Authors
1
Associate Proffesor of Animal Science Department, Ahar Faculty of Agriculture and Natural Resources , University of Tabriz, Iran
2
MSc Graduate of Animal Breeding and Genetics, Ahar Faculty of Agriculture and Natural Resources, University of Tabriz, Iran
3
Associate Proffesor of Animal Science Department, Faculty of Agriculture, University of Tabriz, Iran
4
Assistant Professor, Animal Science Research Department, Khorasan Razavi Agricultural and Natural Resources Research Center, Mashhad, Iran
5
Assistant Professor of Animal Science Department, Ahar Faculty of Agriculture and Natural Resources, University of Tabriz, Iran
10.22069/ejrr.2026.24428.2038
Abstract
Background and Objectives: In dairy cattle breeding, high selection pressure to improve some economic traits along the use of a limited number of superior bulls by using artificial insemination technique has led to an increase in the relationship between cows and also an increase in the average inbreeding of the population. The most important result of inbreeding at the level of commercial herds is a decrease in the level of economic traits, which is called inbreeding depression. Pedigree information is usually used to estimate inbreeding. However, estimates obtained from pedigrees depend largely on the depth of the pedigree and its completeness. In recent years, along with the emergence of genome sequencing techniques, interest in using genomic information to accurately estimate inbreeding coefficients has increased. The aim of the present study was to estimate the genomic inbreeding coefficient in some Holstein cattle herds in East Azerbaijan Province of Iran using dense single nucleotide marker chip data.
Materials and Methods: In this study, genotypic information of 43 heifers belonging to 5 Holstein dairy farms in Tabriz city was used to estimate genomic inbreeding. Hair follicles of each animal (80 to 100 strands) were sampled from the tail tip and after DNA extraction, genotype was determined using Illumina BovineSNP50 BeadChip array. Data quality control was performed using PLINK software. All loci with a genotype call rate of less than 95% and with a minor allele frequency of less than 0.01 were excluded from the data set. Also, loci with a significant deviation from Hardy-Weinberg equilibrium were identified and removed from the data. All SNP markers located on the X and Y sex chromosomes were also removed from the data set. The genomic inbreeding coefficient was estimated using the runs of homozygosity (ROH) criteria.
Results: Out of a total of 41177 genotyped markers, 40904 markers were able to pass various quality control steps. One marker was removed due to a minor allele frequency of less than 0.01%, 264 markers due to a genotyping rate of less than 95% in each sample, and 8 markers due to Hardy-Weinberg disequilibrium. The average number of ROH with lengths of 1-2, 2-4, 4-6, 6-8, and more than 16 Mb was estimated to be 25.7, 25.6, 20, 9.14, and 2.8, respectively. As the length of the desired segments for the ROH increased, the average number of segments in animals decreased. Also, the average length of ROH in the aforementioned length categories was estimated to be 216.3, 216.1, 197.6, 137.1, and 67, respectively. The average genomic inbreeding coefficient estimated using ROH with lengths of 1-2, 2-4, 4-6, 6-8, and more than 16 Mb was 8.6, 8.6, 7, 5, and 2 percent, respectively.
Conclusion: The average genomic inbreeding coefficient of cows, considering the 1 to 2 Mb of ROH segments, was estimated to be 8.6%. By increasing the length of the considered segments for ROH to more than 16 Mb, the average genomic inbreeding of cows decreased to 2%. The higher frequency of shorter ROH compared to longer segments indicated that the majority of inbreeding in cattle is related to past generations and has arisen due to the existence of common ancestors in distant generations of the pedigree. Considering the average inbreeding for the Holstein cattle population, the estimated average inbreeding of 2% in the 16 Mb ROH, which reflects the recent mating system used in the herds, was at an acceptable level.
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