BackgroundTwo bovine species contribute to the Indonesian livestock, zebu (Bos indicus) and banteng (Bos javanicus), respectively. Although male hybrid offspring of these species is not fertile, Indonesian cattle breeds are supposed to be of mixed species origin. However, this has not been documented and is so far only supported by preliminary molecular analysis.Methods and FindingsAnalysis of mitochondrial, Y-chromosomal and microsatellite DNA showed a banteng introgression of 10–16% in Indonesian zebu breeds. East-Javanese Madura and Galekan cattle have higher levels of autosomal banteng introgression (20–30%) and combine a zebu paternal lineage with a predominant (Madura) or even complete (Galekan) maternal banteng origin. Two Madura bulls carried taurine Y-chromosomal haplotypes, presumably of French Limousin origin. In contrast, we did not find evidence for zebu introgression in five populations of the Bali cattle, a domestic form of the banteng.ConclusionsBecause of their unique species composition Indonesian cattle represent a valuable genetic resource, which potentially may also be exploited in other tropical regions.

Running title: Bali cattle breeding: state of the art ContentsBali cattle still represents 27% of the total cattle population in Indonesia, and it is considered the pillar breed for small farmers. Moreover, it is a breed of evolutionary importance regarding its direct ancestry from Banteng. However, there is a need for the establishment of a rational system for the evaluation of breeding soundness for indigenous Bali bulls to be used as sires for artificial insemination breeding programmes. Moreover, there is a need for cryobanking of well identified genetic resources pertaining their use in evolutionary research and application as essential germplasm in breeding programmes.Key words: livestock rearing, banteng, bali cattle, breeding, Indonesia. IntroductionCattle production in Indonesia is generally based on indigenous and imported breeds, the first named usually extensively managed on natural pasture. Bali cattle (Bos sondaicus, Bos javanicus, Bos/Bibos banteng), a domesticated descendant of the wild Banteng (Bibos banteng) represents about 27% of the total cattle population in Indonesia (about 11 million heads in 2004). Bali cattle is the most preferred in the small holding system, due to their rusticity, fertility and low calf mortality and breeding programmes have slowly been built in the country using artificial insemination (AI) with frozen-thawed semen from, largely, phenotypically-selected bull sires. Owing to the randomized application of expansion programmes, and the presence of ill-explored remnants of Banteng colonies in national parks, there is no detailed knowledge of the genetic complexity and purity of these individual species, a pre-requisite when cryobanking of genetic resources and/or their application in breeding programmes is to be attempted. BantengBanteng (Order: Artiodactyla, Family: Bovidae, Subfamily: Bovinae, Genus: Bos, Subgenus: Bibos), an endangered asian wild cattle, is most likely the ancestor to the domestic cattle of Southeast Asia (Nowak, 1991). Banteng is a sexually-dimorphic species, with mature males Swedish Links Indonesia Symposia 2010-2011-ChapterKM-GA-2011 2 being dark chestnut brown and cows and juveniles reddish brown. Both sexes have white rump patches and leggings, carry horns, the latter being much more heavier and larger in males. Adult male Bantengs weigh between 600 and 800 kg, while adult females range 590-670 kg. Their average lifespan in the wild is 11 years, although they can live to 20-25 years of age. It is very common for captive banteng to live into their late teens or mid-twenties. The world population of Banteng is considered to range 5-8,000 heads (2000 IUCN Red Data List) being located in Bangladesh, Brunei Darussalam, Cambodia, India, Indonesia (Kalimantan, Java and Bali), Lao People's Democratic Republic, Malaysia, Myanmar, Thailand and Viet Nam (see map) (Wilson and Reeder, 1993) The known subpopulations in the wild are small (5-6 stable subgroups in Java, having more than 50 Banteng/group) and decreasing in most countries (illegal hunting and ha...

Running title: Conservation genetics of Bali cattle. ContentsBoth Bos indicus (zebu) and Bos javanicus (banteng) contribute to the Indonesian indigenous livestock, which is supposedly of a mixed species origin, not by direct breeding but by secondary cross breeding. Here, the analysis of mitochondrial, Y-chromosomal and microsatellite DNA showed banteng introgression of 10-16% in Indonesian zebu breeds with East-Javanese Madura and Galekan cattle having higher levels of autosomal banteng introgression (20-30%) and combine a zebu paternal lineage with a predominant (Madura) or even complete (Galekan) maternal banteng origin. Two Madura bulls carried taurine Ychromosomal haplotypes, presumably of French Limousin origin. There was no evidence for zebu introgression in five populations of the Bali cattle, a domestic form of the banteng.