Population structure and domestication history of the Javan banteng

Authors: WANG, XI - University Of Copenhagen; ANINTA, SABHRINA - University Of Copenhagen; GARCIA-ERILL, GENIS - University Of Copenhagen; LI, ZILONG - University Of Copenhagen; KHAN, ANUBHAB - University Of Copenhagen; LIU, XIAODONG - University Of Copenhagen; BERTOLA, LAURA - University Of Copenhagen; DHARMAYANTHI, ANIK - Collaborator; YULIANTO - Collaborator; YONATHAN - Collaborator; ROSSI, CONOR - Trinity College Dublin; CAUBLE-SIMS, REAGAN - Texas State University; Rosen, Benjamin; HAGEN, DARREN - Oklahoma State University; Heaton, Michael; Smith, Timothy; LENSTRA, JOHANNES - Utrecht University; MARTINS, NUNO - University Of Copenhagen; SINDING, MIKKEL-HOLGER - University Of Copenhagen; AGIL, MUHAMMAD - Collaborator; HELLER, RASMUS - University Of Copenhagen

Submitted to: Current Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/27/2025
Publication Date: 1/19/2026
Citation: Wang, X., Aninta, S.G., Garcia-Erill, G., Li, Z., Khan, A., Liu, X., Bertola, L.D., Dharmayanthi, A.B., Yulianto, Yonathan, Rossi, C., Cauble-Sims, R., Rosen, B.D., Hagen, D.E., Heaton, M.P., Smith, T.P., Lenstra, J.A., Martins, N.F., Sinding, M.S., Agil, M., Heller, R. 2026. Population structure and domestication history of the Javan banteng. Current Biology. 36(2):458-473. https://doi.org/10.1016/j.cub.2025.11.076.
DOI: https://doi.org/10.1016/j.cub.2025.11.076

Interpretive Summary: Current domesticated dairy cattle production breeds originated in Europe and are not adaptable and productive across all environments found in the U.S. Understanding the genes conveying important production traits for dairy cattle is necessary to ensure these desired production traits can be introduced into breeding programs. In this study, we evaluated the genetic makeup of cattle thriving in a warm, humid environment. There have been multiple events leading to the domestication of cattle across the globe, including the domestication of banteng in Southeast Asia. Little is known about the genes of this close relative of modern cattle. We sequenced the DNA of banteng to generate the first standardized representation of its genome. This digital representation of all the genes for banteng cattle was used to identify 54 genes potentially important in the transition from wild banteng to domesticated cattle. The findings are of interest to farmers and ranchers, as knowledge of genes responsible for desired traits can be used in breeding programs to propagate healthier, more productive livestock, potentially increasing profits. For instance, the identification of variation in the leptin receptor gene, known for roles in metabolism and energy balance may provide farmers new targets for future breeding programs. Moreover, this research aids scientists in understanding cattle adaptation to different environments and may help design improved breeding strategies.

Technical Abstract: The domestication of the banteng in Southeast Asia is one of the least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome sequenced samples of which three are historical samples. We found low heterozygosity and pervasive differentiation, the latter primarily driven by recent genetic drift and inbreeding in two populations, which are clearly attributable to man-made founder events or keeping in captivity. Disregarding this, population structure was limited, and we found that the evolutionary divergence between wild and domestic banteng is limited (FST = 0.14), relatively young (10,356 years), and with post-divergence gene flow. We also found only weak signals of a domestication bottleneck between ~6100-2900 years ago, and genetic diversity is on average higher in domestic than in wild banteng. Despite the soft domestication history, we found 54 candidate genes under selection during domestication, with the leptin receptor gene (LEPR) of particular interest due to the robust selection signal across methods, and its known association to metabolism, obesity and energy homeostasis. Finally, genetic load estimation revealed that Bali cattle in Australia have high realized load, while Bali cattle from Bali have high masked load. These findings provide the first genomic insights into an understudied bovine that is Critically Endangered in its wild form, and agriculturally important in its domesticated form.