hrvatski

Optimal contribution selection: a tool for sustainable management of Banija spotted pig

Breeding programmes for conserved breeds of domestic animals are often oriented to conservation role, although selection for economically important traits in such breeds can be beneficial for the sustainable breeding. Best linear unbiased prediction (BLUP) is the appropriate method for selection in local and autochthonous breeds. However, conservation and selection seem to be opposite breeding goals and optimisation between maintaining genetic diversity and genetic gain is required. For that purpose, tools within optimal contribution frame (OCS) are available. The litter size was the focal trait for the application of the OCS on the Banija Spotted (BS) pig population. Genetic diversity parameters were estimated based on pedigree data including 751 available records and single nucleotide polymorphism (SNP) genotypes for 24 animals. Genotyping was carried out using GP Porcine HD 70 K array. The genomic inbreeding coefficients (FROH) were calculated as the proportion of the autosomal genome covered by runs of homozygosity. Trends of effective population size were estimated from linkage disequilibrium as implemented in SNeP software. Data set contained 224 farrowing records for BS sows. Genetic parameters and breeding values for litter size were estimated using a repeatability model for litter size with herd, mating season, and boar as fixed effects, and permanent environmental and additive genetic effects as random effects in the model. Evolutionary Algorithm (EVA) software was used to estimate pedigree-based genetic diversity parameters of the population and to apply optimal contribution selection in the population of Banija spotted pig. Average pedigree-based inbreeding coefficient in the population was 3.68%. Inbreeding rate per generation (ΔF) in the population based on genealogical analysis was 2.62% and effective population size was 19.06. Genomic inbreeding was 18%, while historical effective population size obtained from molecular information was 54. According to the obtained genetic parameters, Banija spotted pig belongs to the breeds with low genetic diversity. Estimated heritability for the litter size was 0.05. The predefined rate of inbreeding was restricted to 1% in order to optimise the increase of inbreeding and genetic gain. The application of OCS showed that genetic gain of the similar level can be achieved while restricting the increase of ΔF to 1% in the population. As the restriction on the inbreeding rate is relaxed, the number of selected pigs decreases and the maximum contribution for a single selected male and female increases, resulting in the higher genetic gain. The Banija spotted pig population is suitable for a management strategy which jointly optimizes the response to selection and the levels of variability and inbreeding. Further steps include full integration of the molecular information from the microsatellite and SNP markers in the optimum contribution selection procedure.

Pigs ; conservation ; selecion ; optimal contribution

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