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.

Background The Russian White is a gene pool breed, registered in 1953 after crossing White Leghorns with local populations and, for 50 years, selected for cold tolerance and high egg production (EL). The breed has great potential in meeting demands of local food producers, commercial farmers and biotechnology sector of specific pathogen-free (SPF) eggs, the former valuing the breed for its egg weight (EW), EL, age at first egg (AFE), body weight (BW), and the latter for its yield of extraembryonic fluid (YEF) in 12.5-day embryos, ratio of extraembryonic fluid to egg weight, and embryo mass. Moreover, its cold tolerance has been presumably associated with day-old chick down colour (DOCDC) – white rather than yellow, the genetic basis of these traits being however poorly understood. Results We undertook genome-wide association studies (GWASs) for eight performance traits using single nucleotide polymorphism (SNP) genotyping of 146 birds and an Illumina 60KBeadChip. Several suggestive associations ( p < 5.16*10 − 5 ) were found for YEF, AFE, BW and EW. Moreover, on chromosome 2, an association with the white DOCDC was found where there is an linkage disequilibrium block of SNPs including genes that are responsible not for colour, but for immune resistance. Conclusions The obtained GWAS data can be used to explore the genetics of immunity and carry out selection for increasing YEF for SPF eggs production. Electronic supplementary material The online version of this article (10.1186/s12864-019-5605-5) contains supplementary material, which is available to authorized users.

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A b s t r a c tA population of the Russian White chickens, bred at the gene pool farm of ARRIFAGB for 25 generations using individual selection, is characterized by resistance to a lowered temperature in the early postnatal period and white colour of the embryonic down. In 2002-2012, breeding was carried out by panmixia, and by now a new population of the Russian White chickens has been formed on the basis of the surviving stock. Comparison of the genetic variability of this population and the archival DNA of representatives of the 2001 population using microarray screening technology will help to assess the population structure and the preservation of the unique characteristics of its genome. The material for the study was DNA extracted from 162 chicken blood samples. Two groups of the Russian White breed were studied, the 2001 population and the current population. Genome-wide analysis using single nucleotide markers (SNP) included screening by means of the Illumina Chicken 60K SNP iSelect BeadChip microarray. Quality control of genotyping, determination of the population genetic structure by multidimensional scaling (MDS), calculation of linkage disequilibrium (LD) and allele frequency in the groups were carried out using PLINK 1.9 software program. The construction of a cluster delimitation model based on SNP genotypes was carried out using the ADMIXTURE program. According to the MDS analysis results, the current population can be divided into four MDS groups, which, when compared to the data of the pedigree, adequately reflect the origin of the studied individuals. The representatives of the ancestral population were genetically similar to the MDS3 group of the current population. Using the F-statistic of the twoway analysis of variance, a significant effect of the group, chromosome, chromosome in the group, and the distance between SNP markers on LD (r 2 ) values was observed. In the 2001 group, the maximum r 2 and the high incidence of LD equal to 1 were observed for all chromosomes, with a distance between SNP markers being 500-1000 Kb. There was also the greatest number of monomorphic alleles in this group. Based on the SNP analysis, we may conclude that the current Russian White chicken population is characterized by the disintegration of long LD regions of the ancestral population. Modelling clusters using the ADMIXTURE program revealed differences between the current population groups determined by MDS analysis. The groups composed of individuals included in MDS1 and MDS2 had a homogeneous structure and differed from each other at K = 4 and K = 5. The MDS4 group formed a genetically heterogeneous cluster different from the MDS1 and MDS2 groups at K of 2-5. The MDS3 group was phylogenetically close to the 2001 population (at K of 2-5). In general, the analysis of the current gene pool population of the Russian White chickens showed its heterogeneity while one of its groups (MDS3) was similar to the ancestral population of 2001, which in turn is characterized by a large number of monomorphic alleles and...

The aim of this study was to create balanced media for the cryopreservation of rooster semen in pellets to maintain the functional state of the sperm after thawing. Fructose was replaced by trehalose in experimental media in proportions of 10% (LCM-T10) and 20% (LCM-T20), while LCM was used as a control. After artificial insemination of the hens, the eggs were incubated (n = 400). To determine the functional safety of spermatozoa in the genital tract of hens after 5, 10, and 15 days from the last insemination, we used a method for assessing the interaction of sperm with the perivitelline membrane. Significantly higher rates of egg fertilization (82–86%) were obtained when using LCM-T10 and LCM-T20 compared to control (79%, p < 0.05). Egg fertility on the 5th day from the last insemination with the LCM-T20 diluent reached 100% versus 86% in the control; on the 10th day, the fertility rates were 55% versus 20%, respectively. The best results for fertility duration were obtained by freezing spermatozoa with LCM-T20 medium. The numbers of interaction points of spermatozoa with the perivitelline membrane were as follows: on the 5th day from the last insemination with LCM-T20—461.5 ± 11.5 holes/cm2 (LCM-control—13.7 ± 2.7 holes/cm2), p < 0.01; on the 10th day with LCM-T20—319.3 ± 12.9 holes/cm2 (LCM-control—14.9 ± 3.5 holes/cm2); and on the 15th day with LCM-T20—345.2 ± 11.1 holes/cm2 (LCM-control—0 holes/cm2). In conclusion, the use of trehalose in LCM diluent medium can increase the fertility of frozen/thawed sperm and the duration of their fertility in the genital tract of hens.

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

Currently, there is virtually no information on genetic factors affecting the yield of allanto-amniotic fluid, which is the raw material for the production of human and animal vaccines. Association studies including this trait are beneficial for increasing productivity of a biotechnological line of chickens used for the production of 'Clean Eggs'. We examined here a population of the Russian White breed for the effects of indels in the prolactin (PRL) and dopamine receptor D2 (DRD2) genes on the yield of extraembryonic fluid (YEF) and embryo weight at 12.5 days of development. A 24-bp insertion in the 5' flanking region of the PRL gene significantly (P<0.01) increases YEF in the embryos. The heterozygous embryos contained the highest YEF (9.6 mL) than that of the homozygous insertion (9.4 mL) and deletion embryos (8.4 mL). We also found a significant association (P<0.001) between the PRL genotypes and egg weight (EW). The results of the present study suggest a significant association between the PRL gene variation and quantitative traits in the Russian White chickens, contributing to a long-term programme on the effective use of the genetic potential of Russian gene pool breeds and populations of chickens.

This review presents the current progress in and approaches to in vitroconservation of reproductive cells of animals, including birds, such as cryopreservation and freeze-drying, as well as epigenetic conditions for re storing viable spermatozoa and female gametes after conservation. Cryopreservation is an effective way to preserve reproductive cells of various species of animals and birds. In vitrogene pool conservation is aimed primarily to the restoration of extinct breeds and populations and to the support of genetic diversity in populations prone to genetic drift. It is the combination of ex situ in vivoand ex situ in vitromethods that can form the basic principles of the strategy of animal genetic diversity preservation. Also, use of cryopreserved semen allows faster breeding in industrial poultry farming. Despite numerous advances in semen cryobiology, new methods that can more efficiently restore semen fertility after cryopreservation are being sought. The mechanisms underlying the effect of cryopreservation on the semen parameters of cocks are insufficiently understood. The review reflects the results of recent research in the field of cryopreservation of female and male germ cells, embryonic cells, the search for new ways in the field of genetic diversity in vitro (the development of new cryoprotective media and new conservation technologies: freeze-drying). Molecular aspects of cryopreservation and the mechanisms of cryopreservation influence on the epigenetic state of cells are highlighted. Data on the results of studies in the field of male reproductive cell lyophilization are presented. The freeze-drying of reproductive cells, as a technology for cheaper access to the genetic material of wild and domestic animals, compared to cryopreservation, attracts the attention of scientists in Japan, Israel, Egypt, Spain, and France. There is growing interest in the use of lyophilized semen in genetic engineering technologies. Methods of freeze-drying are developed taking into account the species of birds. Organizational and legal ways of solving the problems of in vitroconservation of genetic resources of farm animals, including birds, are proposed.