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The Istrian (IS) and the Pag sheep (PS) are local Croatian breeds which provide significant income for the regional economy and have a cultural and traditional importance for the inhabitants. The aim of this study was to estimate some important population specific genetic parameters in IS (N = 1293) and PS (N = 2637) based on genome wide SNPs. Estimates of linkage disequilibrium effective population size (Ne) evidenced more genetic variability in PS (Ne = 838) compared to IS (Ne = 197), regardless of historical time (both recent and ancient genetic variability). The discrepancy in the recent genetic variability between these breeds was additionally confirmed by the estimates of genomic inbreeding (FROH), which was estimated to be notably higher in IS (FROH>2 = 0.062) than in PS (FROH>2 = 0.029). The average FROH2–4, FROH4–8, FROH8–16, and FROH>16 were 0.26, 1.65, 2.14, and 3.72 for IS and 0.22, 0.61, 0.75, and 1.58 for PS, thus evidencing a high contribution of recent inbreeding in the overall inbreeding. One ROH island with > 30% of SNP incidence in ROHs was detected in IS (OAR6; 34,253,440–38,238,124 bp) while there was no ROH islands detected in PS. Seven genes (CCSER1, HERC3, LCORL, NAP1L5, PKD2, PYURF, and SPP1) involved in growth, feed intake, milk production, immune responses, and resistance were associated with the found autozygosity. The results of this study represent the first comprehensive insight into genomic variability of these two Croatian local sheep breeds and will serve as a baseline for setting up the most promising strategy of genomic Optimum Contribution Selection.

The aim of the study was to estimate genetic diversity parameters for Banija spotted pig population and to apply optimisation methods to control the inbreeding in the population in three different scenarios. The first scenario consisted of minimizing inbreeding by minimizing the average kinship without considering breeding values. The second scenario was to minimize inbreeding by minimizing the average kinship accounting for breeding values. The third scenario was to apply traditional optimal contribution selection by maximizing the breeding value of the offspring. A total of 5 boars and 49 sows were selected to create mating plan minimise inbreeding in the next generation. The average inbreeding coefficient in the population was 6.97, while effective population size was 8.47. In the first scenario, different kinship constrains between candidates resulted in a change in the number of selected animals and a change in the average breeding values, such that the number of selected candidates increased when the constraint on kinship was stronger, with a simultaneous decrease in breeding values. The second scenario resulted in increased inbreeding when additional weight was placed on genetic gain. The Maximisation of breeding values resulted with drastically increased average inbreeding coefficient in the next generation. Due the small total and effective population size, the application of optimisation methods demonstrated that genetic improvement is possible at a high cost of loss of the genetic variability and preservation of diversity remains the first objective in the breeding programme for Banija spotted pig.