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 (N_e) evidenced more genetic variability in PS (N_e = 838) compared to IS (N_e = 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 (F_ROH), which was estimated to be notably higher in IS (F_ROH>2 = 0.062) than in PS (F_ROH>2 = 0.029). The average F_ROH2–4, F_ROH4–8, F_ROH8–16, and F_ROH>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 two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of two donkey breeds, two decades after the start of protection by analyzing their pedigrees and genetic structure. The average generation interval was higher for the Istrian donkey (7.73) than for the Littoral-Dinaric donkey (7.27). The rate of the effective number of founders compared with the effective number of ancestors in the Littoral-Dinaric donkey (1.03; 325/316) and in the Istrian donkey (1.08; 70/65) revealed no evidence of a genetic bottleneck. The inbreeding coefficient (F) and the average relatedness coefficient (AR) was lower in the Littoral-Dinaric donkey population (0.99%; 0.13%) than in the Istrian donkey population (1.77%; 1.10%). Genetic microsatellite analysis showed relatively high genetic diversity in Littoral-Dinaric donkey and Istrian donkey breeds, expressed by mean allele number (5.92; 5.85) and expected heterozygosity (0.650; 0.653). Genetic differentiation between the Littoral-Dinaric donkey and the Istrian donkey has not significantly increased in the last two decades (F_ST = 0.028). Genetic analysis also showed no evidence of high inbreeding or genetic bottleneck in both breeds. A total of 11 haplotypes including 28 polymorphic sites were found in 30 samples. Analysis of mtDNA has shown that the Littoral-Dinaric donkey and Istrian donkey breeds belong to the Equus asinus africanus group. The study confirms the need to use different analytical approaches to get a regular and complete insight into the situation and trends within and between breeds, so that the existing diversity can be fully preserved.

The Croatian Posavina horse (CPH) is native Croatian breed under a conservation program and under various programs of economic use (ecosystem services, agrotourism, and meat production). The aim of this study was to analyze the status of the CPH population through an analysis of their pedigree (28,483 records), phenotype (292 licensed stallions, 255 mares), and genetic structure (292 licensed stallions). The average generation interval was 8.20 years, and the number of complete generations was 1.66. The effective number of founders and ancestors was 138 and 107, respectively, with a ratio of 1.29, and the genetic conservation index was 4.46. As for the morphometric characteristics, the average withers height of the stallions was 142.79 cm, the chest circumference was 194.28 cm, and the cannon bone circumference was 22.34. In mares, the withers height, chest, and cannon bone circumference were lower (139.71 cm, 190.30 cm, and 20.94 cm, respectively). Genetic microsatellite analysis of the 29 sire-lines showed high genetic diversity, expressed as the mean allele number (7.7), allele richness (4.0), and expected heterozygosity (0.740). There was no evidence of high inbreeding or a genetic bottleneck. The genetic and phenotypic data indicate that the CPH is an important and diverse reservoir of genetic diversity and can be conserved because of its special characteristics (adaptability).

The Istrian sheep breed has been subjected to selection for dairy traits for more than two decades. However, a detailed study of some important population-specific parameters such as effective population size ($N_e$) and connectedness between flocks has never been carried out. The aim of the study was to examine the above parameters in dairy Istrian sheep subjected to a national selection program. The $N_e$ was estimated as the mean rate of increase in coancestry, and connectedness was determined using four different statistics. The $N_e$ was estimated at 73 animals with pedigree constraints imposed on 4 equivalent generations and 3 full generations. Analysis of $\Delta N_e$ (“sliding window approach”) revealed a negative $\Delta N_e$ indicating a progressive loss of genetic variability ($\Delta N_e{}_{\mathrm{NEG}\ge 4}$ = −6.6, p < 0.01; $\Delta N_e{}_{\mathrm{NFG}\ge 3}$ = −4.9, p > 0.05). The overall connectedness ($\overline{r}$ ~ 0.0001) was below the acceptable level for unbiased ranking of the animals belonging to different flocks ($r_{i,j}$ = 0.05). OCS appears to be the best option for the long-term survival (self-sufficiency) of the breed, but genetic links between flocks need to be strengthened to allow unbiased ranking of the animals based on the estimated breeding values.

This study aimed to examine the impact of ewe’s age at first lambing (AFL) on days in milk (DIM), average daily milk yield (DMY), and total milk yield (TMY). Symmetrical bimodal distribution of AFL enabled classification of maidens in those mated in the first (47%) or second year of life (53%). After accounting for all available sources of phenotypic variability with the linear mixed model for repeated records, it was estimated that AFL had a statistically significant effect only on DIM (p < 0.001). The litter size had a significant effect only on TMY (p < 0.001), while the effect of the parity was significant for all the examined traits (p < 0.001). The results of the study suggest that prolongation of age at first mating to the second year of life is not justified in dairy-orientated sheep farms. However, more evidence on this issue is needed for generalization, especially considering some other traits that can impact profitability of dual-purpose sheep farms (reproduction traits, growth rate of lambs, etc.).