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 (FROH > 4 Mb = 0.400 and FROH > 8 Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (FROH > 4 Mb = 0.098 and FROH > 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.
Highlights
For thousands of years, pigs have been indispensable to humans as they represent an important part of our everyday diet
Taking advantage of high-throughput genomic analyses, we explored the genetic structure of Black Slavonian and Turopolje pig breeds and their relationships with local and modern breeds worldwide
A closer look at the European and North American clusters (Figure 1, lower part) showed that the commercial breeds Landrace and Pietrain were separated from the breeds in the middle group, which was dominated by the UK and North American local breeds
Summary
Pigs have been indispensable to humans as they represent an important part of our everyday diet. Most local breeds are adapted to specific environments, production systems, geographical regions or human demands. In the last few decades, several breeds such as Large White, Duroc, Landrace, Hampshire and Pietrain (FAO, 2007) and their hybrids have spread internationally and replaced most local breeds, mainly because they are economically more efficient. This poses a problem: the conservation of local breeds is crucial for the future of animal production as they can be important sources of genetic variability (Bruford et al, 2015) and are better adapted for production in sustainable environments (Ollivier et al, 2005)
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