Genomic characterization of Serbian Holstein-Friesian cattle population

Šaran, Momčilo (author), Štrbac, Ljuba (author), Janković, Dobrila (author), Djan, Mihajla (author), Trivunović, Snežana (author), Zorc, Minja (author)

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 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.

• Language: English
• Keywords: single nucleotide polymorphism, genetic diversity, genomic analysis, linkage disequilibrium, haplotype block
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2023
• Number of pages: Str. 486-496
• Numbering: Vol. 68, iss. 12
• PID: 20.500.12556/RUL-154285-00c7df0d-6064-67d7-3e65-760e2e17323b
• UDC: 636.2:575
• ISSN on article: 1212-1819
• DOI: 10.17221/89/2023-CJAS
• COBISS.SI-ID: 178108675
• Publication date in RUL: 05.02.2024

Record is a part of a journal

• Title: Czech Journal of Animal Science
• Shortened title: Czech J. Anim. Sci.
• Publisher: Ústav zemědělských a potravinářských informací, Česká akademie zemědělských věd
• ISSN: 1212-1819
• COBISS.SI-ID: 953736

Licences

• License: CC BY-NC 4.0, Creative Commons Attribution-NonCommercial 4.0 International
• Link: http://creativecommons.org/licenses/by-nc/4.0/
• Description: A creative commons license that bans commercial use, but the users don’t have to license their derivative works on the same terms.

Secondary language

• Language: Slovenian
• Keywords: govedo, pasme, holštajn, frizijsko govedo, genetika, genomika, Srbija

Projects

• Funder: Other - Other funder or multiple funders
• Funding programme: Science Fund of the Republic of Serbia
• Project number: 6066512
• Name: PROMIS project: BioITGenoSelect