engleski

Conservation genomic analyses of Croatian autochthonous pig breeds

Turopolje (TUP) and Black Slavonian (BSP) pigs are the only two recognized Croatian autochthonous pig breeds. Here we analysed 16 animals from each breed using Illumina Infinium PorcineSNP60 v2 BeadChip and estimated genomic inbreeding levels (FROH) and linkage disequilibrium effective population size (NeLD). We also defined genomic position of TUP and BSP with respect to 29 domestic world-wide pig breeds and to six wild boar populations. The inbreeding level based on runs of homozygosity (FROH) was much higher in TUS then in BSP for both FROH>2Mb, 0.43 vs 0.12, and FROH>8Mb, 0.33 vs 0.07, respectively. Estimated NeLD for TUP was very small, 18 (95%CI: 14-22) while higher NeLD estimates, 48 animals (95%CI: 37-59), were obtained for BSP. Principal Components Analysis of the overall dataset (666 animals) positioned TUP close to the Mangalica and some Mediterranean autochthonous breeds (MED cluster), not so far from the European wild boar populations. BSP was remote from MED cluster in direction of UK and USA breeds (Berkshire, Large black, Tamworth). To our knowledge, this is the first genomic analysis of TUP and BSP providing insight into their conservation status. Although BSP population is genetically small, an organised management program has been established in the last decade. In contrast, extremely high inbreeding level and small effective population size in TUP, ring alarm bells for an urgent conservation management plan

inbreeding ; genomic ; runs of homozygosity ; linkage disequilibrium effective population size

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