In Indonesia, cattle are not just cattle. The large island-nation houses a variety of different breeds, locally preferred for their unique set of physical attributes and strongly linked to culture and ceremonies. There is even a distinct species of domesticated bovine here, namely the Bali cattle, a domesticated version of the wild banteng (see Box 1). Little is known about the history of cattle in this archipelago, which is positioned at a crossroad between major historical trading empires and cultures, notably India and China. Local cattle are known to carry genetic ancestry from both zebu cattle (Box 1) and banteng, but their proportions and which genes derive from each ancestral species remain unknown. It is also not known when, why and how this mixing took place.
A new study led by researchers from University of Copenhagen and IPB University sheds light on these questions by generating the first whole-genome data from Indonesian cattle, including six local breeds and several populations of Bali cattle.
“We were quite surprised to find that cattle were most likely not introduced from India, which was a significant cultural and mercantile influence around the era of Hindu-Buddhist kingdoms in the beginning of Indonesia’s historical period, but rather from mainland Southeast Asia. These mainland cattle were coming into Indonesia via at least two different waves, one into Sumatra and one into Java,” says Sabhrina Gita Aninta, a postdoc involved in the study from the Department of Biology. “This knowledge redefines our understanding of the cultural and maritime links in Asia around the start of the Common Era and suggests that Southeast Asia had more internal connectivity than previously believed.”
The researchers also investigated which parts of the individual Indonesian cattle genomes originate from a zebu and which from a banteng.
“We found that different breeds have different amounts of banteng genetics, with one breed - the Madura - having up to 36% of banteng ancestry. This makes the Madura effectively a hybrid between two different species, and totally unique in the world. Due to this high amount of banteng genetics, Madura cattle are also the most genetically diverse cattle in the world. They carry more than 3.5 million new genetic variants that are currently unknown to cattle geneticists around the globe,” says Associate Professor Rasmus Heller from UCPH, lead author on the study.
If the function of these new genetic resources can be catalogued, they could help genetically improve cattle elsewhere by modern breeding techniques (Box 2). For example, some of these genetic variants could have a positive impact on disease resistance, productivity under tropical conditions, or even greenhouse gas emissions. All of which would be immensely beneficial to the environment and to economies, as the cattle population in the tropics is predicted to grow substantially to feed a growing demand.
“Our results also help us understand which genetic variants can be introduced from other bovine species into cattle, by presenting us with a valuable ‘natural experiment’ running over about 1500 years, and showcasing which banteng variants have been retained, and which have been removed by natural selection in the admixed Indonesian cattle,” says Sabhrina.
These results are of immense significance for Indonesia - they provide the first whole-genome data from a severely understudied, and highly unique cattle system. Cattle genomics in Europe, India, China, the Americas and even Africa have been studied quite extensively, but Southeast Asian cattle have so far been omitted.
“With these data and results in hand, we have formed a baseline for future genomic studies on Indonesian cattle and answered many open questions about how the different breeds came to be what they are. I have no doubt that these findings will be the starting point for much fascinating research on Indonesian cattle and showcase how understudied local cattle can hold the key to important global questions,” says Professor Bambang Purwantara from IPB University, a co-author on the study.
The study is a collaboration between the University of Copenhagen and IPB University, with contributions from several other Danish, Indonesian, Australian, Indian, Chinese, American and European research institutions. It was funded mainly by the Independent Research Fund Denmark and the European Research Council. The scientific paper for this study is published in the renowned journal Nature Communications.
Nature Communications
The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression
25-Sep-2025