Genomic analysis of conservation status, population structure and admixture in local Czech and Slovak dairy goat breeds.

While dairy goat production, characterized by traditional production on small farms, is an important source of income in the Czech Republic and Slovakia, locally adapted breeds have not been fully consolidated over the last 100 years due to large fluctuations in population size and inconsistent breeding programs that allowed for different crossbreeding strategies. Our main objective in this study was therefore to assess the conservation status of 4 Czech (Alpine Goat, White Shorthair, Brown Shorthair and Czech Landrace) and one Slovak (Slovak White Shorthair) local goat breeds, to analyze their population structure and admixture, and to estimate their relatedness to several neighboring breeds. Our analyses included 142 goats belonging to 5 local breeds genotyped with the Illumina 50K BeadChip and 618 previously genotyped animals representing 15 goat breeds from Austria and Switzerland (all analyses based on 46,862 autosomal SNPs and 760 animals). In general, the conservation status of the Czech and Slovak local goat breeds was satisfactory, with the exception of the Brown Shorthair goat, as the analyzed parameters (heterozygosity, haplotype richness, ROH-based inbreeding and effective population size) were mostly above the median of 20 breeds. However, for all 5 Czech and Slovakian breeds, an examination of historical effective population size indicated a substantial decline about 8 to 22 generations ago. In addition, our study revealed that the Czech and Slovakian breeds are not fully consolidated; for instance, White Shorthair and Brown Shorthair were not clearly distinguishable. Considerable admixture, especially in Czech Landrace (effective number of parental clusters equal to 4.2), and low but numerous migration rates from other Austrian and Swiss breeds were found. These results provide valuable insights for future breeding programs and genetic diversity management of local Czech and Slovak goat breeds.

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep.

This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.

Chemical composition and fatty acid content in lamb and adult sheep meat.

The aim of the present study was to compare the chemical composition and fatty acid (FA) content of the muscle tissues of lambs and adult sheep bred for meat production. Throughout the research period, the animals were managed in a confinement indoor system under uniform environmental conditions. After slaughter, meat samples collected from the musculus biceps femoris were used to determine the basic chemical composition and fatty acid content in the intramuscular fat. The analyses showed that, compared to lambs, meat from adult animals exhibited a more beneficial ratio of n-6 to n-3 FAs, as well as a favorable percentage of OFAs (dietary fatty acids having an undesirable hypercholesterolemic effect on humans). The results of this study support the inclusion of dietitian-recommended mutton into the human diet and the promotion of the production of meat from adult animals as a high-value product. The sheep industry could benefit economically, particularly in countries where this meat type has not enjoyed a high standing in consumer preferences.

Fatty acids in intramuscular fat of Ile de France lambs in two different production systems.

The fatty acid (FA) composition in the intramuscular fat (IMF) of the musculus longissimus dorsi (MLD) of Ile de France purebred lambs in two different production systems in Slovakia was evaluated using gas chromatography. In the first production system, lambs and ewes were assigned to pasture without access to concentrates (P). In the second system, lambs and ewes were confined indoors with hay/silage and access to concentrates (S). An analysis of variance with the following factors was employed: production system, sex, and production system-sex interactions. The proportions of arachidonic, eicosapentaeonic, docosapentaeonic, and docosahexaenoic FAs, i.e. long-chain polyunsaturated FA (PUFA), were significantly higher in P lambs (1.83, 0.82, 0.92, 0.29 g 100 g - 1 FAME, respectively) than in S lambs (0.45, 0.14, 0.30, 0.09 g 100 g - 1 FAME, respectively). The proportions of conjugated linoleic acid (CLA), n-6 PUFA, n-3 PUFA, and essential FA (linoleic and α -linolenic) were also significantly higher in P lambs (2.10, 8.50, 4.55, and 8.80 g 100 g - 1 FAME, respectively) than in S lambs (0.65, 3.27, 1.50, and 3.64 g 100 g - 1 FAME, respectively). The proportions of palmitic acid and myristic acid as important individual saturated FAs (SFA) were significantly higher in S lambs (28.51 and 8.30 g 100 g - 1 FAME, respectively) than in P lambs (21.80 and 5.63 g 100 g - 1 FAME, respectively). The proportion of all SFAs was also significantly higher in S lambs (57.87 g 100 g - 1 FAME) than in P lambs (48.70 g 100 g - 1 FAME). From a nutrition and human health point of view (i.e. higher proportions of PUFA, CLA, and essential FAs and lower proportions of SFAs), meat from P lambs was found to be more favourable and would be more highly recommended for consumption.