A polymorphism analysis of dysferlin gene locus in chicken gene pool

Disferlin refers to proteins involved in the repair of the muscle membrane. It is assumed that some mononucleotide substitutions in the dysferlin gene ( DYSF ) are associated with the formation of muscle mass in poultry. In this work, for the first time in chickens of the Russian White breed, four mononucleotide substitutions have been identified that are in intron 32 on chromosome 4: rs317801013 (G/A) at position 90672849, rs16455118 (C/A) at 90672756, rs318045896 (A/G) at 90672862, and T/G at 90672805. Mononucleotide polymorphism T/G on chromosome 4 at position 90672805 was submitted for registration to the ENSEMBL database, since it was detected for the first time in the species Gallus gallus . In addition, for the first time, we assessed the frequency of occurrence of genotypes and the deviation of the observed genotype distribution from the expected Hardy-Weinberg equilibrium in the gene pool chickens of the Russian White breed. The aim of this work was to study single nucleotide polymorphisms (SNPs) of the dysferlin gene in chicken gene pools and to identify possible associations of DYSF gene polymorphisms with economically valuable traits. We studied meat (Cornish) chickens, laying hen (Russian White, Rhode Island, Aurora, Black-and-White Austrolorp, Leningrad Calico) and decorative breeds (Russian Crested, Light Brahma, Bare-Necked) from the gene pool population of the Genetic Collection of rare and endangered breeds of chickens (RRIFAGB, St. Petersburg-Pushkin). DNA was isolated from blood collected from the axillary vein by phenol extraction. Illumina Chicken 60K SNP iSelect BeadChip chip (Illumina, Inc., USA) was used to analyze the rs16455118 polymorphism. The observed and expected frequencies of genotypes АА , АС , СС and their deviations from the Hardy-Weiberg equilibrium were analyzed in laying hens based on the replacement of adenine for cytosine in the dysferlin gene (rs16455118). The reliability of the data obtained was assessed using the Pearson χ2 test. Dysferlin gene polymorphism was analyzed by sequencing a 237 bp DYSF gene region on chromosome 4 in 76 Russian White hens. We analyzed the NCBI and ENSEMBL databases to identify the SNPs found. An analysis of the frequency of genotypes and alleles was carried out for four identified substitutions. Genotyping of 185 hens using Illumina Chicken 60K SNP iSelect BeadChip technology revealed a single nucleotide polymorphism SNP rs16455118. It was found that the allele frequencies shifted towards an increase in heterozygous genotypes of AC in decorative chickens while the AA genotype was present in the minority. In laying hen, the homozygous genotype AA had the highest frequency of occurrence, the CC genotype was small in number, and it was completely absent in the population of chickens of the Aurora breed. The Cornish beef breed had a more even distribution of genotypes as compared to decorative and laying hens. Sequencing of the 237 bp dysferlin gene region located on chromosome 4 in Russian White chickens identified mononucleotide substitutions in the intron 32. Single nucleotide substitutions G/A (rs317801013), C/A (rs16455118), A/G (rs318045896) corresponded to those in the publicly available chicken genome in the databases NCBI (https://www.ncbi.nlm.nih.gov/SNP) and ENSEMBL (https://www.ensembl.org/index.html). The single nucleotide polymorphism T/G at 90672805 has been detected for the first time. The shift in the genetic balance in the gene pool of Russian White hens indicates the effect of the founder or selection pressure on the region of the SNP rs16455118. The almost complete absence of heterozygotes in laying hen may indicate inbreeding or strong selection pressure. Our findings can be helpful in the future search for SNPs associated with productivity trait in chickens to create a system of molecular markers to accelerate breeding progress.