A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits

Media type: E-Article
Title: A meta-analysis of genetic and phenotypic diversity of European local pig breeds reveals genomic regions associated with breed differentiation for production traits
Contributor: Poklukar, Klavdija; Mestre, Camille; Škrlep, Martin; Čandek-Potokar, Marjeta; Ovilo, Cristina; Fontanesi, Luca; Riquet, Juliette; Bovo, Samuele; Schiavo, Giuseppina; Ribani, Anisa; Muñoz, Maria; Gallo, Maurizio; Bozzi, Ricardo; Charneca, Rui; Quintanilla, Raquel; Kušec, Goran; Mercat, Marie-José; Zimmer, Christoph; Razmaite, Violeta; Araujo, Jose P.; Radović, Čedomir; Savić, Radomir; Karolyi, Danijel; Servin, Bertrand
imprint: Springer Science and Business Media LLC, 2023
Published in: Genetics Selection Evolution
Language: English
DOI: 10.1186/s12711-023-00858-3
ISSN: 1297-9686
Keywords: Genetics ; Animal Science and Zoology ; General Medicine ; Ecology, Evolution, Behavior and Systematics
Origination:
Footnote:
Description: <jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Intense selection of modern pig breeds has resulted in genetic improvement of production traits while the performance of local pig breeds has remained lower. As local pig breeds have been bred in extensive systems, they have adapted to specific environmental conditions, resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds that have been genetically characterized using DNA-pool sequencing data and phenotypically characterized using breed level phenotypes related to stature, fatness, growth, and reproductive performance traits. These data were analyzed using a dedicated approach to detect signatures of selection linked to phenotypic traits in order to uncover potential candidate genes that may underlie adaptation to specific environments.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>Analysis of the genetic data of European pig breeds revealed four main axes of genetic variation represented by the Iberian and three modern breeds (i.e. Large White, Landrace, and Duroc). In addition, breeds clustered according to their geographical origin, for example French Gascon and Basque breeds, Italian Apulo Calabrese and Casertana breeds, Spanish Iberian, and Portuguese Alentejano breeds. Principal component analysis of the phenotypic data distinguished the larger and leaner breeds with better growth potential and reproductive performance from the smaller and fatter breeds with low growth and reproductive efficiency. Linking the signatures of selection with phenotype identified 16 significant genomic regions associated with stature, 24 with fatness, 2 with growth, and 192 with reproduction. Among them, several regions contained candidate genes with possible biological effects on stature, fatness, growth, and reproductive performance traits. For example, strong associations were found for stature in two regions containing, respectively, the <jats:italic>ANXA4</jats:italic> and <jats:italic>ANTXR1</jats:italic> genes, for fatness in a region containing the <jats:italic>DNMT3A</jats:italic> and <jats:italic>POMC</jats:italic> genes and for reproductive performance in a region containing the <jats:italic>HSD17B7</jats:italic> gene.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>In this study on European local pig breeds, we used a dedicated approach for detecting signatures of selection that were supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems.</jats:p> </jats:sec>
Access State: Open Access

Search in field:

Recently searched for: