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...

Preserving breed uniqueness and purity is vitally important in developing conservation/breeding programs for a germplasm collection of rare and endangered chicken breeds. The present study was aimed at analyzing SNP genetic variability of 21 small local and imported purebred and F1 crossbred populations and identifying crossbreeding events via whole-genome evaluation of runs of homozygosity (ROH). The admixture models more efficiently reflected population structure, pinpointing crossbreeding events in the presence of ancestral populations but not in their absence. Multidimensional scaling and FST-based analyses did not discriminate properly between purebred populations and F1 crossbreds, especially when comparing related breeds. When applying the ROH-based approach, more and longer ROHs were revealed in purebred individuals/populations, suggesting this as an effective implement in genome-wide analysis of germplasm breed purity.

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Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.

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.