Evolution is the source of the huge variation between and within species worldwide. All species are related to each other through a common origin and new species will develop in the future from the existing species nowadays. Modern biology defines evolution as the differences in allele frequencies over time and these differences can be used for characterization of populations. In this study the genetic variability between different indigenous cattle breeds in Indonesia were investigated. For this purpose, genomic and mitochondrial DNA from160 cattle from the Aceh province, 10 Bali cattle, two Madura cattle, two Pesisir cattle and two Ongole descendent were used. For the analysis of the species origin, 20 microsatellite markers in the genome were used and tracing of maternal lineage and history of the herd was performed by analysis of the mitochondrial DNA (mtDNA), D-loop. The microsatellites were polymorphic in all breeds, ranging from two to twelve detected alleles with the exception for the Banteng where HEL 13 and INRA35 were monomorphic. Mean heterozygosity computed across the 16 loci for each breed ranged between 0, 3924 (Banteng) and 0, 7860 (Ongole). The inbreeding coefficient FIS which indicates within breed genetic variation ranged from 0, 08851 (Pesisir) to 0, 14251 (Madura). In the Neighbor Joining tree, genetic relationships among the mtDNA sequences revealed that all samples with different origin clustered together, Bos taurus, Bos indicus, Bos banteng. In the median joining network the sequences with Bos indicus origin grouped into two star-like clusters with predominant haplotypes in the centres. The two clusters are separated by four mutations and one haplotype unique for the Aceh cattle. In summary, Banteng, the endangered ancestor of Bali cattle, exhibited low genetic variation compared with the other breeds in the study. The Aceh cattle showed highest level of genetic variation and is probably a breed which has been created using a large par...
