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

Although 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 yr 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 1 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).

Genome-wide screening for selection signatures in native and cosmopolitan cattle breeds reared in Türkiye.

Via long-term natural and artificial selection pressure, homozygosity may extend across the genome, leaving genomic patterns called selection signatures. This study is the first attempt to assess genome-wide selection signatures in six native Turkish and two cosmopolitan cattle breeds by 211.119 bi-allelic SNPs recovered using the double digest restriction associated DNA sequencing method.

Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations.

In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups.

Genome-wide genetic variation and population structure of native and cosmopolitan cattle breeds reared in Türkiye.

This is the first comprehensive study to reveal genetic variation and population structure at genome level in six Anatolian (Anatolian Black, East Anatolian Red, South Anatolian Red, South Anatolian Yellow, Turkish Grey Steppe, and Zavot) and two cosmopolitan (Brown Swiss and Holstein Friesian) cattle breeds reared in Türkiye. Being 20 samples from each population, a total of 160 blood samples retrieved from representative herds were utilized to generate genomic libraries by ddRADseq method. Genomic libraries sequenced by Illumina HiSeq X Ten instrument revealed a total of 211,119 bi-allelic SNPs with high call rate.

Mitochondrial DNA diversity of D-loop region in three native Turkish cattle breeds.

This study aimed to reveal the genetic variability of mitochondrial DNA (mtDNA) displacement-loop (D-loop) region in 62 animals belonging to three native Turkish cattle breeds, namely Anatolian Black (AB), East Anatolian Red (EAR) and Zavot (ZAV), and to conduct phylogenetic relationship analyses to obtain deeper information on their genetic origin and breeding history by comparison of 6 taurine and 11 indicine breeds, together with 66 polymorphic sites, a total of 31 haplotypes, of which 15, 10 and 6 were detected in AB, EAR and ZAV, respectively. Mean nucleotide and haplotype diversity were 0.01 and 0.

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.

Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions.

This study evaluates the diversity of the so-called 'Moroccan Royal lions' using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of 'Moroccan Royal lions' seems to be significantly endangered by the loss of diversity due to the effective population size decrease.

Czechoslovakian Wolfdog Genomic Divergence from Its Ancestors , German Shepherd Dog, and Different Sheepdogs of European Origin.

This study focused on the genomic differences between the Czechoslovakian wolfdog (CWD) and its ancestors, the Grey wolf (GW) and German Shepherd dog. The Saarloos wolfdog and Belgian Shepherd dog were also included to study the level of GW genetics retained in the genome of domesticated breeds. The dataset consisted of 131 animals and 143,593 single nucleotide polymorphisms (SNPs).

Genetic diversity of local cattle.

The Slovak Pinzgau breed faces the bottleneck effect and the loss of diversity due to unequal use of founders and a significant population decline. Further population size reduction can lead to serious problems. Information obtained here and in other studies from high-throughput genotyping of 179 individuals was used to characterise genetic diversity and differentiation of Slovak Pinzgau, Austrian Pinzgau, Cika and Piedmontese cattle by Bayesian clustering algorithm.

Genetic polymorphisms of leptin and leptin receptor genes in relation with production and reproduction traits in cattle.

Leptin and leptin receptor genes are considered as production traits markers in dairy or beef cattle. The aim of this study was to verify the associations of polymorphisms in bovine LEP and LEPR genes with production and reproduction traits in Slovak Spotted and Pinzgau cows. Long-life production was evaluated: milk, protein, and fat yield and reproduction traits: age at first calving, calving interval, days open, and insemination interval.