The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression
Genetic diversity is a crucial resource in livestock, determining their traits and ability to respond to selection. Indonesian cattle are unique due to their history of admixture involving both zebu (Bos indicus) and banteng (B. javanicus), and may therefore contain novel cattle genetic resources. We generated whole genome sequences from 126 Indonesian cattle, 51 domesticated banteng and three captive banteng. We show that Indonesian cattle have very high genetic diversity, especially the Madura breed due to introgression from banteng and possibly other Bos species, contributing up to 36.6% of the Madura's genome. We find that Indonesian zebu ancestry can be traced to at least three distinct ancestral populations, two of which were introduced more than 1345 years ago from mainland Southeast or eastern Asia. Peaks and valleys in banteng ancestry across the genome in admixed breeds suggest that both negative and positive selection act on introgressed haplotypes. Despite adaptive introgression being mainly breed-specific, we found evidence that some phenotypes, such as coat color, have experienced convergent adaptive introgression. Overall, our results provide insights into the historical movement of cattle in Asia, and showcase the potential for genetic improvement of cattle by identifying ~3.5 million novel SNPs introgressed into Indonesian cattle.
Authors
- Rasmus Heller (ORCID: https://orcid.org/0000-0001-6583-6923)
- Johannes Arjen Lenstra (ORCID: https://orcid.org/0000-0003-1745-7739)
- Muhammad Agil (ORCID: https://orcid.org/0000-0003-3591-4219)
- Mikkel‐Holger S. Sinding (ORCID: https://orcid.org/0000-0003-1371-219X)
- Alam Putra Persada Putra Persada
- Darren E. Hagen (ORCID: https://orcid.org/0000-0001-8295-020X)
- Cynthia Dewi Gaina (ORCID: https://orcid.org/0000-0002-0322-1373)
- Greger Larson (ORCID: https://orcid.org/0000-0002-4092-0392)
- Laura D. Bertola (ORCID: https://orcid.org/0000-0002-3445-0355)
- Josiah Kuja (ORCID: https://orcid.org/0000-0002-3202-9540)
- Laurent Frantz (ORCID: https://orcid.org/0000-0001-8030-3885)
- Pita Sudrajad (ORCID: https://orcid.org/0000-0001-8148-9095)
- Dedy Duryadi Solihin (ORCID: https://orcid.org/0000-0002-7507-6320)
- Bambang Purwantara (ORCID: https://orcid.org/0000-0002-6652-4902)
- Yu Jiang (ORCID: https://orcid.org/0000-0003-4821-3585)
- Kristian Hanghøj (ORCID: https://orcid.org/0000-0003-1941-5495)
- Jonas Meisner (ORCID: https://orcid.org/0000-0002-9540-6673)
- Casia Nursyifa (ORCID: https://orcid.org/0000-0002-7803-9664)
- Sabhrina Gita Aninta (ORCID: https://orcid.org/0000-0002-0736-4750)
- Michael P. Heaton (ORCID: https://orcid.org/0000-0003-1386-1208)
- Timothy P. L. Smith (ORCID: https://orcid.org/0000-0003-1611-6828)
- Dwi Sendi Priyono (ORCID: https://orcid.org/0000-0001-5828-7559)
- Anubhab Khan (ORCID: https://orcid.org/0000-0002-6342-6522)
- Corey J. A. Bradshaw (ORCID: https://orcid.org/0000-0002-5328-7741)
- Yuli Arif Tribudi (ORCID: https://orcid.org/0000-0002-7852-9452)
- Genís Garcia‐Erill (ORCID: https://orcid.org/0000-0003-3150-1708)
- Benjamin D. Rosen (ORCID: https://orcid.org/0000-0001-9395-8346)
- Amal Al‐Chaer
- Thomas Bøggild
- Xi Wang (ORCID: https://orcid.org/0009-0009-5146-8408)
- Reagan Cauble-Sims
Institutions
- Oklahoma State University (US)
- Tanjungpura University (ID)
- University of Copenhagen (DK)
- United States Department of Agriculture (US)
- Australian Research Council (AU)
- Universitas Gadjah Mada (ID)
- Queen Mary University of London (GB)
- Flinders University (AU)
- Utrecht University (NL)
- National Centre for Biological Sciences (IN)
- Aarhus University (DK)
- IPB University (ID)
- Tencent (China) (CN)
- Novo Nordisk Foundation (DK)
- Agriculture and Forestry University (NP)
- Copenhagen University Hospital (DK)
- University of Nusa Cendana (ID)
- University of Oxford (GB)
- North West Agriculture and Forestry University (CN)
- Beltsville Agricultural Research Center (US)
- Roman L. Hruska U.S. Meat Animal Research Center (US)
- Oxford Archaeology (GB)
- National Nuclear Energy Agency of Indonesia (ID)
- Indian Institute of Science Bangalore (IN)
- Ludwig-Maximilians-Universität München (DE)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-09-25
- DOI
- https://doi.org/10.1038/s41467-025-62692-z
- Citations
- 1
- Primary Topic
- Genetic and phenotypic traits in livestock
- Type
- article
- Field-Weighted Citation Impact
- 1.82