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Whole-Genome Sequencing of European Autochthonous and Commercial Pig Breeds Allows the Detection of Signatures of Selection

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Whole-Genome Sequencing of European Autochthonous and Commercial Pig Breeds Allows the Detection of Signatures of Selection Bovo et al. Genet Sel Evol (2020) 52:33 https://doi.org/10.1186/s12711-020-00553-7 Genetics Selection Evolution RESEARCH ARTICLE Open Access Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to diferent breeding and production systems Samuele Bovo1, Anisa Ribani1, Maria Muñoz2, Estefania Alves2, Jose P. Araujo3, Riccardo Bozzi4, Marjeta Čandek‑Potokar5, Rui Charneca6, Federica Di Palma7, Graham Etherington7, Ana I. Fernandez2, Fabián García2, Juan García‑Casco2, Danijel Karolyi8, Maurizio Gallo9, Vladimir Margeta10, José Manuel Martins6, Marie J. Mercat11, Giulia Moscatelli1, Yolanda Núñez2, Raquel Quintanilla12, Čedomir Radović13, Violeta Razmaite14, Juliette Riquet15, Radomir Savić16, Giuseppina Schiavo1, Graziano Usai17, Valerio J. Utzeri1, Christoph Zimmer18, Cristina Ovilo2 and Luca Fontanesi1* Abstract Background: Natural and artifcial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to diferent environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo‑Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow‑Bellied Mangalitsa, Schwäbisch‑Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European com‑ mercial 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 identi‑ fed by using a single‑breed approach with two statistics [within‑breed pooled heterozygosity (H P) and fxation index (FST)] and group‑based FST approaches, which compare groups of breeds defned according to external traits and use/ specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared popula‑ tions and identifed 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 afect 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 *Correspondence: [email protected] 1 Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127 Bologna, Italy Full list of author information is available at the end of the article © The Author(s) 2020. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creat iveco mmons .org/publi cdoma in/ zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Bovo et al. Genet Sel Evol (2020) 52:33 Page 2 of 19 signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions: Our fndings 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. Background to design sustainable conservation programs for these Natural and artifcial directional selection have shaped genetic resources, most of which are still unexplored, livestock genomes and led to many breeds and popu- the frst step is to characterize genetically their popula- lations, which are considered the main reservoir of tions [18]. genetic diversity in farmed animals [1–3]. Under posi- To date, a few whole-genome investigations have been tive selection pressure, the frequency of favourable performed, which are mainly based on single nucleo- alleles increases rapidly in a population and generates a tide polymorphism (SNP) arrays and include only a few high level of population diferentiation, with impacts on European local pig breeds [19–21]. Most of these stud- haplotype structures and extended linkage disequilib- ies are based on small numbers of animals and provide rium between the mutated sites and neighbouring loci preliminary information on their population structure. [4]. Signatures of selection that remain in the livestock In the case of the Iberian and Casertana breeds, quanti- genomes are the result of combined human-driven and tative trait loci (QTL) and genome scans have identifed natural selection events, which have contributed to the genomic regions and mutations associated with morpho- adaptation of genetic resources to diferent environ- logical, production, meat and carcass traits [9, 10, 16, 17, ments and production systems. 22–24]. Other studies have compared SNP datasets from Livestock genomes can be analysed by applying dif- Italian autochthonous and commercial breeds to iden- ferent genomic and statistical measures and approaches tify population-informative markers and analyse their [e.g. Wright’s fxation index (FST) within or between inbreeding levels [25, 26]. Muñoz et al. [27] and Ribani populations and pooled heterozygosity (H P), among et al. [28] analysed candidate markers in major genes in other statistics] to reveal regions under selection. 20 European local pig breeds and wild boar populations, Tese regions can provide insights into the biological which provided information on the segregation of rel- mechanisms that explain domestication and lead to evant polymorphisms for breeding or traceability pur- morphological diferentiation, specialized production poses [29]. A follow-up study on these breeds included performances and, in some cases, disease resistance the analysis of linkage disequilibrium, F ST and efective and resilience (e.g. [5–10]). population size using a medium-density SNP array [30]. Since the frst domestication events, pig has been Other studies that involved a few Asian and European subject to artifcial directional selection that has pro- pig breeds investigated signatures of selection in the por- foundly diferentiated domestic genetic pools from cine genome using SNP chip or partial/reduced or whole- the original European and Asian wild boar popula- genome re-sequencing datasets and highlighted loci of tions [11–14]. Although today the pig industry uses a economic importance [7, 31–42]. few cosmopolitan highly selected breeds and lines in Tus, it is important to take further the analyses of the intensive production systems, a large number of local genome of autochthonous and cosmopolitan pig genetic breeds still exist in many regions around the world. resources, including unexplored and poorly investigated Tese autochthonous genetic resources are less per- breeds, which were developed under diferent human- forming than commercial populations and, mainly in driven evolutionary conditions (i.e. selection programs) Europe, they are associated with local and traditional and production systems. niche markets [15]. Other common characteristics of In this study, we analysed the genome of 19 European these breeds are good adaptation to their local agro- autochthonous pig breeds from nine countries, three climatic and environmental conditions, high rustic- commercial Italian breeds and wild boars to identify sig- ity, slower growth rate, high adipogenic potential and, natures of selection by mining whole-genome sequenc- for some of them, superior meat quality traits. Tey ing data obtained by using a DNA-pool sequencing are usually raised under extensive or semi-extensive approach. SNPs were called and allele frequencies were production systems and in marginal areas [15]. Tey estimated. Signatures of selection were identifed by are also characterized by a variety of coat colour phe- computing both within-breed HP and FST statistics and notypes and specifc morphological traits, which can comparing diferent groups according to domestication/ have interesting scientifc values [11, 16, 17]. In order selection levels (i.e. autochthonous vs. commercial vs. Bovo et al. Genet Sel Evol (2020) 52:33 Page 3 of 19 wild boars) and morphological (coat colours and pat- and distributed across nine European countries (from terns and body size) criteria. Tese breeds, some of them West to East and then North; Fig.
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