authors.lastname: Pilla
authors.affiliation: Istituto di Zootecnica, Università Cattolica del Sacro Cuore, via Emilia Parmense, 84, 29122, Piacenza, Italy. paolo.ajmone@unicatt.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Ajmone-Marsan
authors.affiliation: DIVET, Università degli Studi di Milano, via Celoria 10, 20133, Milan, Italy. paola.crepaldi@unimi.it.
authors.forename: Paola
authors.initials: P
authors.lastname: Crepaldi
mesh_terms: D000818:Animals; D051456:Gene Flow; D040961:Genetic Drift; D005838:Genotype; D006041:Goats / Q000145:classification* / Q000235:genetics*; D007178:Inbreeding; D007558:Italy; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide