BIODIVERSITAS ISSN: 1412-033X Volume 20, Number 1, January 2019 E-ISSN: 2085-4722 Pages: 17-22 DOI: 10.13057/biodiv/d200103 Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences TETY HARTATIK 1,♥ , DWI NUR HAPPY HARIYONO 1 , YUDI ADINATA 2 1 Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada. Jl. Fauna No. 3, Bulaksumur, Depok, Sleman 55281, Yogyakarta, Indonesia. Tel.: +62-274-4333373, Fax.: +62-274-521578, ♥ email: tety@ugm.ac.id, tetyharuta@yahoo.com 2 Beef Cattle Research Station. Jl. Pahlawan, Grati, Pasuruan 67184, East Java, Indonesia Manuscript received: 9 July 2018. Revision accepted: 1 December 2018. Abstract. Hartatik T, Hariyono DNH, Adinata Y. 2019. Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas 20: 17-22. Genetic diversity and phylogenetic relationships of two Indonesian local cattle breeds (Pasundan and Pacitan cattle) were investigated using mitochondrial DNA (mtDNA) cytochrome b (cyt b) gene analysis. Partial sequences of cyt b gene, 404 bp in length, were determined for 21 individuals from the two breeds. Genetic diversity of the breeds was assessed based on the number of polymorphic sites, number of haplotypes, haplotype diversity, nucleotide diversity and average number of differences. In addition, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura’s two-parameter model. Among the two breeds, haplotype and nucleotide diversity of Pacitan cattle were the highest with values of 0.3778 and 0.00099, respectively. In contrast, Pasundan cattle had the lowest value for haplotype (0.1818) and nucleotide (0.00045) diversity. Four haplotypes (Hap_16, Hap_17, Hap_18 and Hap_19) were found across the two breeds and around 85.71% of investigated individuals were classified as Hap_16. Phylogenetic analysis with the inclusion of the cyt b sequences from 39 cattle breeds from Genbank database, showed that Indonesian cattle made a separated lineage together with Bos javanicus, B. bison, and B. bonasus. Pasundan and Pacitan cattle were considered from the same lineage based on haplotype distribution as well as phylogenetic analysis. This study may help the future researchers and livestock breeders for designing a breeding program based on a better understanding of the genetic diversity and history of local breeds. Keywords: Cytochrome b, Genetic diversity, Indonesian cattle, mtDNA, phylogenetic analysis INTRODUCTION During its uncertain history, a number of local cattle breeds have contributed to the Indonesian livestock industry to date. Mostly, Indonesian local cattle breeds are descendants of the Indian zebu (Bos indicus) and banteng (B. javanicus) (Mohamad et al. 2009). As a part of the local cattle breeds in Indonesia, Pasundan and Pacitan cattle are known for being well adapted to harsh environmental conditions with fluctuation in feed quality. Pasundan cattle (B. javanicus x B. indicus) are commonly found in the province of West Java particularly in Ciamis (Sutarno and Setyawan 2015). Whereas, Pacitan cattle are bred across Pacitan of East Java. Their role is clear, they provide a source of immediate income and food for households. To date, for the sustainable use of livestock breeds, there are major barriers and mostly, these are probably due to lack of information regarding the existing local breeds or populations, geographical locations and genetic characteristics (Long 2008). In addition, current proper strategies for livestock utilization mainly depend on the deep understanding of genetic variation, which exists within and between breeds. In both Pasundan and Pacitan cattle, no molecular information is available so far. A considerable effort has focused on molecular characterization in major cattle breeds in Indonesia, such as Bali (Winaya et al. 2009; Hartatik et al. 2015; Septian et al. 2015; Sutarno et al. 2015) and Madura cattle (Hartatik et al. 2013). With the advanced growth of molecular techniques, employment of molecular markers will be the best approach to understand the existing genetic variation of the analyzed local breeds. Mitochondrial DNA (mtDNA) represents only a tiny fraction of organism genome size, yet it has been by far the most popular marker of molecular diversity in animals over the last three decades (Galtier et al. 2009). From a populational perspective, it could be considered as a system of small, sexually isolated demes, or clonal lineages, with an evolutionary rate 5 to 10 times faster than the nuclear genome, and such characteristics, therefore, make this molecule ideal for evolutionary studies (Castro et al. 1998). In mtDNA, the cytochrome b (cyt b) gene contains abundant phylogenetic information among intra- and interspecies and it is considered to be a good marker to study the genetic differentiation as well as phylogenetic relationships among species within the same genus or the same family (Browers et al. 1994; Zardoya and Meyer 1996). The mtDNA has been proven to be useful markers for elucidating genetic diversity and relationships of domestic animals including chicken, goat, pig, horse, and cattle (Zhu et al. 2014; Sepehri and