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
Author
Bovo, Samuele
Ribani, Anisa
Muñoz, Maria
Alves, Estefania
Araujo, Jose P.
Bozzi, Riccardo
Čandek-Potokar, Marjeta
Charneca, Rui
Di Palma, Federica
Etherington, Graham
Fernandez, Ana I.
García, Fabián
García-Casco, Juan
Karolyi, Danijel
Gallo, Maurizio
Margeta, Vladimir
Martins, José Manuel
Mercat, Marie J.
Moscatelli, Giulia
Núñez, Yolanda
Radović, Čedomir
Razmaite, Violeta
Riquet, Juliette
Savić, Radomir
Schiavo, Giuseppina
Usai, Graziano
Utzeri, Valerio J.
Zimmer, Christoph
Ovilo, Cristina
Fontanesi, Luca
Publication date
2020-06-26ISSN
0999-193X
Abstract
Background
Natural and artificial 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 different 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 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 (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.
Results
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.
Conclusions
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.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
636 - Animal husbandry and breeding in general. Livestock rearing. Breeding of domestic animals
Pages
19
Publisher
BMC
Is part of
Genetics Selection Evolution
Citation
Bovo, Samuele, Anisa Ribani, Maria Muñoz, Estefania Alves, Jose P. Araujo, Riccardo Bozzi, and Marjeta Čandek-Potokar et al. 2020. "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". Genetics Selection Evolution 52 (1). doi:10.1186/s12711-020-00553-7.
Grant agreement number
EC/COST/CA15112/EU/Functional Annotation of Animal Genomes-European network/FAANG-Europe
EC/H2020/634476/EU/Diversity of local pig breeds and production systems for high quality traditional products and sustainable pork chains/TREASURE
Program
Genètica i Millora Animal
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2831]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/