AGRICULTURAL RESEARCH COMMUNICATION CENTRE www.arccjournals.com/www.ijaronline.in *Corresponding author’s e-mail: veeramani@tanuvas.org.in. Indian J. Anim. Res., 50 (4) 2016 : 626-628 Print ISSN:0367-6722 / Online ISSN:0976-0555 Phylogenetic analysis of six duck populations P. Veeramani*, R. Prabakaran, S.N. Sivaselvam, T. Sivakumar, S.T. Selvan and S.M.K. Karthickeyan Postgraduate Research Institute in Animal Sciences, (TNVASU), Kattupakkam-603 203, India. Received: 01-03-2015 Accepted: 15-01-2016 DOI:10.18805/ijar.9301 ABSTRACT Indigenous ducks play a vital role in sustainable livelihood of the poor duck farmers. In Tamil Nadu, two popular indigenous duck varieties viz., Sanyasi and Keeri are being reared traditionally by the duck farmers under nomadic system. In the same way, Kuttanad ducks are popular in Kerala and Assam ducks are popular in Assam. The present research work was undertaken to study the genetic distance between and within the indigenous ducks and exotic duck breeds by using duck specific microsatellite markers. From the blood samples the genomic DNA was isolated and characterized genetically. With the molecular data, dendrogram was constructed. This revealed that, Keeri, Sanyasi, Kuttanad and Assam ducks formed the first group with White Pekin in the second group and Muscovy in the third cluster. Among the Indian duck varieties, Keeri and Sanyasi ducks of Tamil Nadu were found to be closer to each other as indicated by the genetic distance value of 0.11. However, within this group, 26.33 and 29.87 per cent of differentiation were noticed between Assam and Sanyasi and Assam and Keeri ducks respectively. Higher genetic distance value of 0.92 (92 per cent) was observed between two exotic ducks. Based on the genetic distance and genetic diversity between the indigenous ducks, the duck varieties of Tamil Nadu, Kerala and Assam may be classified as distinct breeds. Key words: Duck, Phytogenetic. Asia is considered as the homeland for ducks holding 90 per cent of the world duck population. In India, out of the country’s total egg production, 5.3 per cent comes from ducks and indigenous ducks contribute 92 per cent of the same. On the other hand, 30 per cent of the total meat production in the country is of poultry origin. The contribution of ducks in meat production also cannot be neglected. The distribution and demographic dynamics of duck population revealed that they are mainly concentrated in eastern, north eastern and southern states of the country. The leading states in duck population are West Bengal, Assam, Kerala, Andhra Pradesh, Tamil Nadu, Bihar and Orissa. The common Indian breeds/genetic groups of ducks are Indian Runner, Nageswari, Sythetmete, Kuttanad, Arni etc. Besides, non-descript ducks are also available in large numbers in many states of the country, contributing significantly to the total duck population. These indigenous ducks have innate potential to produce eggs and meat at considerable quantity with lesser input and they are a good dietary source of proteins. However, information on these duck populations, their physical and production characteristics are very scanty and there have been very few systematic studies of ducks in India. In order to conserve this genetic resource, study on genetic diversity within and between duck populations using microsatellite markers would provide information for taking priority decisions towards preservation. Microsatellite markers are frequently used in genotype identification, pedigree analysis and estimation of genetic diversity and genetic distance (Chen et al., 2003; Yan et al., 2005) and may be useful in resolving the phylogenetic relationships between closely related populations (Takezaki and Nei, 1996). The characterization of genetic diversity by employing molecular tools is a prerequisite in developing strategies for conservation, utilization of duck genetic resources and to the establishment of a sensible genetic preservation strategy for these populations. Hence, the present research was conducted to evaluate genetic diversity and relationships within and between Indian breeds of ducks based on microsatellite markers. A total of 190 blood samples were collected from unrelated birds of both sexes of Sanyasi, Keeri in the study area, Kuttanad ducks from Kerala, Assam ducks, White Pekin and Muscovy ducks for molecular characterisation and phylogenetic analysis of the duck populations. From the blood samples, the genomic DNA was isolated by standard protocol. The FAO recommended 23 microsatellite markers with labelled forward primers were used for molecular characterization. These microsatellite primers were standardised for their annealing temperatures. Molecular characterization of various duck varieties was carried out using standard PCR protocol and the PCR amplicons were