World Journal of Fish and Marine Sciences 4 (4): 430-435, 2012 ISSN 2078-4589 © IDOSI Publications, 2012 Corresponding Author: Suresh Chandra, Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research (ICAR), Bhimtal-263136, Nainital, Uttarakhand, India. Tel: +91-9696692623. 430 DNA Bar-Coding of Indian Coldwater Fishes of Genus Schizothorax (Family: Cyprinidae) from Western Himalaya Suresh Chandra, Ashoktaru Barat, Mahender Singh, Birender Kumar Singh and Rakesh Matura 1 1 2 3 1 Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research, 1 (ICAR), Bhimtal-263136, Nainital, Uttarakhand, India International Centre for DNA Barcoding, National Bureau of Fish Genetic Resources, 2 (ICAR), Dilkusha, Lucknow-226002, (U.P.), India Department of Zoology, Kumaun University, Nainital, Uttarakhand, India 3 Abstract: The rapid and accurate characterization of species using morphological data is a critical constraint. To overcome this, species identification using molecular tools has been supplemented in many studies in present era. The present study was designed to test the utility of Cytochrome Oxidase I (COI) DNA barcodes for the identification of two commercially important coldwater species of Genus Schizothorax (Snow trout), Family Cyprinidae, from Uttarakhand Himalayas. COI gene (655 bp) was amplified using PCR and sequenced. The mean intra-specific nucleotide sequence divergence was 1.75% (range 0.00-3.50%) and inter-specific divergence of S. richardsonii is 0.00% (range 0.00040-0.00080%) and S. progastus is 0.00% (range 0.00036- 0.000206), respectively. Although, DNA bar-coding aims to develop species identification systems, some phylogenetic signal was apparent in the data. It was concluded that COI sequencing or ‘bar-coding’, was found to be suitable for the identification of coldwater fish species. Key words: Cytochrome Oxidase Subunit I %Bar-coding %Fish %MtDNA %Schizothorax INTRODUCTION by a particular sequence or by a tight cluster of very Accurate and unambiguous identification of fish Species identification by DNA bar-coding is based and fish products, from eggs to adult, is important in on sequencing a short standardized genomic region of the many areas. It would enable retail substitutions of target specimen and comparing this information to a species to be detected, assist in managing fisheries for sequence library from known species. The proposed long-term sustainability and improve ecosystem standard barcode sequence for animal species is a 650-bp research and conservation. Hitherto, a wide variety of fragment of the mitochondrial gene cytochrome c oxidase protein and DNA based methods have been used for I (COI). Many benefits of DNA bar-coding for species the genetic identification of fish species [1-4]. DNA identification and discovery have been discussed [6], sequence analysis has been used for 30 years to assist although the concept continues to be hotly debated [7]. species identifications, but different sequences have In addition to species identification, the construction of been used for different taxonomic groups and in barcode database could expose novel DNA barcodes that different laboratories [5]. Proposed that a single gene may indicate provisional new species [8]. Genetic sequence would be sufficient to differentiate all, or interrelationships of Cyprinid subfamilies have been at least the vast majority of, animal species and extensively investigated from morphological, anatomical proposed the use of the mitochondrial DNA gene and molecular perspectives [9-12]. Two studies mainly cytochrome oxidase subunit I (COI) as a global bio- based on morphological and anatomical characters have identification system for animals. The sequence was investigated phylogenetic relationships among genera likened to a barcode, with species being delineated and species and explored the taxonomic status of these similar sequences.