An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis
Open accessAbstract
The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.
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Indochinese and Chinese cattle populations are dominant in the zebu ancestry, specifically Y-chromosomal sub-haplogroup Y3a and the maternal sub-haplogroup I1a.
“Indochinese and Chinese cattle populations are dominant in the zebu ancestry, specifically Y-chromosomal sub-haplogroup Y3a and the maternal sub-haplogroup I1a [10,60,61].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [60]
The Results (Population ancestries and migration events; page unavailable) describe Thai cattle as part of an indicine group and report Bos indicus introgression into Chinese cattle. They do not establish that zebu ancestry is dominant in Indochinese and Chinese populations, and our copy does not report the Y3a or I1a sub-haplogroups. (LLM, conf=0.83)
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- Authors
- Sudrajad, P., Subiharta, S., Adinata, Y., Lathifah, A., Lee, J. H., Lenstra, J. A., & Lee, S. H.
- Affiliations
- Ministry of Agriculture (ID)
- Diponegoro University (ID)
- Chungnam National University (KR)
- Utrecht University (NL)
- Corresponding author
- Sudrajad, Pita
- ORCID
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2020-11-10
- Volume
- 15
- Issue
- 11
- Pages
- e0241038
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC7654832
- OpenAlex
- W3105184072
- Cited by
- 22
- References
- 50
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 2 · 2023: 5 · 2022: 2 · 2021: 3
- FWCI
- 1.46
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Funders
- Kementerian Riset Teknologi Dan Pendidikan Tinggi Republik Indonesia (13/E/KPT/2018)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
- Keywords
- cattle domestication, Bos javanicus, Bos indicus, hybrid cattle, genetic diversity, demographic history, effective population size, breed purity, whole-genome genotyping
- MeSH terms
- Data Analysis, Animals, Breeding, Cattle, Biological Evolution, Genotype, Indonesia, Genome, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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