Discovering genomic regions associated with the phenotypic differentiation of European local pig breeds

Poklukar, K.; Mestre, C.; Skrlep, M.; Candek-Potokar, M.; Ovilo, C.; Fontanesi, L.; Riquet, J.; Bovo, S.; Schiavo, G.; Ribani, A.; Munoz, M.; Bozzi, R.; Charneca, R.; Quintanilla, R.; Kusec, G.; Mercat, M.-J.; Zimmer, C.; Razmaite, V.; Araujo, J. P.; Radovic, C.; Karolyi, D.; Servin, B.

doi:10.1101/2022.02.22.481248

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bioRxiv · 10.1101/2022.02.22.481248

Discovering genomic regions associated with the phenotypic differentiation of European local pig breeds

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Abstract

BackgroundIntensive selection of modern pig breeds resulted in genetic improvement of productive traits while local pig breeds remained less performant. As they have been bred in extensive systems, they have adapted to specifical environmental conditions resulting in a rich genotypic and phenotypic diversity. This study is based on European local pig breeds 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 selection signatures linked to phenotypic traits in order to uncover potential candidate genes that may be under adaptation to specific environments. ResultsGenetic data analysis of European pig breeds revealed four main axes of genetic variation represented by Iberian and 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 phenotypic data distinguished between larger and leaner breeds with better growth potential and reproductive performance on one hand and breeds that were smaller, fatter, and had low growth and reproductive efficiency on the other hand. Linking selection signatures 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 effect on stature, fatness, growth and reproduction performance traits. For example, strong associations were found for stature in two regions containing the ANXA4 and ANTXR1 genes, for fatness containing the DNMT3A and POMC genes and for reproductive performance containing the HSD17B7 gene. ConclusionsThe present study on European local pig breeds used a dedicated approach for searching selection signatures supported by phenotypic data at the breed level to identify potential candidate genes that may have adapted to different living environments and production systems. Results can be useful to define conservation programs of local pig breeds.

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Poklukar, K., Mestre, C., Skrlep, M., Candek-Potokar, M., Ovilo, C., Fontanesi, L., Riquet, J., Bovo, S., Schiavo, G., Ribani, A., Munoz, M., Bozzi, R., Charneca, R., Quintanilla, R., Kusec, G., Mercat, M.-J., Zimmer, C., Razmaite, V., Araujo, J. P., Radovic, C., Karolyi, D., Servin, B.. 2022-02-22. Discovering genomic regions associated with the phenotypic differentiation of European local pig breeds. https://doi.org/10.1101/2022.02.22.481248

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