The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression

Xi Wang, Casia Nursyifa, Sabhrina Gita Aninta, Genís Garcia-Erill, Laura D. Bertola, Anubhab Khan, Josiah Kuja, Kristian Hanghøj, Jonas Meisner, Thomas Bøggild, Corey J. A. Bradshaw, Amal Al-Chaer, Alam Putra Persada, Dwi Sendi Priyono, Yuli A. Tribudi, Pita Sudrajad, Cynthia Dewi Gaina, Yu Jiang, Johannes A. Lenstra, Reagan Cauble-Sims, Benjamin D. Rosen, Darren E. Hagen, Michael P. Heaton, Timothy P. L. Smith, Laurent Frantz, Greger Larson, Mikkel-Holger S. Sinding, Dedy Duryadi Solihin, Muhammad Agil, Bambang Purwantara and Rasmus Heller ()
Additional contact information
Xi Wang: University of Copenhagen
Casia Nursyifa: University of Copenhagen
Sabhrina Gita Aninta: University of Copenhagen
Genís Garcia-Erill: University of Copenhagen
Laura D. Bertola: University of Copenhagen
Anubhab Khan: University of Copenhagen
Josiah Kuja: University of Copenhagen
Kristian Hanghøj: University of Copenhagen
Jonas Meisner: University of Copenhagen
Thomas Bøggild: University of Copenhagen
Corey J. A. Bradshaw: Flinders University
Amal Al-Chaer: University of Copenhagen
Alam Putra Persada: IPB University
Dwi Sendi Priyono: Universitas Gadjah Mada
Yuli A. Tribudi: Universitas Tanjungpura
Pita Sudrajad: National Research and Innovation Agency
Cynthia Dewi Gaina: Universitas Nusa Cendana
Yu Jiang: Northwest Agriculture and Forestry University
Johannes A. Lenstra: Utrecht University
Reagan Cauble-Sims: Ten Triple X Ranch
Benjamin D. Rosen: Animal Genomics and Improvement Laboratory
Darren E. Hagen: Oklahoma State University
Michael P. Heaton: U.S. Meat Animal Research Center
Timothy P. L. Smith: U.S. Meat Animal Research Center
Laurent Frantz: Ludwig Maximilian University
Greger Larson: University of Oxford
Mikkel-Holger S. Sinding: University of Copenhagen
Dedy Duryadi Solihin: IPB University
Muhammad Agil: IPB University
Bambang Purwantara: IPB University
Rasmus Heller: University of Copenhagen

Nature Communications, 2025, vol. 16, issue 1, 1-19

Abstract: Abstract 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-62692-z Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62692-z

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-62692-z

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().