A Fundamental Statistical Tools Application for Livestock Diversity Studies from Microsatellite Data—A Mini Review


The conservation of genetic variation is essential for meeting future unpredictable breeding requirements. Therefore, the foremost priority must be given to assessment of the population variation status. Among several markers, a DNA based microsatellite is a choice for the population studies, currently. We reviewed some important statistical tools for assessing the farm animal biodiversity. Firstly, the reliability of the results which is mainly based on the number of microsatellite loci genotyped and unrelated sample size per population was discussed. Secondly, we argued genetic parameters which are estimated while reporting the state of population variations. Thirdly, supplementing information to variations was also presented. Fourthly, we briefly discussed the types and constructing phylogenetic tree and the role of principal component analysis. Finally, we presented the important web-based statistical packages for genetic data analysis. This shall assist in devising appropriate conservation strategy for our farm animal genetic resources.

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Dorji, N. and Daugjinda, M. (2014) A Fundamental Statistical Tools Application for Livestock Diversity Studies from Microsatellite Data—A Mini Review. Open Access Library Journal, 1, 1-8. doi: 10.4236/oalib.1100572.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Baumung, R., Simianer, H. and Hoffmann, I. (2004) Genetic Diversity Studies in Farm Animals—A Survey. Journal of Animal Breeding and Genetics, 121, 361-373.
[2] Soller, M., Weigend, S., Romanov, M.N., Dekkers, J.C.M. and Lamont, S.J. (2006) Strategies to Assess Structural Variation in the Chicken Genome and Its Association with Biodiversity and Biological Performances. Poultry Science, 85, 2061-2078.
[3] Ellagra, H. (2004) Microsatellites: Simple Sequences with Complex Evolution. Nature Review Genetics, 5, 435-445.
[4] Muchadeyi, F.G., Wollny, C.B.A., Eding, H., Weigend, S., Makuza, S.M. and Simianer, H. (2007) Variation in Village Chicken Production Systems among Agro-Ecological Zones of Zimbabwe. Tropical Animal Health and Production, 39, 413-461.
[5] Toro, M.A. and Caballero, A. (2005) Characterization and Conservation of Genetic Diversity in Subdivided Populations. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1367-1378.
[6] Hillel, J., Martien, A.M., Groenen, A.M., Boichard, M.T., Abraham, B., Korol, A.B., David, V., Kirzhner, V.M., Burke, T., Barre-Dirief, A., Crooijmans, R.P.M.A., Elo, K., Feldman, M.W., Paul, J., Freidlin, P.J., Mäki-Tanila, A., Oortwijn, W., Thomson, P., Vigna, A., Wimmers, K. and Weigend, S. (2003) Biodiversity of 52 Chicken Populations Assessed by Microsatellite Typing of DNA Pools. Genetic Selection Evolution, 35, 533-557.
[7] Norberg, E. and Sørensen, A.C. (2007) Inbreeding Trend and Inbreeding Depression in the Danish Populations of Texel, Shropshire, and Oxford Down. Journal of Animal Science, 85, 299-304.
[8] Miglior, F., Burnside, E.B. and Hohenboken, W.D. (1994) Heterogeneity among Families of Holestien Cattle in Inbreeding Depression for Production Traits. Proceedings of the 5th WCGALP, 18, 479-482.
[9] Rathje, T.A. (2000) Strategies to Manage Inbreeding Accumulation in Swine Breeding Company Nucleus Herds: Some Case Studies. Journal of Animal Science, 79, 1-8.
[10] Culbertson, M.S., Mabry, J.W., Misztal, I. and Bertrand, J.K. (1997) Effect of Inbreeding and Outbreeding in Purebred and Hampshire and Duroc Swine. The Professional Animal Scientist, 13, 194-197.
[11] Sewalem, A., Johansson, K., Wilhelmson, M. and Lillpers, K. (1999) Inbreeding and Inbreeding Depression on Reproduction and Production Traits of White Leghorn Lines Selected for Egg Production Traits. British Poultry Science, 40, 203-208.
