Comparison of different parameters of invasive and non invasive sampling methods for microsatellite genotyping: a case study from Red Junglefowl and its application for other Galliformes
Abstract
In studies dealing with genetic and disease prognosis, biological sampling is a prerequisite. Earlier, blood and muscle samples were taken after live captures. These invasive procedures are of considerable risk when sampling endangered species. Therefore, non invasive samples like shed feathers/hairs, faeces and hatched or predated egg shells are the alternative source for genetic study. We collected 18 Red Junglefowl feather samples (plucked feathers n= 6; shed feathers n=12) across its northwestern distribution range in India. The DNA yield was compared with other sample types i.e. blood, egg shell and faeces (n=6 for each sample type). We found a gradient in DNA yield as blood (770 μg/ml) > plucked feathers > shed feathers > egg shell = faeces (30 μg/ml). DNA extracts from feathers were amplified for four microsatellite loci. Three samples (17%) for all 4 microsatellite loci, four samples (22%) for 3 and 2 loci each, and seven samples (39%) for 1 locus were successfully genotyped. We found that the successful amplification of multilocus genotypes were dependant on the condition of the starting material and the type of sample. There are few studies that have compared the quality and quantity of DNA being produced through varying degree of invasiveness. None have considered effort (time) and the cost involved in procuring the samples from field and processing samples in lab. We scaled all the aspects of cost and efforts from 1 (low) to 10 (high) and here presenting a comparative analysis for the efficacy of invasive and non-invasive sampling methods
References
Ali S and Ripley SD. 1983. Handbook of the Birds of India and Pakistan. Oxford University Press, Delhi.
Brisbin IL Jr. 1995. Conservation of the wild ancestors of domestic animals. Conserv. Biol., 9:1327.
Bub H. 1991. Bird trapping and bird banding. Cornell University Press, New York.
Bush KL, Vinsky MD, Aldridge C L, Paszkowski, CA. 2005. Comparison of sample types varying in invasiveness for use in DNA sex determination in an endangered population of greater Sage-Grouse (Centrocercus uropihasianus), Conservation Genetics 6:867.
Fernandes M, Mukesh S, Sathyakumar, Rahul Kaul, Rajiv S Kalsi and Deepak Sharma, 2009. Conservation of Red Junglefowl Gallus gallus in India. International Journal for Galliformes Conservation 1:94.
Fernandes M, Mukesh, Sathyakumar S, Kaul R and Kalsi, R S. 2008. Conservation of Red Junglefowl Gallus gallus in India. Interim Report – Phase I. Wildlife Institute of India, Dehradun, 49.
Fiona E, Hogan, Raylene Cooke, Christopher P. Burridge and Janette A. Norman. 2008. Optimizing the use of shed feathers for genetic analysis, Mol. Ecol. Resources 8:561.
Gagnex P, Boesch C, Woodruff D. 1997. Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Mol Ecol, 6:861.
Gerloff U, Schlötterer C, Rassmann K, Rambold I, Hohmann G, Fruth B and Tautz D. 1995. Amplification of hypervariable simple sequence repeats (microsatellites) from excremental DNA of wild living bonobos (Pan paniscus). Mol. Ecol., 4:515-518.
Jason CB, Elizabeth AA, Russell CVH, Cynthia JM and Susan CA. 2005. Locus effects and sources of error in noninvasive genotyping, Mol. Ecol.Notes 5:680-683.
Johnsgard PA. 1986. The Pheasants of the World. Oxford University Press, New York. 300.
Kohn M, Knauer F, Stoffella A, der Schröder W and Paabo S. 1995. Conservation genetics of the European brown bear: A study using excremental PCR of nuclear and mitochondrial sequences. Mol. Ecol., 4:95-103.
Kohn MH, York EC, Kamradt DA, Haught G, Sauvajot RM, Wayne RK. 1999. Estimating population size by genotyping faeces. Proceedings of the Royal Society of London, Series B: Biological Sciences 266, 657.
Mackey K, Williams P, Seim S, Chomczynski P. 1996. The use of DNAzol® for the rapid isolation of genomic DNA from whole blood. Biomedical Products Supplement 13.
Morejohn VG. 1968. Study of Plumage of the four species of the genus Gallus. The Condor 70:56.
Morin PA, Chambers KE, Boesch C, Vigilant L. 2001. Quantitative Polymerase chain reaction of DNA from non-invasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol Ecol, 10:1835.
Navidi W, Arnheim N, Waterman MS. 1992. A multiple-tubes approach for accurate genotyping of very small DNA samples by using PCR: statistical considerations. Am J Hum Genet., 50:347–359.
Ramesh K, Sathyakumar S, Rawat GS. 2008. Methods of capture and radio tracking of western tragopan Tragopan melanocephalus J.E. Gray 1829 in the Great Himalayan National Park, India, J Bombay Nat Hist Soc., 105, 2, 127.
Segelbacher G, Steinbrück G. 2001. Bird faeces for sex identification and microsatellite analysis. Vogelwarte 41, 139.
Sharma D. 2006. Comparative genomic studies on wild and domesticated avian species. Annual Progress Report, Submitted to the Department of Biotechnology, New Delhi.
Sivakumar K, Goyal SP, Mukherjee SK. 2007. Identification of Galliformes using the Microstructure of Feathers: Preliminary Findings. (IN) Sathyakumar, S., Sivakumar, S., (Eds.). Galliformes of India. ENVIS Bulletin: Wildlife and Protected Areas, 10 (1), Wildlife Institute of India, Dehradun, India. 197.
Taberlet P, Bouvet J. 1991. A single plucked feather as a source of DNA for bird genetic studies. Auk, 108, 959.
Taberlet P, Griffin S, Goossens B. 1996. Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Res, 24:3189-3194.
Vidya TNC and Sukumar R. 2005. Amplification success and feasibility of using microsatellite loci amplified from dung to population genetic studies of the Asian elephant (Elephas maximus), Curr Sci, 88(3):489-492.
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http://gallus.forestry.uga.edu/genetics/protocols/pdf/feather.pdf, Accessed on 5th March, 09.
