Optimization of DNA from Musk Deer (Moschus chrysogaster) Hair Follicle: extraction, PCR Amplification for discriminatory analysis of RAPD markers
Paper Details
Optimization of DNA from Musk Deer (Moschus chrysogaster) Hair Follicle: extraction, PCR Amplification for discriminatory analysis of RAPD markers
Abstract
Of 62 hair follicle samples of Himalayan musk deer ((Moschus chrysogaster) collected by hair-snares appreciable quantity of DNA was isolated from 60.70%. Largest quantity of DNA (220.11±15.09ng/µL) was obtained by modified phenol-chloroform method, followed by phenol-chloroform (199.13±11.09ng/µL) and Qiagen kit (146.34 ±20.42ng/µL) methods. The qualities of extracted DNA by Qiagen kit and modified phenol-chloroform method were not significantly different within (paired t =1.68, df =33, P≥ 0.05; paired t=1.75, df=33, P≥0.05) but significantly higher (paired t=2.56, df=33, P≤0.05) than phenol-chloroform. Of 35 RAPD markers tested, 29 amplified. Optimal conditions varied for responding for PCR-amplification, as optimum concentration of: MgCl2; ranged minimum 1.5mm, 4 (13.79%) to maximum 2.5mm (6.89%), template DNA; ranged 30-50ng/µL, primer; majority,0.25 (16, 55.17%) to 0.15 (6, 20.68%), by using of A PCR profiles (Ta=26oC -37oC) for better and consistent amplification. Polymorphic information content (PIC) found higher (FA-18; 0.54) and lower (FA-9; 0.07) with resolution power (Rp) ranged 13.14-32.22. RAPD marker loci and molecular indices suggested significant correlation between PIC and Rp; (r2=0.95; P≤0.01), followed MI and PIC; (r2=0.67; P≤0.05) and MI and Rp (r2=0.63: P≤0.05). The probability of identical by chance ranged between 0.0012 (OPA-20) and 0.0357 (FA-14), and total probability by multiplying of 4.234 × 10-61. However, discriminatory indices of RAPD markers are indicative of high resolution and have potentials of significance, for using in DNA finger printing which can be employed for efficient identification, conservation and breeding approaches of musk deer.
Akram A. 2010. Optimization of the conditions for the assessment of genetic diversity in Asiatic bears. M. Phil. Thesis (Unpublished) Dept. of Zoology., PMAS Agri. Univ. Rawalpindi, Pakistan. 63pp.
Allen M, Engstrom AS, Meyers S, Handt O, Saldeen T, Haeseler A, Paabo S, Gyllensten U. 1998. Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. Journal of Forensic Sciences 43, 453-464.
Avise JC. 2004. Molecular markers, natural history and evolution. Sinauer Associates, Sunderland, Massachusetts. Banhos, A., Hrbek,
CITES. 2008. Appendices I, II and III. Convention on International Trade in Endangered Species of Wild Fauna and Flora. Official documents. UNEP Lausanne, Switzerland.
Dhikari S, Saha S, Biswas A, Bandyopadhyay TK, Ghosh P. 2017. Randomly primed improved PCR approach for genetic characterization and identification of Cymbopogon germplasms. Rendiconti Lincei 28(2), 379-392.
Eggert LS, Maldonado JE, Fleischer RC. 2005. Nucleic acid isolation from ecological samples-animal scat and other associated materials. Methods in Enzymology 395, 73-87.
Emara MG, Kim H. 2003. Genetic markers and their application in Poultry Breeding. Poultry Science 82, 952-957.
Exadactylos AA, Geffen J, Panagiotaki P, Thorpe JP. 2003. Population structure of Dover sole Solea solea: RAPD and allozyme data indicate divergence in European stocks. Marine Ecology Progress Series 246, 253-264.
Fernandez M, Figueiras A, Benito C. 2002. Theoretical and Applied Genetics 104, 845.
Foran DR, Crooks KR, Minta SC. 1997. Species identification from scat: an unambiguous genetic method. Wildlife Society Bulletin 25(4), 835-839.
Gagneux P, Boesch C, Woodruff DS. 1997. Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Molecular Ecology 6, 861-868.
Goossens B, Waits LP, Taberlet P. 1998. Plucked hair samples as a source of DNA: reliability of dinucleotide microsatellite genotyping. Molecular Ecology 7, 1237-1241.
Guan T, Zeng B, Peng Q, Yue B, Zou F. 2009. Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation. Biochemical Systematics and Ecology 37, 166-173.
Huifang B, Hongfa X, Houji L. 1999. Studies on forest musk deer and alpine musk deer using random amplied polymorphic DNA (RAPD). Acta Theriologica Sinica 4, 241-246.
