Veterinary World

     Open access and peer reviewed journal  

ISSN (Online): 2231-0916

ISSN (Print): 0972-8988


Home l Editorial board l Instructions for authors l Reviewer guideline l Open access policy l Archives l FAQ

Open Access

Copyright: The authors. This article is an open access article licensed under the terms of the Creative Commons Attribution License

( which permits unrestricted use, distribution and reproduction in any medium, provided the work is properly cited.

Research (Published online: 27-09-2014)

20. Genetic architecture and bottleneck analyses of Salem Black goat breed based on microsatellite markers - A. K. Thiruvenkadan,

V. Jayakumar, P. Kathiravan and R. Saravanan

Veterinary World, 7(9): 733-737



   doi: 10.14202/vetworld.2014.733-737



A. K. Thiruvenkadan: Department of Animal Husbandry Statistics and Computer Applications, Veterinary College and Research Institute,

Namakkal - 637 002, Tamil Nadu, India;

V. Jayakumar: Veterinary Dispensary, Department of Animal Husbandry, Namakkal - 637 001, Tamil Nadu, India;

P. Kathiravan: Livestock Geneticist, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria;

R. Saravanan: Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Namakkal - 637 002, Tamil Nadu, India;


Received: 05-05-2014, Revised: 12-08-2014, Accepted: 19-08-2014, Published online: 27-09-2014


Corresponding author: A. K. Thiruvenkadan, e-mail:

Aim: The present study was undertaken in Salem Black goat population for genetic analysis at molecular level to exploit the breed for planning sustainable improvement, conservation and utilization, which subsequently can improve the livelihood of its stakeholders.

Materials and Methods: Genomic DNA was isolated from blood samples of 50 unrelated Salem Black goats with typical phenotypic features in several villages in the breeding tract and the genetic characterization and bottleneck analysis in Salem Black goat was done using 25 microsatellite markers as recommended by the Food and Agricultural Organization, Rome, Italy. The basic measures of genetic variation were computed using bioinformatic software. To evaluate the Salem Black goats for mutation drift equilibrium, three tests were performed under three different mutation models, viz., infinite allele model (IAM), stepwise mutation model (SMM) and two-phase model (TPM) and the observed gene diversity (He) and expected equilibrium gene diversity (Heq) were estimated under different models of microsatellite evolution.

Results: The study revealed that the observed number of alleles ranged from 4 (ETH10, ILSTS008) to 17 (BM64444) with a total of 213 alleles and mean of 10.14±0.83 alleles across loci. The overall observed heterozygosity, expected heterozygosity, inbreeding estimate and polymorphism information content values were 0.631±0.041, 0.820±0.024, 0.233±0.044 and 0.786±0.023 respectively indicating high genetic diversity. The average observed gene diversities (He) pooled over different markers was 0.829±0.024 and the average expected gene diversities under IAM, TPM and SMM models were 0.769±0.026, 0.808±0.024 and 0.837±0.020 respectively. The number of loci found to exhibit gene diversity excess under IAM, TPM and SMM models were 18, 17 and 12 respectively.

Conclusion: All the three statistical tests, viz., sign test, standardized differences test and Wilcoxon sign rank test, revealed significant deviation of Salem Black goats from mutation-drift equilibrium under IAM and TPM models, however, nonsignificant deviation under SMM model. The qualitative test of mode shift analysis supported the results under SMM indicating the absence of the genetic bottleneck in the recent past in Salem Black goats.

Keywords: bottleneck, genetic diversity, microsatellites, Salem Black.

