Vet World Vol.15 February-2022 Article-28
Research Article
Veterinary World, 15(2): 449-454
https://doi.org/10.14202/vetworld.2022.449-454
Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data
2. Department of Animal Science, Faculty of Agriculture, Universitas Sebelas Maret, Surakarta, 57126, Indonesia.
3. Research Center for Biotechnology, Research Organization for Life Sciences, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional), Cibinong, Jawa Barat, 16911, Indonesia.
Background and Aim: Bali Cattle (Bos j. javanicus) is a local breed originating in Indonesia, accounting for 32.3% of the total cattle population. To date, no studies of the genetic structure and demographic status of Bali cattle have been conducted, even though the breeding of Bali cattle has a long and unique history that is likely to have impacted its genetic diversity. Therefore, a study that used molecular breeding technologies to characterize the demography of Bali cattle would be timely. This study aimed to examine genome diversity in Bali cattle and estimate the linkage disequilibrium (LD) and effective population size (Ne) values in the cattle population.
Materials and Methods: In this study, we explored the population structure and genetic diversity of Bali cattle using genomic-level analyses. Our study primarily studied cattle that had been bred in livestock breeding centers since these breeds had subsequently spread throughout Indonesia. We focused on characterizing the genetic structure, determining the level of LD present, and estimating the Ne of the Bali cattle population. The genomic data used for this study were obtained from DNA samples of 48 Bali cattle collected at the Breeding Center of Bali Cattle as well as 54 genomic samples from Bali cattle collected elsewhere in Indonesia that had been used in recent publications. This genomic dataset included exclusively 50K single nucleotide polymorphisms (SNP) array (Illumina Bovine 50SNP bead chip, Illumina, USA) data.
Results: We found that the LD values of Bali cattle from the breeding center and those raised elsewhere were 0.48±0.43 and 0.39±0.40, respectively. Subsequently, the Ne value of Bali cattle from the breeding center and farmers was 151 and 96, respectively.
Conclusion: Our results suggest that the selection program of the breeding center is beneficial for maintaining the genetic diversity of Bali cattle. Keywords: Bali cattle, effective population size, genomic data, genetic structure, linkage disequilibrium.
Keywords: Bali cattle, effective population size, genomic data, genetic structure, linkage disequilibrium.
How to cite this article: Sudrajad P, Kusminanto RY, Volkandari SD, Cahyadi M (2022) Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data, Veterinary World, 15(2): 449-454.
Received: 18-09-2021 Accepted: 20-01-2022 Published online: 25-02-2022
Corresponding author: Muhammad Cahyadi E-mail: mcahyadi@staff.uns.ac.id
DOI: 10.14202/vetworld.2022.449-454
Copyright: Sudrajad, 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.