Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.

The aim of this study was to determine the variability of birth weight and growth of piglets in hyper prolific sow line. Data collected from 25 litters from Pen Ar Lan Naima sow line were used to evaluate the variability of piglets' birth weight and its consequences on subsequent growth performances. All piglets were individually weighted five times from the birth until the end of nursery period. Pre-weaning mortality was the highest in piglets with birth weight less than 1,000 g. The difference in the final live weight at the end of nursery period between the lightest and heaviest piglets was more than 10 kg. Birth weight of piglets had a significant influence on pre-weaning mortality and subsequent growth performances. In large litters produced by highly prolific sows, the variability of birth weight of piglets together with an increased number of lighter piglets become a new challenge for pig producers.

Istrian shorthaired hound is an old indigenous Croatian dog breed with historical traces of its origin, which date back to the 14th century. Due to its intelligence and great hunting abilities, it is considered an excellent hunting dog. Despite its ancient origin, there is no data on genetic diversity, population structure, and degree of inbreeding that could be used for advanced management and conservation of this breed. Our study aimed to provide a high-resolution population structure of the Istrian shorthaired hound using a 220K HD SNP array, to compare the obtained data with the genealogical records and to place the breed in a broader context of world dog populations. Relatively high population size and low inbreeding coefficient estimated from genealogical data indicate a preserved genetic diversity in this breed. The principle component analysis, the NeighborNet network, and TreeMix were used to determine the genetic relationship between the Istrian shorthaired hound and other breeds. The Istrian shorthaired hound was found to be genetically related to Italian hunting dogs sharing the same branch with the Segugio Italiano a Pelo Raso and Segugio Italiano a Pelo Forte. The ADMIXTURE analysis indicated that the Istrian shorthaired hound could be involved in the development of some other hunting dog breeds. The estimated effective population size (Ne) based on SNP data was similar to Ne calculated from genealogical data indicating the absence of bottlenecks and well-balanced use of breeding animals. The low genomic inbreeding coefficient, together with the higher number of short runs of homozygosity, observed in the Istrian shorthaired hound, confirms the ancient origin of the breed based on historical documents. The analysis of selective sweeps identified genomic regions with the strongest selection signals in the vicinity of the genes associated with cognitive performance and behavior. Genome analysis proved to be a useful tool for estimating population parameters and can be implemented in the conservation plan for this indigenous breed.

Anthropogenic activities and rapidly increasing climate change have led to a significant loss of genetic diversity in domestic animals. Genealogical data have traditionally been used to monitor genetic diversity. However, due to dependency on pedigree completeness and significant errors that can occur in genealogical records, inaccurate estimation of population parameters, such as the inbreeding coefficient or effective population size, might occur. To reduce possible errors, it is necessary to combine genealogical data with molecular data. An integrated approach using genealogical and molecular data leads to the optimization of breeding programs while controlling the inbreeding that can occur within the population of domestic animals. Molecular techniques such as single nucleotide polymorphism (SNP) genotyping, whole-genome sequencing (WGS), or genome-wide association studies (GWASs) enable a detailed understanding of breed-specific genetic profiles and their use in conservation programs. In addition, molecular methods such as structural variation (SV) analysis and pangenome and epigenomic profiling provide a more comprehensive insight into genetic diversity. The conservation of genetic diversity is of particular importance for an autochthonous domestic breed due to its resilience to unfavorable climatic conditions, its specific productive traits, and its disease resistance. A combined approach of genealogical and molecular data helps to maintain genetic diversity and sustainable agricultural systems under evolving environmental challenges.

The inclusion of linseed in cattle diets can improve the fatty acid (FA) profile of meat, but the effects of supplementation at different ages have been insufficiently studied. Hence, this study examined the effects of linseed supplementation and slaughter age on beef cattle carcass and meat quality, FA profile, and lipid oxidation. Eighty Simmental bulls (initial age 221 ± 9 days) were evenly allocated the experimental treatments, consisting of a control diet and a linseed-enriched diet (around 1% whole linseed) fed to the bulls until slaughter at 13 or 17 months of age, in a 2 × 2 factorial design. After slaughter, carcass traits, meat quality, FA profile, and oxidative stability (TBARS test) of the longissimus thoracis muscle were determined. Linseed feeding increased the dressing percentage (p < 0.01) at both slaughter ages but had limited effects on overall carcass and meat quality. The intramuscular fat of linseed-fed bulls contained less saturated FA (p < 0.01) and more beneficial n-3 PUFAs, such as eicosapentaenoic (p < 0.05) and α-linolenic acid (p < 0.001), especially in younger bulls. Although the atherogenic index and n-6/n-3 ratio improved, they remained above the recommended values. Lipid oxidation was higher in linseed-fed (p < 0.05) and younger bulls (p < 0.001). These results suggest that linseed supplementation can improve the beef’s FA composition, but higher levels, especially in older animals, and antioxidant strategies may be required to optimise meat stability and nutritional value.

The Turopolje pig (TP) is a local Croatian pig breed that almost became extinct in the second half of the 20th century. Today, the TP is still endangered, and a new conservation strategy based on products with higher added value is needed to preserve the breed. There is little information on the quality of TP meat products such as smoked and dry-cured ham, including the impact of natural feeds or processing innovations such as smoke reduction. This study, therefore, investigated the effects of the animal’s diet (either conventionally fed or acorn-supplemented) and the processing method (standard or lightly smoked) on the quality traits of dry-cured TP ham. Twenty hams, evenly distributed among the treatments, were processed for 15 months and then analysed for physicochemical and textural traits, volatiles and sensory profile. The hams from acorn-supplemented pigs lost less weight during processing (p ≤ 0.05). Otherwise, the diet had no significant effect on most examined ham traits. The exceptions were protein content and the texture parameter hardness, which decreased (p ≤ 0.05), and the degree of proteolysis and colour parameters, which increased (p ≤ 0.05) as a result of acorn supplementation. However, these effects were generally small and varied between the inner (m. biceps femoris) and outer (m. semimembranosus) muscles. Furthermore, acorn supplementation was associated with less typical ham odour and lower sensory scores for sweetness and colour uniformity (p ≤ 0.05). The smoke reduction had no effect on the physicochemical and colour properties but resulted in a significant reduction (p ≤ 0.05) in the volatile phenolic compounds and an improved texture to the hams. This was reflected both in reduced (p ≤ 0.05) hardness, identified in the instrumental analysis, and in an increased (p ≤ 0.05) softness, solubility and moistness, identified in the sensory evaluation. To summarize, the quality of the TP ham under the conditions studied was only slightly affected by acorn supplementation, whereas reduced smoking had a more significant effect, which was mainly reflected in an improved texture.