Studying the Structure of a Gene Pool Population of the Russian White Chicken Breed by Genome-Wide SNP Scan

Abstract

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...

Genetic Variability in Local and Imported Germplasm Chicken Populations as Revealed by Analyzing Runs of Homozygosity

“…The original Russian White population (RW1) existed from 1953–2003, had one founder and underwent intensive selection for chick tolerance to cold [ 7 , 26 ]. In 2005, in order to maintain genetic diversity in a small population of this breed, a single introductory crossing with White Leghorns resulted in producing the present population RW2.…”

“…Assessment of the genome-wide diversity plays a significant role in conserving local and imported genetic resources and maintaining an effective program for breeding commercial populations (e.g., [ 1 , 2 , 3 ]). Previously, in the framework of a poultry germplasm conservation and utilization research project, we assessed a broad spectrum of the world’s chicken germplasm populations for genetic variation at economically important loci [ 4 , 5 ] and multiple single nucleotide polymorphisms (SNP) loci [ 6 , 7 , 8 , 9 ].…”

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

“…. 123,202,074 bp), which could reflect the long-term selection of RW chickens for cold tolerance at the earlier stage of breed development [11][12][13]. Moreover, this region contains a causal SNP associated with day-old chick down color in RW chickens [15].…”

“…As a result of the long-term selection for critically low temperatures, the RS phenotypes were characterized by exceptional cold tolerance of neonatal chicks; their snowy-white down at day-old presumably caused by a recessive mutant gene, sw, for snow-white down [14,15]; and elevated resistance to a few neoplastic diseases, such as Marek's disease, leukemia, and carcinomas [11]. The current RG population was more recently derived from the RS as a result of a one-time telic crossing with White Leghorns in 2006 not selected further for cold tolerance and subjected to random mating in 2000-2013 [12,[16][17][18].…”

Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens

“…The RW population maintained at the Russian Research Institute of Farm Animal Genetics and Breeding (RRIFAGB) was put under strong selection pressure for 50 years (1953 to 2003) [3, 7, 8]. Derived from one founder, its breeding was carried out selecting for tolerance to cold in chicks [7].…”