M. G. Smaragdov, A. A. Kudinov
All-Russian Research Institute of Genetics and Breeding of Farm Animals – the branch of Federal Scientific Center of Animal Husbandry – L. K. Ernst All-Russian Research Institute of Animal Husbandry, Moskovskoe sh., 55a, Sankt-Peterburg, 196601, Russian Federation
Abstract. Modern molecular genetics allows identifying runs of homozygosity (ROH) in the animal genome indicating the presence of closely related crosses in the pedigree. The purpose of the research was to calculate the inbreeding coefficient for cows based on the full genome ROH data of Holsteinized Black-and-White cows from four breeding farms of the Leningrad region. From each herd from 46 to 85 animals were selected, a total of 263 heads. DNA for genotyping with BovineSNP50 chip was isolated from the blood by the phenol-chloroform method. Criteria for editing genotypes were the following: SNPs (single nucleotide polymorphism) with the frequency of occurrence in the genome of cows less than 5% were removed; SNPs genotypes that did not satisfy the Hardy-Weinberg distribution with confidence p=0.0001 were removed. As a result of the editing of 54,609 SNPs, 43,298 SNPs remained. The quality of genotyping (QS) was 0.99. ROHs in the cow genome were identified using Plink 1.9 software. The ROH selection criteria were as follows: the scanning frame included 50 SNPs; heterozygous SNPs in ROH were banned; the number of missing SNPs in ROH was no more than two. The scanning of the genome of 263 cows showed that the average number of ROH per genome varied from 23 to 25. The average length of ROH in the cow genome varied from 6729 kbp to 7220 kbp (kilobase pairs). Thus, the total ROH length of individual animals ranged from 24 Mbp to 380 Mbp (megabase pairs). The calculated inbreeding coefficient for individual cows varied from 1.0 to 15.1%. The average inbreeding coefficient in four herds varied from 5.5% to 8.0%. Thus, molecular indicators based on ROH allow evaluating the inbreeding coefficient of cows in herds, and this method should be used in breeding.
Keywords: ROH; inbreeding; dairy cattle; herds.
Author Details: M. G. Smaragdov, Cand. Sc. (Biol.), senior research fellow (e-mail: Этот адрес электронной почты защищён от спам-ботов. У вас должен быть включен JavaScript для просмотра.); A. A. Kudinov, research fellow (e-mail: Этот адрес электронной почты защищён от спам-ботов. У вас должен быть включен JavaScript для просмотра.).
For citation: Smaragdov M. G., Kudinov A.A. Full Genome Inbreeding Assessment of Dairy Cattle. Dostizheniya nauki i tekhniki APK. 2019. Vol. 33. No 6. Pp. 51–53 (in Russ.). DOI: 10.24411/0235-2451-2019-10612.