Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data

Research (Published online: 25-02-2022)

28. Genomic structure of Bali cattle based on linkage disequilibrium and effective population size analyses using 50K single nucleotide polymorphisms data

Pita Sudrajad, Richi Yuliavian Kusminanto, Slamet Diah Volkandari and Muhammad Cahyadi

Veterinary World, 15(2): 449-454

Pita Sudrajad: Assessment Institute for Agricultural Technology - Central Java, Indonesian Agency for Agricultural Research and Development, Ministry of Agriculture, Semarang, 50552, Indonesia.

Richi Yuliavian Kusminanto: Department of Animal Science, Faculty of Agriculture, Universitas Sebelas Maret, Surakarta, 57126, Indonesia.

Slamet Diah Volkandari: Research Center for Biotechnology, Research Organization for Life Sciences, National Research and Innovation Agency (Badan Riset dan Inovasi Nasional), Cibinong, Jawa Barat, 16911, Indonesia.

Muhammad Cahyadi: Department of Animal Science, Faculty of Agriculture, Universitas Sebelas Maret, Surakarta, 57126, Indonesia.

doi: www.doi.org/10.14202/vetworld.2022.449-454

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Article history: Received: 18-09-2021, Accepted: 20-01-2022, Published online: 25-02-2022

Corresponding author: Muhammad Cahyadi

E-mail: mcahyadi@staff.uns.ac.id

Citation: 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.

Abstract

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 (N_e) 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 N_e 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 N_e 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.