1. Mahmoudi, B., Esteghamat, O., Shahriyar1, A., and Babayev, M.S.H. (2012) Genetic characterization and bottleneck analysis of Korki Jonub Khorasan goats by microsatellite markers. J. Cell. Mol. Biol., 10: 61-69.
2. Aggarwal, R.A.K., Dixit, S.P., Verma, N.K., Ahlawat, S.P.S., Kumar, Y., Kumar, S., Chander, R. and Singh, K.P. (2007) Population genetic analysis of Mehsana goat based on microsatellite markers. Curr. Sci., 92: 1133-1137.
3. Rout, P.K., Joshi, M.B., Mandal, A., Laloe, D., Singh, L. and Thangaraj, K. (2008) Microsatellite-based phylogeny of Indian domestic goats. BMC. Genet., 9: 11, 2008.
PMid:18226239 PMCid:PMC2268706
4. Ramamoorthi, J., Thilagam, K., Sivaselvam, S.N. and Karthickeyan, A.M.K. (2009) Genetic characterization of Barbari goats using microsatellite markers. J. Vet. Sci., 10(1): 72-76.
5. Dixit, S.P., Aggarwal, R.A.K., Verma, N.K., Vyas, M.K., Rana, J., Sharma, A. and Chander, R. (2011) Genetic variability and bottleneck analyses of Kanniadu goat breed based on microsatellite markers. Indian J. Anim. Sci., 81: 40-43.
6. Thiruvenkadan, A.K. and Karunanithi, K. (2006) Characterization of Salem black goats in their home tract. Anim. Genet. Resour. Inf., 38: 67-75.
7. Miller, S.A., Dykes, D.D. and Polesky, H.F. (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic. Acids. Res., 16(3): 1215.
PMid:3344216 PMCid:PMC334765
8. Dieringer, D. and Schlötterer, C. (2003) Microsatellite analyzer (MSA): A platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes., 3: 167-169.
9. Excoffier, L., Laval, G. and Schneider, S. (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol. Bioinformatics. Online., 1: 47-50.
10. Peakall, R. and Smouse, P.E. (2006) GENALEX 6: Genetic analysis in excel. Population genetic software for teaching and research. Mol. Ecol. Notes., 6: 288-295.
11. Piry, S., Luikart, G. and Cornuet, J.M. (1999) Bottleneck: A computer program for detecting recent reductions in the effective population size using allele frequency data. J. Hered., 90: 502-503.
12. Sharma, R., Kumar, D., Pandey, A.K., Dixit, S.P. and Ahlawat, S.P.S. (2008) Genetic variability and bottleneck analysis of Barbari goat population using microsatellite markers. Indian J. Anim. Sci., 78: 391-396.
13. Mishra, P., Ali, A.S., Aggarwal, R.A.K., Dixit, S.P., Kawitkar, V.S., Dangi, P.S. and Verma, N.K. (2012) Genetic diversity and bottleneck analysis of Konkan Kanyal goats. Anim. Genet. Resour., 50: 43-48.
14. Botstein, D., White, R.L., Skolnick, M. and Davis, R.W. (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J. Hum. Genet., 32: 314-331.
PMid:6247908 PMCid:PMC1686077
15. Wimmers, K., Ponsuksili, S., Hardge, T., Valle-Zarate, A., Mathur, P.K. and Horst, P. (2000) Genetic distinctness of African, Asian and South American local chickens. Anim. Genet., 31: 159-165.
16. Li, J.Y., Chen, H., Lan, X.Y., Kong, X.J. and Min, L.J. (2008) Genetic diversity of five Chinese goat breeds assessed by microsatellite markers. Czech. J. Anim. Sci., 53: 315-319.
17. Cornuet J.M. and Luikart, G. (1996) Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genet., 144: 2001-2014.
18. Luikart GL, Allendorf FW, Cornuet JM, Sherwin WB. (1998) Distortion of allele frequency distributions provides a test for recent population bottlenecks. J. Hered., 89: 238-247.
19. Mburu, D.N. and Hanotte, O. (2005) Comparative genetic analysis of molecular diversity of African cattle. In: The Proceedings Of International Workshop On The Role Of Biotechnology For The Characterization And Conservation Of Crop, Forestry, Animal And Fishery Genetic Resources, 5-7 March, 2005, Villa Gualino, Turin, Italy.
20. Glowatzki-Mullis, M.L., Muntwyler, J., Baumle, E. and Gaillard, C. (2008) Genetic diversity measures of Swiss goat breeds as decision making support for conservation policy. Small. Rumin. Res., 74: 202-211.
21. Bray, T.C., Chikhi, L., Sheppy, A.J. and Bruford, M.Q. (2009) The population genetic effects of ancestry and admixture in a subdivided cattle breed. Anim. Genet., 40: 393-400.
22. Ganapathi, P., Rajendran, R. and Kathiravan, P. (2012) Detection of occurrence of a recent genetic bottleneck event in Indian hill cattle breed Bargur using microsatellite markers. Trop. Anim. Health Prod., 44(8): 2007-2013.
23. Tantia, M.S., Behl, R., Sheoran, N., Singh, R., and Vijh, R.K. (2007) Microsatellite data analysis for conservation of two goat breeds. Indian J. Anim. Sci., 74: 761-767.
24. Fatima, S., Bhonga, C.D, Ranka, D.N. and Joshi, C.G. (2008) Genetic variability and bottleneck studies in Zalawadi, Gohilwadi and Surti goat breeds of Gujarat (India) using microsatellites. Small Rumin. Res., 77: b58-64.
25. Mishra, P., Verma, N.K., Aggarwal, R.A.K. and Dixit, S.P. (2010) Breed characteristics and genetic variability in Changthangi goats. Indian J. Anim. Sci., 80: 1203-1208.