Vet World   Vol.18   April-2025  Article - 28 

Analysis of genetic diversity and phylogenetic relationships among Indonesian native cattle breeds using microsatellite markers: A review

Rini Hastarina^1,2 , Agung Purnomoadi¹ , Sutopo Sutopo¹ , Dela Ayu Lestari¹ , Fatmawati Mustofa¹ , Putu Novia Gariri^1,3 , Pupus Galau Prahara¹ , Firda Tasya Kamila¹ , Syaddad Verahry Philco¹ , Maulida Arkaan Muhammad Da’i¹ , and Asep Setiaji¹

Background and Aim: Indonesia is home to a diverse array of native cattle breeds - such as Aceh, Bali, Madura, and Sumba Ongole - that are uniquely adapted to their regional environments and integral to the country’s agricultural and cultural heritage. This review synthesizes current research on the genetic diversity and phylogenetic relationships of Indonesian native cattle using microsatellite markers, a robust molecular tool for assessing genetic variation. Analysis of multiple studies reveals that geographical isolation, selective breeding, and human-mediated practices have shaped the genetic structure of these populations. Notably, Bali and Madura cattle exhibit distinctive genetic clusters reflecting island isolation and long-standing breeding traditions. Findings also underscore concerns regarding genetic erosion caused by uncontrolled crossbreeding with exotic breeds, which threatens local adaptability and increases the risk of inbreeding. Key genetic parameters - including allele richness, heterozygosity, and inbreeding coefficients - suggest varying degrees of genetic integrity among the breeds, with several populations showing signs of inbreeding depression. Microsatellite data further demonstrate clear phylogenetic separation among breeds, offering valuable insights for breed identification and conservation planning. The primary strength of this review lies in its comprehensive integration of genetic studies across diverse breeds and islands, providing a national-scale perspective. However, limitations include the underrepresentation of certain breeds and reliance on microsatellite data without integration of high-resolution genomic tools. Future research should incorporate advanced molecular techniques e.g., sngle-nucleotide polymorphism arrays and whole-genome sequencing) and longitudinal monitoring to inform targeted conservation strategies. This review advocates for the incorporation of molecular genetic data into national breeding and conservation programs. Strengthening such initiatives is essential for preserving Indonesia’s indigenous cattle as valuable genetic resources for climate-resilient, sustainable livestock production.

Keywords: breed conservation, genetic diversity, inbreeding, Indonesian cattle, microsatellite markers, phylogenetics, sustainable livestock.

How to cite this article: Hastarina R, Purnomoadi A, Sutopo S, Lestari DA, Mustofa F, Gariri PN, Prahara PG, Kamila FT, Philco SV, Da’i MAM, and Setiaji A (2025) Analysis of genetic diversity and phylogenetic relationships among Indonesian native cattle breeds using microsatellite markers: A review, Veterinary World, 18(4): 1036-1046.

Received: 28-12-2024   Accepted: 28-03-2025   Published online: 30-04-2025

Corresponding author: Asep Setiaji    E-mail: asepsetiaji93@gmail.com

DOI: 10.14202/vetworld.2025.1036-1046

Copyright: Hastarina, 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.