Genomic characterization of Serbian Holstein-Friesian cattle population

Momčilo Šaran, Ljuba Štrbac, Dobrila Janković, Mihajla Djan, Snežana Trivunović and Minja Zorc
Additional contact information
Momčilo Šaran: Department of Animal Science, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
Ljuba Štrbac: Department of Animal Science, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
Dobrila Janković: Department of Animal Science, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
Mihajla Djan: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
Snežana Trivunović: Department of Animal Science, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
Minja Zorc: Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia

Czech Journal of Animal Science, 2023, vol. 68, issue 12, 486-496

Abstract: The use of genomic data makes it possible to examine genetic variability and calculate the genetic parameters of the population in an efficient and precise way. The aim of this research was to analyse linkage disequilibrium (LD), contemporary effective population size (Nec), haplotype block structure, minor allele frequency (MAF), observed (HO) and expected heterozygosity (HE), calculate the genomic relationship matrix and perform a principal component analysis (PCA) in the Serbian Holstein-Friesian cattle population using SNP data from the GGP Bovine 100K chip. After quality control (QC), 83 208 SNPs and 1 575 cows were retained for further analysis. LD on autosomes had an average value of ≥ 0.2 up to a distance of 50-60 kb (r2 = 0.211), while on BTX r2 ≥ 0.2 was represented at distances of 80-90 kb (r2 = 0.211). LD differed between chromosomes. The average HO for autosomes and X chromosome SNPs was 0.412 and 0.422, respectively. 81.30% of SNPs that passed QC had MAF > 0.2. The total number of haplotype blocks in the studied population was 15 642. On average, blocks contained 2.932 SNPs. The average block length was 32.657 kb and ranged from a minimum of 0.019 kb (BTA21 and BTA26) to a maximum of 999.562 kb (BTX). The estimated value of Nec in the this cattle population was 142. The results of PCA showed a significant variability of genotypes in the population, but there was no clear stratification of the population. The obtained results will serve as a basis for future genomic analyses such as the detection of QTLs for important economic traits and the implementation of genomic selection.

Keywords: single nucleotide polymorphism; genetic diversity; genomic analysis; linkage disequilibrium; haplotype block (search for similar items in EconPapers)
Date: 2023
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
http://cjas.agriculturejournals.cz/doi/10.17221/89/2023-CJAS.html (text/html)
http://cjas.agriculturejournals.cz/doi/10.17221/89/2023-CJAS.pdf (application/pdf)
free of charge

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:caa:jnlcjs:v:68:y:2023:i:12:id:89-2023-cjas

DOI: 10.17221/89/2023-CJAS

Access Statistics for this article

Czech Journal of Animal Science is currently edited by Bc. Michaela Polcarová

More articles in Czech Journal of Animal Science from Czech Academy of Agricultural Sciences
Bibliographic data for series maintained by Ivo Andrle ().