Mitochondrial 12S rRNA has proven to be a useful molecular marker for better conservation and management of the endangered species. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the mitochondrial 12S rRNA gene has proven to be a reliable and efficient tool for the identification of different Indian deer species of family cervidae. In the present study, mitochondrial 12S rRNA gene sequence of mouse deer (Moschiola indica) belonging to the family Tragulidae was characterized and analysed in silico for its use in species identification. Genomic DNA was isolated from the hair follicles and mitochondrial 12S rRNA gene was amplified using universal primers. PCR product was cloned and sequenced for the first time. The sequence of mouse deer showed 90.04, 90.08, 90.04, 91.2, 90.04, and 90.08% identities with sika deer, sambar, hog deer, musk deer, chital, and barking deer, respectively. Restriction mapping in Lasergene (DNAstar Inc., Madison, WI, USA) revealed that mouse deer mitochondrial 12S rRNA gene sequence can be differentiated from the other deer species in PCR-RFLP using RsaI, DdeI, BsrI, and BstSFI. With the help of predicted pattern, mouse deer can be identified using genomic DNA from a variety of biomaterials, thereby providing molecular aid in wildlife forensics and conservation of the species. 1. Introduction Use of different molecular markers has evolved as a powerful tool in species identification. Earlier, techniques like liquid chromatography [1], immunoassay [2], electrophoresis [3], and so forth were used in species identification. In recent years, use of DNA has been popularized due to its specificity and stability. Among types of DNA [4, 5], mitochondrial DNA has been used extensively due to high copy number of mitochondria in cell. Mitochondria follow clonal inheritance [6] as only mother to contributes to mitochondria; its genome does not undergo recombination; thus, genetic material will be passed onto the next generation unchanged. Reports also suggest that mitochondrial genome is accumulating high percentage of neutral mutations which is helpful in species identification. Different mitochondrial genes have been used in species differentiation. PCR amplification of cytochrome b gene has been used in differentiation of meats from buffalo, emu, and crocodile [7]. Cytochrome b has also been used in differentiation of processed products like canned tuna, vegetable oil, and tomato sauce [8]. Other mitochondrial genes like 12S and 16S rRNA are extensively used in mammalian species identification. Numerous
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