The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers

Abstract

Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: NeighborJoining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.

Sequence variation of captive Malayan Gaur (Bos gaurus hubbacki) based on mitochondrial D-loop region DNA sequences

“…DNA was extracted from these samples using QIAGEN QIAamp DNA Micro Kit and amplified with Polymerase Chain Reactions (PCRs) using an Eppendorf Mastercycler. One pair of specific primers were used to amplify the D-loop region: Walid F (TCA CCG TCA ACT CCC AAA GCT GA) and Walid R (AGG GGG AAG TTT TAT GGA AGG GGG) (Syed-Shabthar et al 2013). PCR components used in this study were Taq DNA polymerase (5 U/µL), 10X PCR Buffer, 50 mM MgCl 2 and 10 mM dNTP.…”

“…All the phylogenetic tree topologies showed a significant separation between the outgroup (bison and water buffalo) and the ingroup (Malayan gaur). The outgroup was selected based on previous studies that also used the Bos genus in their studies (Rosli et al 2011(Rosli et al , 2016Syed-Shabthar et al 2013). For the NJ tree, clade A was formed by the separation of bison from Malayan gaur, supported with a 100% bootstrap value.…”

“…Mitochondrial DNA (mtDNA) of the displacement loop (D-loop) region was chosen because this locus has a potential for molecular studies at the population level (Ang et al 2011;Ang et al 2012;Abdul-Latiff et al 2014a;Md-Zain et al 2017). The Dloop region has a high mutation rate compared to other mtDNA regions and has the ability to provide high resolution data on phylogenetic relationships (Syed-Shabthar et al 2013). Thus, the main objective of this study is to infer the sequence variation in the mtDNA D-loop region of B. g. B I O DI VE RS I T A S 19 (5): 1601-1606, September 2018 1602 hubbacki in captivity with a focus on the two captive centers.…”

Phylogenetic tree of Kuantan cattle by DNA barcoding

“…Some research reports using DNA barcode on birds (Herbert et al 2004), Indonesian local cattle (Febriana 2011), chicken (Gao et al 2011), cetartiodactyla (Zein & Fitri 2012), bali cattle (Syed-Shabthar et al 2013) and Indonesian local buffalo (Saputra et al 2013) has been reported.…”

A New Subspecies Identification and Population Study of the Asian Small-Clawed Otter (Aonyx cinereus) in Malay Peninsula and Southern Thailand Based on Fecal DNA Method

“…However, fecal samples are important in studies that require DNA sources from risky or highly endangered subjects before samples are collected in the wild [4, 9]. With several nonconventional DNA extraction kits and enhanced PCR chemicals available today, DNA analysis of fecal sources is no longer impossible [10]. In this study, we focused on extracting DNA from fecal samples that are believed to be otter feces, collected from several regions, to identify species.…”