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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>4Mb=0.400 and FROH>8Mb=0.332)
that considerably exceeded the level of full-sib mating, while Black
Slavonian pig showed much lower inbreeding (FROH>4Mb=0.098 and
FROH>8Mb=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.
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