Species identification, molecular sexing and genotyping using non‐invasive approaches in two wild bovids species: Bos gaurus and Bos javanicus

Abstract

Since the second Indochina war, habitat destruction and overhunting has resulted in fragmentation of the remaining populations of Bos javanicus and B. gaurus. Nowadays, both species are in serious danger, especially the gaur. In Vietnam, where these species have become almost impossible to capture in the wild, noninvasive investigations are the only feasible approach to obtain data on populations. However, non-invasive derived DNA, especially in tropical areas, is usually characterized by low concentrations, poor quality and/or contamination from alien DNA. To assist in tropical conservation management, baseline information is provided here on assessing the reliability of species identification, molecular sexing and microsatellite genotyping using fecal DNA from B. gaurus and B. javanicus. For species identification using bovine fecal samples, cytochrome b fragment between positions 867 and 1140 was found to contain species diagnostic sites, which distinguishes the four species encountered in the region: B. gaurus, B. indicus, B. javanicus and B. taurus. For sex determination, primers were initially tested on DNA obtained from blood. Then, these primers were successfully used on DNA derived from fecal material. Finally, we also evaluate the feasibility of non-invasive microsatellite genotyping on fecal samples collected in Vietnamese nature reserves. The results presented here improve on current molecular methods based on fecal material obtained from tropical areas.

Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences

“…This is due to the higher variation of the Cyt b gene as compared to that of other functional areas, the fact that it is detected easily and the availability of high-definition phylogenetic information, especially for species level classification (Irwin et al, 1991). In the Bovinae tribe, Cyt b has been used for the determination of phylogenetic relationships of gayal (Ma et al, 2007), investigation of the taxonomic status of kouprey (Hassanin and Ropiquet, 2004), in the study of species identification, molecular sexing and genotyping of gaur and banteng (Rivière-Dobigny et al, 2009) and related species (Verkaar et al, 2004). However, only few studies have used molecular techniques on the Malaysian subspecies of gaur (Brennan, 1995).…”

A new high-frequency allele of the BM2113 locus in the Yunnan mithun population

“…Allele 121 bp was absent in European cattle breeds (MacHugh et al, 1997), Brazilian Gir (Bicalho et al, 2006), Vietnamese cattle and wild gaur (Nguyen et al, 2007), Indian Kangayam cattle (Karthickeyan et al, 2009), Colombia Brahman cattle (Novoa and Usaquén, 2010), Uruguayan Creole cattle (Armstrong et al, 2013), Mongolian and Russian yak (Xuebin et al, 2005), Swiss yak (Nguyen et al, 2005), and Chinese yak (Liao et al, 2008;Zhang et al, 2008). No detailed data were shown for other bovid species in the previous studies on the BM2113 locus (Kantanen et al, 2000;Ritz et al, 2000;Kim et al, 2002;Zhang et al, 2007aZhang et al, ,b, 2011Mao et al, 2008;Wang et al, 2008;Rivière-Dobigny et al, 2009;Li and Kantanen, 2010;Azam et al, 2012). Herein, the PIC value was high and had a mean of 0.6170, the expected and observed heterozygosity was moderate with values of 0.6427 and 0.6000, respectively, and the BM2113 locus was in H-W equilibrium (P = 0.2897) in the Yunnan mithun population.…”

Detection of parasitizing coccidia and determination of host crane species, sex and genotype by faecal DNA analysis

“…Recently, a noninvasive molecular approach, in which samples such as hair and faeces were collected and used to obtain DNA, has been employed to determine species, sex and microsatellite genotyping of some animals (e.g. Hedmark et al 2004;Bhagavatula & Singh 2006;Rivière-Dobigny et al 2009). To our knowledge, such an approach has been applied to only wild apes during infectious disease research (Keele et al 2006;Liu et al 2010).…”