Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

Boris Lukić; Maja Ferenčaković; Dragica Šalamon; Mato Čačić; Vesna Orehovački; Laura Iacolina; Ino Curik; Vlatka Cubric-Curik

doi:10.3389/fgene.2020.00261

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

Front Genet. 2020 Mar 31:11:261. doi: 10.3389/fgene.2020.00261. eCollection 2020.

Authors

Boris Lukić¹, Maja Ferenčaković², Dragica Šalamon², Mato Čačić³, Vesna Orehovački³, Laura Iacolina^{4

5}, Ino Curik², Vlatka Cubric-Curik²

Affiliations

¹ Department for Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, J.J. Strossmayer University of Osijek, Osijek, Croatia.
² Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.
³ Ministry of Agriculture, Zagreb, Croatia.
⁴ Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
⁵ Department for Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia.

Abstract

The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (F_ROH _> ₄ _Mb = 0.400 and F_ROH _> ₈ _Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (F_ROH _> ₄ _Mb = 0.098 and F_ROH _> ₈ _Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.

Keywords: diversity; genomics; inbreeding; local breeds; population structure.

Associated data

Dryad/10.5061/dryad.wpzgmsbhq