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Open Access Highly Accessed Open Badges Research article

Microsatellite-based phylogeny of Indian domestic goats

Pramod K Rout1, Manjunath B Joshi2, Ajoy Mandal1, D Laloe3, Lalji Singh2 and Kumarasamy Thangaraj2*

Author affiliations

1 Central Institute for Research on goats, Makhdoom, Farah, Mathura-281122, India

2 Centre for cellular and Molecular biology, Uppal Road, Hyderabad-500007, India

3 Station de Génétique Quantitative et Appliquée, INRA, 78352 Jouy-en-Josas, France INRA, Cedex, France

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Citation and License

BMC Genetics 2008, 9:11  doi:10.1186/1471-2156-9-11

Published: 28 January 2008



The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones.


The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The DA measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution.


Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information.