The relationship between genomic and estimated inbreeding in the population of Holstein cattle in Sverdlovsk region.

Abstract

Abstract. The purpose of this paper is to study the inbreeding change of Holstein cattle in Sverdlovsk region and to show the correlation between genomic and estimated inbreeding. Methods. The study was conducted in six farms of the Sverdlovsk region and included 512 cows and heifers with date of birth from 2007 to 2022 and 12 breeding bulls. Chips GGP Bovine 150K (Neogen, USA) and Bovine 50K (Illumina, USA) were used for genotyping. Genome inbreeding estimates F were conducted with --het function in PLINK v1.9. Homozygosity inbreeding coefficient FROH was calculated with “sliding window” package of detectRUNS; FPED was taken from SELEX database, where it was calculated by pedigrees with Wright-Kislovsky formula. Scientific novelty. The comparison of genomic inbreeding for different age groups and estimation of correlations with pedigree inbreeding was conducted in Sverdlovsk region for the first time. Results. Our studies show that inbreeding coefficients increase radically from younger to older age groups. Holstein breed bulls show the highest value of inbreeding. At the same time heterozygosity level, estimated with sMLH tends to decrease with age. In addition, a strong correlation between estimated by pedegree inbreeding FPED and date of birth, as well as weak correlations between FPED and genomic coefficients (which have strong correlations with each other) were established.