Abstract
BackgroundNatural 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.ResultsWe 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.ConclusionsOur 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.
Highlights
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
Bovo et al Genet Sel Evol (2020) 52:33 signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding occurred with wild boars
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
Summary
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. Livestock genomes can be analysed by applying different genomic and statistical measures and approaches [e.g. Wright’s fixation index (FST) within or between populations and pooled heterozygosity (HP), among other statistics] to reveal regions under selection These regions can provide insights into the biological mechanisms that explain domestication and lead to morphological differentiation, specialized production performances and, in some cases, disease resistance and resilience Other common characteristics of these breeds are good adaptation to their local agroclimatic and environmental conditions, high rusticity, slower growth rate, high adipogenic potential and, for some of them, superior meat quality traits They are usually raised under extensive or semi-extensive production systems and in marginal areas [15]. In order to design sustainable conservation programs for these genetic resources, most of which are still unexplored, the first step is to characterize genetically their populations [18]
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