http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–7 ! 2013 Informa UK Ltd. DOI: 10.3109/19401736.2013.823170 RESEARCH ARTICLE Genetic characterization of Golden mahseer (Tor putitora) populations using mitochondrial DNA markers Jyoti Sati, Rohit Kumar, Prabhati Kumari Sahoo, Rabindar S. Patiyal, Shahnawaz Ali, and Ashoktaru Barat Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal, Nainital, Uttarakhand, India Abstract Golden Mahseer (Tor putitora) is an economically important fish of India and Southeast Asia. The present study examined the genetic variations between seven geographically isolated populations of T. putitora using Cyt b (Cytochrome b) and ATPase6/8 gene sequences of mitochondrial DNA. Analysis of 133 sequences of Cyt b (1141 bp) and 130 sequences of ATPase6/8 gene (842 bp) revealed 47 and 44 haplotypes, respectively. The estimated haplotype and nucleotide diversity was high in River Jia Bhoreli (Bhalukpong) population (h ¼ 1.00000,  ¼ 0.007121 for Cyt b and h ¼ 0.90441  ¼ 0.004867 for ATPase6/8). Results of AMOVA indicated that majority of the genetic variations in both genes were due to variation among populations (60.79% for Cyt b and 51.41% for ATPase6/8 gene). The pairwise F ST comparison and neighbor-joining tree revealed high genetic divergence of River Jia Bhoreli population from other populations. The understanding of genetic variations of T. putitora populations will play a key role in conservation and management of this endangered fish species. Keywords ATPase6/8, cytochrome b, genetic differentiation, haplotype diversity, nucleotide diversity History Received 1 May 2013 Revised 13 June 2013 Accepted 22 June 2013 Published online 10 September 2013 Introduction The Golden Mahseer (Tor putitora, Family: Cyprinidae) is an economically important cold water fish of the Himalayan region. It is an important food as well as game fish distributed in the large rivers, lakes and reservoirs all along the Eastern, Western and Central Himalayas (Islam & Tanaka, 2007). Presently the natural stock of T. putitora in various ecosystems has declined due to various anthropogenic effects such as loss of habitat, excessive fishing pressure and pollution (Nautiyal et al., 1994, 1996). At present it is assigned the status of ‘‘endangered’’ in IUCN red list of threatened species (Jha & Rayamajhi, 2010). Thus, the conservation and maintenance of natural stock of this fish species is very essential. The careful selection of appropriate wild stock based on genetic diversity can offer immense potential for species-recovery and stock management. In recent years, different molecular tools have been successfully used to characterize the fish populations (Yoon & Park, 2002). It was observed through comprehensive literature survey that genetic variability in T. putitora populations were studied so far using different molecular markers viz. allozymes, microsatellite and rRNA markers (Gopalakrishnan et al., 2008; Mohindra et al., 2004; Singh et al., 2009). However, genetic studies based on mtDNA markers were not reported as far as we are aware. Mitochondrial DNA (mtDNA) markers show maternal mode of inheritance and are highly variable. They have been used to study genetic differentiation and phylogenetic relationships between species and populations (Avise et al., 1987; Briky et al., 1983; Faulks et al., 2008; Ferguson & Danzmann, 1998). Mitochondrial DNA markers such as Cyt b and ATPase6/8 genes have been used by researchers for population studies in several fish species (Luhariya et al., 2012; Xin-ong et al., 2004). The earlier reports on genetic diversities of Labeo rohita populations by using Cyt b (Luhariya et al., 2012) and Channa marulius populations by ATPase 8 and ATPase 6 genes (Habib et al., 2012) have highlighted the usefulness of these markers for assessing genetic variation at intrapopulation and interpopulation level. In the present study, we attempted to assess genetic variability and to construct a dendogram of seven populations of T. putitora with respect to nucleotide sequence variations of Cyt b and ATPase6/8 genes. This information will provide some important insight into present genetic status of T. putitora, which will ultimately help in drawing appropriate strategies for conservation and stock improvement program. Materials and methods Sample collection Live specimens of T. putitora were collected from seven different geographically isolated locations of India namely River Jia Bhoreli (Bhalukpong, Assam), River Satluj (Bhakara, Himachal Pradesh), River Beas (Jogindernagar, Himachal Pradesh), River Kosi (Ramnagar, Uttarakhand), Walwhan dam (Lonavala, Maharashtra), River Chenab (Anji, Jammu & Kashmir) and River Ravi (Basoli, Jammu & Kashmir) during April 2009 to May 2011 (Table 1, Supplementary 1: Geographical locations of Sampling sites). Fin tissues were collected by non-invasive technique (Wasko et al., 2003) followed by proper antiseptic treatment of organism before they were reverted to their habitat. All the fishes were handled according to the approved guide line of Directorate of Coldwater Fisheries Research ethical committee. Caudal fin samples were preserved in 2 ml vials containing 75% ethanol and stored in 20  C till further processing. Correspondence: Dr. Ashoktaru Barat, PhD, Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, Indian Council of Agricultural Research, Bhimtal 263136, Nainital, Uttarakhand, India. Tel: +91 5942 247280. Mobile: +91 9410341899. Fax: +91 5942 247693. E-mail: abarat58@hotmail.com Mitochondrial DNA Downloaded from informahealthcare.com by Texas State Univ San Marcos on 09/20/13 For personal use only.