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."
Discovering a hybrid cattle breed
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.
Understudied cattle can hold solutions to global problems
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.
Box 1: The cattle of Indonesia
- Indonesia has a large number of recognized cattle breeds, each typically the preferred one in a particular region or island, while some others are more widespread through the archipelago. The ones included in this study are: Aceh and Pesisir from Sumatra; Pasundan, Jabres and Madura from Java; Ongole from Sumba.
- Cattle often play significant cultural roles in the local community, e.g. Madura cattle have been used for centuries for rice field racing (kerapan sapi) and highly ritualized beauty contests (sonok).
- In addition to these, Indonesia also has its own unique livestock species, namely the Bali cattle, which is a domesticated form of the wild and critically endangered bovine species, the banteng. Bali cattle are the most popular and widespread bovine type in Indonesia, as it is hardy and able to thrive under tropical conditions and with low-quality feed.
Box 2: Genomics in cattle breeding
- Genomic data is increasingly used in livestock breeding to e.g. predict the breeding value of a given individual. These techniques have for example dramatically increased the amount of milk produced by European dairy cattle in recent decades.
- Genomic data can also be used to identify specific genetic variants associated with desirable traits, e.g. disease resistance, growth, or even methane emission. These can then be spread in the population either by selective breeding or by genetic engineering.
- Despite the utility of genomic data in improving livestock, tropical livestock is severely underrepresented in genomic catalogs of existing variation. This means there are probably many unknown, but potentially useful, genetic variants segregating among understudied cattle.
- Unfortunately, local cattle breeds are under pressure everywhere as highly productive cattle from e.g. Europe are being introduced into tropical settings where they may produce short-term gains but are likely to lead to a loss of cattle genetic resources over time, making the global cattle gene pool smaller and less diverse.
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.
