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.

It is well known that the chicken gene pools have high adaptive abilities, including adaptation to cold environments. This research aimed to study the genomic distribution of runs of homozygosity (ROH) in a population of Russian White (RW) chickens as a result of selection for adaptation to cold environments in the early postnatal period, to perform a structural annotation of the discovered breed-specific regions of the genome (compared to chickens of the Amroks breed) and to suggest key candidate genes associated with the adaptation of RW chickens to cold environments. Genotyping of individual samples was performed using Illumina Chicken 60K SNP BeadChip® chips. The search for homozygous regions by individual chromosomes was carried out using the PLINK 1.9 program and the detectRuns R package. Twelve key genes on breed-specific ROH islands were identified. They may be considered as potential candidate genes associated with the high adaptive ability of chickens in cold environments in the early postnatal period. Genes associated with lipid metabolism (SOCS3, NDUFA4, TXNRD2, IGFBP 1, IGFBP 3), maintaining body temperature in cold environments (ADIPOQ, GCGR, TRPM2), non-shivering thermogenesis (RYR2, CAMK2G, STK25) and muscle development (METTL21C) are perspectives for further research. This study contributes to our understanding of the mechanisms of adaptation to cold environments in chickens and provides a molecular basis for selection work.

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.

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.

The CRISPR / Cas9 genome editing system is a very convenient and promising method for creating highly productive chickens of meat direction with improved productive qualities. The biological feature of the amniotes structure creates certain difficulties for the an editing structure introduction into a unicellular zygote. The aim of the study is to optimize technological approaches for obtaining PGCs (Primordial Germ Cells) in Pushkin chickens from the Bioresource collection RRIFAGB “Genetic collection of rare and endangered chicken breeds” (Pushkin, St. Petersburg) for further transformation by the CRISPR / Cas9 system. All experiments on chickens were conducted with the ethical approval of the Russian Research Institute of Farm Animal Genetics and Breeding ‐ Branch of the L.K. Ernst Federal Research Center for Animal Husbandry (Protocol Number: 2020–3). The optimal egg weight varied from 55 to 62 grams for incubation It has been revealed that embryos obtained from large eggs from 62 grams or more developed poorly or did not reach the stage of PGCs selection at all. The eggs were incubated with occasional shaking at 37–38 ° C and 65–70% relative humidity. It was better to select PGCs of Pushkin breed chickens on the 3rd day of incubation from the dorsal aorta of embryos (Hamburger Hamilton stage 14). Cell selection was performed using a microinjector (Narishige IM‐11‐2, Japan). The cells were cultured for 21 days at 37 ° C with 5% CO2. PGCs have been found to reproduce better in a serum‐free medium (MEM Non‐Essential Amino Acids Solution, Gibco, Thermo Fisher) of a specific chemical composition than in a medium containing serum (Opti‐MEM with Chicken Serum, Gibco, Thermo Fisher). The expression of PGCs various genes characteristic was determined by real‐time PCR using conservative primer sets.