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Metadata of the article that will be visualized in OnlineFirst ArticleTitle The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions Article Sub-Title Article CopyRight Springer Science+Business Media New York (This will be the copyright line in the final PDF) Journal Name Mammalian Genome Corresponding Author Family Name Bertolini Particle Given Name Francesca Suffix Division Department of Animal Science Organization Iowa State University Address Ames, IA, USA Phone +1-515 294-6114 Fax Email [email protected] URL ORCID Author Family Name Andrea Particle Given Name Talenti Suffix Division Dipartimento di Medicina Veterinaria Organization Università degli Studi di Milano Address Milan, Italy Phone Fax Email URL ORCID Author Family Name Pagnacco Particle Given Name Giulio Suffix Division Dipartimento di Medicina Veterinaria Organization Università degli Studi di Milano Address Milan, Italy Phone Fax Email URL ORCID Author Family Name Pilla Particle Given Name Fabio Suffix Division Dipartimento Agricoltura, Ambiente e Alimenti Organization Università degli Studi del Molise Address via Francesco De Sanctis s.n.c., 86100, Campobasso, Italy Phone Fax Email URL ORCID Author Family Name Ajmone-Marsan Particle Given Name Paolo Suffix Division Istituto di Zootecnica Organization Università Cattolica del Sacro Cuore Address via Emilia Parmense, 84, 29122, Piacenza, Italy Phone Fax Email URL ORCID Author Family Name Rothschild Particle Given Name Max F. Suffix Division Department of Animal Science Organization Iowa State University Address Ames, IA, USA Phone Fax Email URL ORCID Author Family Name Crepaldi Particle Given Name Paola Suffix Division Dipartimento di Medicina Veterinaria Organization Università degli Studi di Milano Address Milan, Italy Phone Fax Email URL ORCID Received 5 July 2016 Schedule Revised Accepted 26 January 2017 Abstract The Valdostana goat is an alpine breed, raised only in the northern Italian region of the Aosta Valley. This breed’s main purpose is to produce milk and meat, but is peculiar for its involvement in the “Batailles de Chèvres,” a recent tradition of non-cruel fight tournaments. At both the genetic and genomic levels, only a very limited number of studies have been performed with this breed and there are no studies about the genomic signatures left by selection. In this work, 24 unrelated Valdostana animals were screened for runs of homozygosity to identify highly homozygous regions. Then, six different approaches (ROH comparison, Fst single SNPs and windows based, Bayesian, Rsb, and XP-EHH) were applied comparing the Valdostana dataset with 14 other Italian goat breeds to confirm regions that were different among the comparisons. A total of three regions of selection that were also unique among the Valdostana were identified and located on chromosomes 1, 7, and 12 and contained 144 genes. Enrichment analyses detected genes such as cytokines and lymphocyte/leukocyte proliferation genes involved in the regulation of the immune system. A genetic link between an aggressive challenge, cytokines, and immunity has been hypothesized in many studies both in humans and in other species. Possible hypotheses associated with the signals of selection detected could be therefore related to immune-related factors as well as with the peculiar battle competition, or other breed-specific traits, and provided insights for further investigation of these unique regions, for the understanding and safeguard of the Valdostana breed. Footnote Information Talenti Andrea and Francesca Bertolini have contributed equally to the work. Electronic supplementary material The online version of this article (doi:10.1007/s00335-017-9678-7) contains supplementary material, which is available to authorized users. Mamm Genome DOI 10.1007/s00335-017-9678-7 1 The Valdostana goat: a genome-wide investigation 2 of the distinctiveness of its selective sweep regions 3 Talenti Andrea1 · Francesca Bertolini2 · Giulio Pagnacco1 · Fabio Pilla3 · 4 Paolo Ajmone-Marsan4 · Max F. Rothschild2 · Paola Crepaldi1 · The Italian Goat 5 Consortium 6 7 Received: 5 July 2016 / Accepted: 26 January 2017 © Springer Science+Business Media New York 2017 8 Abstract The Valdostana goat is an alpine breed, raised 7, and 12 and contained 144 genes. Enrichment analyses 25 9 only in the northern Italian region of the Aosta Valley. This detected genes such as cytokines and lymphocyte/leuko- 26 10 breed’s main purpose is to produce milk and meat, but is cyte proliferation genes involved in the regulation of the 27 11 peculiar for its involvement in the “Batailles de Chèvres,” a immune system. A genetic link between an aggressive chal- 28 12 recent tradition of non-cruel fight tournaments. At both the lenge, cytokines, and immunity has been hypothesized in 29 13 genetic and genomic levels, only a very limited number of many studies both in humans and in other species. Possible 30 14 studies have been performed with this breed and there are hypotheses associated with the signals of selection detected 31 15 no studies about the genomic signatures left by selection. In could be therefore related to immune-related factors as well 32 16 this work, 24 unrelated Valdostana animals were screened as with the peculiar battle competition, or other breed-spe- 33 17 for runs of homozygosity to identify highly homozygous cific traits, and provided insights for further investigation of 34 18 regions. Then, six different approaches (ROH comparison, these unique regions, for the understanding and safeguard 35 19 Fst single SNPs and windows based, Bayesian, Rsb, and of the Valdostana breed. 36 20 XP-EHH) were applied comparing the Valdostana dataset 21 with 14 other Italian goat breeds to confirm regions that 22 were different among the comparisons. A total of three Introduction 37 23 regions of selection that were also unique among the Val- 24 dostana were identified and located on chromosomes 1, Over the past several years, the increase of genomic tech- 38 nologies and molecular information has given researchers 39 40 A1 Talenti Andrea and Francesca Bertolini have contributed equally the chance of developing useful tools for genome-wide A2 to the work. analyses in livestock. Since 2008, a series of single-nucle- 41 otide polymorphism (SNP) chips of medium and high 42 A3 Electronic supplementary material The online version of this density have been developed and assessed for the major 43 A4 article (doi:10.1007/s00335-017-9678-7) contains supplementary livestock species (Nicolazzi et al. 2015). These tools have 44 A5 material, which is available to authorized users. provided the opportunity to investigate the underlying 45 A6 * Francesca Bertolini structure of genomes for several purposes such as detec- 46 A7 [email protected] tion of selective sweeps, breed differentiation, genome- 47 48 1 UNCORRECTEDwide association studies PROOF (GWAS), and genomic selection in A8 Dipartimento di Medicina Veterinaria, Università degli Studi 49 A9 di Milano, Milan, Italy cattle, pigs, sheep, horses, and chickens (Meuwissen et al. 50 2 2013; Nicolazzi et al. 2015). A10 Department of Animal Science, Iowa State University, Ames, 51 A11 IA, USA The selective sweep can be defined as a reduction or 52 3 elimination of variation among the nucleotides in genomic A12 Dipartimento Agricoltura, Ambiente e Alimenti, Università 53 A13 degli Studi del Molise, via Francesco De Sanctis s.n.c., regions adjacent to a mutation that become fixed from nat- A14 86100 Campobasso, Italy ural or artificial selective pressure.