Runs of homozygosity analysis and genomic inbreeding estimation in Sumba Ongole cattle (Bos indicus) using a BovineSNP50K BeadChip

Vet World Vol.17 August-2024 Article - 29

Research Article

Veterinary World, 17(8): 1914-1919

https://doi.org/10.14202/vetworld.2024.1914-1919

Widya Pintaka Bayu Putra¹, Hartati Hartati², Redi Aditama³, Eko Handiwirawan², Endang Tri Margawati¹, and Simon Elieser²

1. Research Center for Applied Zoology, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia.
2. Research Center for Animal Husbandry, National Research and Innovation Agency (BRIN), Bogor 16911, Indonesia.
3. Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor 16911, Indonesia.

Background and Aim: Runs of homozygosity (ROH) is a biocomputational technique for identifying homozygous regions in the genomics of livestock. This study aimed to determine the ROH in Sumba Ongole (SO) bulls (n = 48) using the BovineSNP50K BeadChip.

Materials and Methods: GenomeStudio 2.0 software was used to generate the BovineSNP50K BeadChip output. The ROH and ROH-based inbreeding coefficients (F_ROH) were determined using the detect RUNS R v4.1.0 package. Using the following filtering criteria, PLINK v1.90 software was used to perform genotype quality control: (1) Individuals and single-nucleotide polymorphism (SNPs) had call rates >0.95; (2) more than 0.05 was the minor allele frequency; (3) the list contained only SNPs linked to autosomes; and (4) SNPs that strongly deviated (p < 1e-6) from Hardy–Weinberg equilibrium were removed. Subsequently, 25,252 autosomal SNP markers were included in the ROH and FROH analyses.

Results: In general, the number and length of ROH segments in pool animals were 149.77 ± 16.02 Mb and 486.13 ± 156.11 Mb, respectively. Furthermore, the ROH segments in the animals under study can be discriminated into two classes of 1–4 Mb (83.33%) and 4–8 Mb (16.67%). Subsequently, Bos taurus autosomes (BTA) 1, BTA6, and BTA14 had significant homozygous segments comprising 13 genes. Despite this, the average F_ROH in pool animals was 0.20 ± 0.06.

Conclusion: These findings indicate that a recent inbreeding event in SO cattle occurred many generations ago. Furthermore, the candidate genes identified from the ROH analysis indicate phenotypic attributes associated with environmental adaptation and economic traits.

Keywords: BovineSNP50K BeadChip, Bos taurus autosomes, F_ROH, runs of homozygosity, Sumba Ongole.

How to cite this article: Putra WPB, Hartati H, Aditama R, Handiwirawan E, Margawati ET, and Elieser S (2024) Runs of homozygosity analysis and genomic inbreeding estimation in Sumba Ongole cattle (Bos indicus) using a BovineSNP50K BeadChip, Veterinary World, 17(8): 1914-1919.

Received: 2024-05-03 Accepted: 2024-07-30 Published online: 2024-08-27

Corresponding author: Hartati Hartati E-mail: hart018@brin.go.id

DOI: 10.14202/vetworld.2024.1914-1919

Copyright: Putra, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/ by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.