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Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, B\u00edsara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Kr\u0161kopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schw\u00e4bisch-H\u00e4llisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (H<jats:sub>P<\/jats:sub>) and fixation index (F<jats:sub>ST<\/jats:sub>)] and group-based F<jats:sub>ST<\/jats:sub> approaches, which compare groups of breeds defined according to external traits and use\/specialization\/type.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Results<\/jats:title>\n<jats:p>We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.<\/jats:p>\n<\/jats:sec><jats:sec>\n<jats:title>Conclusions<\/jats:title>\n<jats:p>Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.<\/jats:p>\n<\/jats:sec>","DOI":"10.1186\/s12711-020-00553-7","type":"journal-article","created":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T05:02:44Z","timestamp":1593147764000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":74,"title":["Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems"],"prefix":"10.1186","volume":"52","author":[{"given":"Samuele","family":"Bovo","sequence":"first","affiliation":[]},{"given":"Anisa","family":"Ribani","sequence":"additional","affiliation":[]},{"given":"Maria","family":"Mu\u00f1oz","sequence":"additional","affiliation":[]},{"given":"Estefania","family":"Alves","sequence":"additional","affiliation":[]},{"given":"Jose P.","family":"Araujo","sequence":"additional","affiliation":[]},{"given":"Riccardo","family":"Bozzi","sequence":"additional","affiliation":[]},{"given":"Marjeta","family":"\u010candek-Potokar","sequence":"additional","affiliation":[]},{"given":"Rui","family":"Charneca","sequence":"additional","affiliation":[]},{"given":"Federica","family":"Di Palma","sequence":"additional","affiliation":[]},{"given":"Graham","family":"Etherington","sequence":"additional","affiliation":[]},{"given":"Ana I.","family":"Fernandez","sequence":"additional","affiliation":[]},{"given":"Fabi\u00e1n","family":"Garc\u00eda","sequence":"additional","affiliation":[]},{"given":"Juan","family":"Garc\u00eda-Casco","sequence":"additional","affiliation":[]},{"given":"Danijel","family":"Karolyi","sequence":"additional","affiliation":[]},{"given":"Maurizio","family":"Gallo","sequence":"additional","affiliation":[]},{"given":"Vladimir","family":"Margeta","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 Manuel","family":"Martins","sequence":"additional","affiliation":[]},{"given":"Marie J.","family":"Mercat","sequence":"additional","affiliation":[]},{"given":"Giulia","family":"Moscatelli","sequence":"additional","affiliation":[]},{"given":"Yolanda","family":"N\u00fa\u00f1ez","sequence":"additional","affiliation":[]},{"given":"Raquel","family":"Quintanilla","sequence":"additional","affiliation":[]},{"given":"\u010cedomir","family":"Radovi\u0107","sequence":"additional","affiliation":[]},{"given":"Violeta","family":"Razmaite","sequence":"additional","affiliation":[]},{"given":"Juliette","family":"Riquet","sequence":"additional","affiliation":[]},{"given":"Radomir","family":"Savi\u0107","sequence":"additional","affiliation":[]},{"given":"Giuseppina","family":"Schiavo","sequence":"additional","affiliation":[]},{"given":"Graziano","family":"Usai","sequence":"additional","affiliation":[]},{"given":"Valerio J.","family":"Utzeri","sequence":"additional","affiliation":[]},{"given":"Christoph","family":"Zimmer","sequence":"additional","affiliation":[]},{"given":"Cristina","family":"Ovilo","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7050-3760","authenticated-orcid":false,"given":"Luca","family":"Fontanesi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,6,26]]},"reference":[{"key":"553_CR1","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/35052563","volume":"2","author":"L Andersson","year":"2001","unstructured":"Andersson L. 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No treatments or other procedures with animals were performed that would demand ethical protocols according to Directive 2010\/63\/EU (2010). Collected DNA or samples from previous projects were also re-used in this study.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethic statement"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"33"}}