Janis CM, Scott KM. 1988. The phylogeny of the Ruminantia (Artiodactyla, Mammalia). In: The phylogeny and classification of the tetrapods, Mammals. M. J. Benton (Ed.). Vol. 2. Clarendon Press, Oxford, U.K. 273-282.
Klinbunga S, Ampayup P, Tassanakajon A, Jarayabhand P, Yoosukh W. 2000. Development of species-specific markers of the tropical oyster (Crassostrea belcheri) in Thailand. Marine Biotechnology 2, 476-484.
Linacero R, Rueda J, Vasquez MA. 1998. Quantization of DNA. in molecular tools for screening biodiversity (K. Angela, P.G. Isaac & D.S. Ingram, eds). Chapman and Hall, London. pp. 18-21.
Merante F, Raha S, Reed JK, Proteau G. 1994. The simultaneous isolation of RNA and DNA from tissue cells, in Methods in molecular Biology. Vol 31. Protocol for gene analysis (Harwood, A.J, Ed), Humana, Totowa, NJ, 113-120.
Milbourne D, Meyer R, Bradshaw J, Braid E, Bonar N, Provan J, Powell W, Waught R. 1997. Comparison of PCR-based marker systems for the analysis of genetic relationships in cultivated potato. Molecular Breeding 3, 127-136.
Powell W, Margenta M, Andre C, Hanfrey M, Vogel J, Tingey S, Rafalsky A. 1996. The utility of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding 2, 225-238.
Prevost A, Wilkinson MJ. 1999. A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theoretical and Applied Genetics 98, 107-112.
Qamar ZQ, Anwar M, Minhas RA. 2008. Distribution and Population status of Himalayan musk deer (Moschus Chrysogaster) in the Machiara National Park, AJK. Pakistan Journal of Zoology 40(3), 159-163.
Roberts TJ. 1997. The mammals of Pakistan. Oxford University Press. Karachi, 525 p.
Roldan-Ruiz I, Dendaun J, Vanbockstaele E, Depicker D, Loose M. 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lollium spp.). Molecular Breeding 6, 125-134.
Roon DA, Waits LP, Kendall KC. 2003. A quantitative evaluation of two methods for preserving hair samples. Molecular Ecology Notes 3, 163-166.
Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory, New York, Appendix E. 3-5.
Sheikh KM, Molur S. 2005. Status and Red List of Pakistan’s Mammals. IUCN Pakistan. pp. 344.
Sloane MA, Sunnucks P, Alpers D, Beheregaray LB, Taylor AC. 2000. Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method. Molecular Ecology, 9, 1233-1240.
Staub JJ, Bacher J, Poeter K. 1996. Sources of potential errors in the application of random amplified polymorphic DNAs in cucumber. Horticulture Science 31, 262-266.
Sunnucks P. 2000. Efficient genetic markers for population biology. Trends in Ecology and Evolution 15, 199-203.
Taberlet P, Camarra J-J, Griffin S, Uhrès E, Hanotte O, Waits LP, Dubois-Paganon C, Burke T, Bouvet J. 1997. Non-invasive genetic tracking of the endangered Pyrenean brown bear population. Molecular Ecology 6, 869-876.
Waits LP, Paetkau D. 2005. New non-invasive genetic sampling tools for wildlife biologists: a review of applications and recommendations for accurate data collection. The Journal of Wildlife Management 69, 1419-1433.
Waldschmidt AN, Salomao TMF, deBarros EG, Campos LAO. 1997. Extraction of genomic DNA from Melipona quadrifasciata (Hymenoptera: Apidae, meliponinae). Brazilian Journal of Genetics 20(iii), 1-5.
Welsh J, McClelland M. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18, 7213-7218.
Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531-6535.
Wilson GA, Strobeck CM. 1999. Genetic variation within and relatedness among wood and plains bison populations. Genome 42, 483-496.
Zargar SM, Farhat S, Mahajan R, Bhakhri A, Sharma A. 2016. Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean. Saudi Journal of Biological Sciences 23(1), 139-149.
Zou FD, Yue BS, Ln X, Zhang YZ. 2005. Isolation and characterization of microsatellite loci from forest musk deer (Moschus berezovskii). Journal of Zoological Sciences 22, 593-598.
Inayat-Ullah Malik, Fakhar-i-Abbas, Muhammad Sajid Nadeem, Ghazala Kaukab, Zahid Sharif Mirza (2018), Optimization of DNA from Musk Deer (Moschus chrysogaster) Hair Follicle: extraction, PCR Amplification for discriminatory analysis of RAPD markers; IJB, V13, N2, August, P257-264
https://innspub.net/optimization-of-dna-from-musk-deer-moschus-chrysogaster-hair-follicle-extraction-pcr-amplification-for-discriminatory-analysis-of-rapd-markers/
Copyright © 2018
By Authors and International
Network for Natural Sciences
(INNSPUB) https://innspub.net
This article is published under the terms of the
Creative Commons Attribution License 4.0