To adjust breeding programs for local, commercial, and fancy breeds, and to implement molecular (marker-assisted) breeding, a proper comprehension of phenotypic and genotypic variation is a sine qua non for breeding progress in animal production. Here, we investigated an evolutionary subdivision of domestic chickens based on their phenotypic and genotypic variability using a wide sample of 49 different breeds/populations. These represent a significant proportion of the global chicken gene pool and all major purposes of breed use (according to their traditional classification model), with many of them being characterized by a synthetic genetic structure and notable admixture. We assessed their phenotypic variability in terms of body weight, body measurements, and egg production. From this, we proposed a phenotypic clustering model (PCM) including six evolutionary lineages of breed formation: egg-type, meat-type, dual purpose (egg-meat and meat-egg), game, fancy, and Bantam. Estimation of genotypic variability was carried out using the analysis of five SNPs, i.e., at the level of genomic variation at the NCAPG-LCORL locus. Based on these data, two generally similar genotypic clustering models (GCM1 and GCM2) were inferred that also had several overlaps with PCM. Further research for SNPs associated with economically important traits can be instrumental in marker-assisted breeding programs.

Milk is an integral and therefore complex structural element of mammalian nutrition. Therefore, it is simple to conclude that lactation, the process of producing milk, is as complex as the mammary gland, the organ responsible for this biochemical activity. Nutrition, genetics, epigenetics, disease pathogens, climatic conditions, and other environmental variables all impact breast productivity. In the last decade, the number of studies devoted to epigenetics has increased dramatically. Reports are increasingly describing the direct participation of microRNAs (miRNAs), small noncoding RNAs that regulate gene expression post-transcriptionally, in the regulation of mammary gland development and function. This paper presents a summary of the current state of knowledge about the roles of miRNAs in mammary gland development, health, and functions, particularly during lactation. The significance of miRNAs in signaling pathways, cellular proliferation, and the lipid metabolism in agricultural ruminants, which are crucial in light of their role in the nutrition of humans as consumers of dairy products, is discussed.

Modern dairy farming is characterised by high selection intensity and the use of a limited number of bulls-producers. This increases the likelihood of widespread genetic defects in livestock populations. Genome-wide studies have identified DNA loci associated with the disruption of foetal embryonic development and its death, which have been called “fertility haplotypes”. The aim of this study is to analyse the occurrence of АН1 haplotype or rs475678587 in Ayrshire bulls (n = 186) used in the artificial insemination system of Russia and to evaluate the reproductive and productive qualities of their daughters. The proportion of genetic defect carrier bulls in the analysed sample cohort was 16.66%. Analysis of the proportion of carriers of unwanted haplotype depending on the place of birth of the bull for service showed that the highest frequency was observed in bulls of Canadian origin (26.66%). Based on data on 97 478 cow and heifer calvings, stillbirth and abortion rates were analysed and cow reproduction rates were based on an AH1 status for the bull-father and bull for service. We observed a significant increase (P < 0.05 and P < 0.001) in the incidence of stillbirths when crossing the daughters of AH1-C bulls with AH1-C bulls. There was no negative association of abortion rates and reproductive qualities with AH1 haplotype. The high incidence of AH1 haplotype among animals of Ayrshire breed requires regular screening for the carriers of this haplotype not only among bulls, but also in cows.

Objective. To assess the variability of egg production traits for nine SNPs, to search for traces of selection in the genome of Russian white chickens based on ROH patterns. Methods. The material for the study was DNA isolated from the blood of Russian white chickens (n = 141). Nine SNPs associated with egg production at p 5.16 105 according to GWAS data were selected for analysis. The frequencies of alleles and genotypes, the relationship between genotypes and characteristics of egg production were calculated, and ROH patterns were identified. Results. Significant differences between genotypes were found in terms of age of laying the first egg (p 0.005) and egg weight (p 0.05). The genomic regions surrounding the target SNPs were analyzed according to the distribution of homozygous regions in them. Conclusions. The substitutions rs317565390 and rs16625488 located in the 4.810.2 Mb region on chromosome 8 showed polymorphism, despite the fact that homozygous loci in this region of the genome are found in 58% of animals. For most SNPs, the prevalence of the frequency of one of the alleles was observed. As a cluster of increased selection pressure, a chick genome region in the 4.810.2 Mb region on chromosome 8 was identified.

Objective:The semen quality of stallions including sperm motility is an important target of selection as it has a high level of individual variability. However, effects of the molecular architecture of the genome on the mechanisms of sperm formation and their preservation after thawing have been poorly investigated. Here, we conducted a genome-wide association study (GWAS) for the sperm motility of cryopreserved semen in stallions of various breeds.Methods: Semen samples were collected from the stallions of 23 horse breeds. The following semen characteristics were examined: progressive motility (PM), progressive motility after freezing (FPM), and the difference between PM and FPM. The respective DNA samples from these stallions were genotyped using Axiom™ Equine Genotyping Array. Results:We performed a GWAS search for single nucleotide polymorphism (SNP) markers and potential genes related to motility properties of frozen-thawed semen in the stallions of various breeds.As a result of the GWAS analysis, two SNP markers, rs1141327473 and rs1149048772, were identified that were associated with preservation of the frozen-thawed stallion sperm motility, the relevant putative candidate genes being NME8, OR2AP1 and OR6C4. Potential implications of effects of these genes on sperm motility are herein discussed. Conclusion:The GWAS results enabled us to localize novel SNPs and candidate genes for sperm motility in stallions. Implications of the study for horse breeding and genetics are a better understanding of genomic regions and candidate genes underlying stallion sperm quality, and improvement in horse reproduction and breeding techniques. The identified markers and genes for sperm cryotolerance and the respective genomic regions are promising candidates for further studying the biological processes in the formation and function of the stallion reproductive system.