[12] Gómez, M.D., Valera, M., Molina, A., Gutiérrez, J.P. and Goyache, F. (2009) Assessment of Inbreeding Depression for Body Measurements in Spanish Purebred (Andalusian) Horses. Livestock Science, 122, 149-155.
[13] Dorji, N., Daujginda, M. and Phasuk, Y. (2011) Genetic Characterization of Thai Indigenous Chickens Compared with Commercial Lines. Tropical Animal Health and Production, 43, 779-785.
[14] Nidup, K. and Moran, C. (2011) Genetic Diversity of Domestic Pigs as Revealed by Microsatellites: A Mini Review. Genomics and Quantitative Genetics, 2, 5-18.
[15] Food and Agriculture Organization/ISAG (2004) Measurement of Domestic Animal Diversity—A Review of Recent Diversity Studies.
[16] Groeneveld, L.F., Lenstra, J.A., Eding, H., Toro, M.A., Scherf, B., Pilling, D., Negrini, R., Finlay, E.K., Jianlin, H., Groeneveld, E. and Weigend, S. (2010) Genetic Diversity in Farm Animals—A Review. Animal Genetics, 41, 6-31.
[17] Nassiry, M.R., Javanmard, A. and Tohidi, R. (2009) Application of Statistical Procedures for Analysis of Genetic Diversity in Domestic Animal Populations. American Journal of Animal & Veterinary Sciences, 4, 136-141.
[18] Tadano, R., Sekino, M., Nishibori, M. and Tsudzuki, M. (2007) Microsatellite Marker Analysis for the Genetic Relationships among Japanese Long-Tailed Chicken Breeds. Poultry Science, 86, 460-469.
[19] Osman, S.A., Sekino, M., Nishibori, M., Kawamoto, Y., Kinoshita, K., Yamamoto, Y. and Tsudzuki, M. (2004) Genetic Variability and Relationships of Japanese Native Chickens Assessed by Means of Microsatellite Profiling Approach-Focusing on the Oh-Shamo (Japanese Large Game) and Its Related Breeds. Journal of Poultry Science, 41, 94-109.
[20] Frankham, R., Ballou, J.D. and Briscoe, D.A. (2004) A Primer of Conservation Genetics. Cambridge University Press, London.
[21] Hanotte, O. and Jianlin, H. (2005) Genetic Characterization of Livestock Populations and Its Use in Conservation Decision-Making. The Role of Biotechnology, Turin, 5-7 March 2005, 131-136.
[22] Toro, M.A., Fernandez, J. and Caballero, A. (2009) Molecular Characterization of Breeds and Its Use in Conservation. Livestock Science, 120, 174-195.
[23] Kalinowski, S.T. (2004) Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs. Conservation Genetic, 5, 539-543.
[24] Nei, M. (1978) Estimation of Heterozygosity and Genetic Distance from a Small Number of Individuals. Genetics, 89, 583-590.
[25] Allendorf, F.W. (1986) Genetic Drift and the Loss of Alleles versus Heterozygosity. Zoo Biology, 5, 181-190.
[26] Lauretto, M.S., Nakano, F., Faria Jr., S.R., Pereira, C.A.B. and Stern, J.M. (2009) A Straightforward Multiallelic Significance Test for the Hardy-Weinberg Equilibrium Law. Genetics and Molecular Biology, 32, 619-625.
[27] Rousset, F. and Raymond, M. (1997) Statistical Analyses of Population Genetic Data: New Tools, Old Concept. Trends in Ecology & Evolution, 12, 313-317.
[28] Weir, B.S. (1996) Genetic Data Analysis II: Methods for Discrete Population Genetic Data. Sinauer Associates, Inc., Sunderland.
[29] Wright, S. (1951) The Genetical Structure of Populations. Annals of Eugenics, 15, 323-354.
[30] Holsinger, K.E. and Weir, B.S. (2009) Genetics in Geographically Structured Populations: Defining, Estimating and Interpreting FST. Nature Reviews Genetics, 10, 639-650.
[31] Kalinowski, S.T. (2002) Evolutionary and Statistical Properties of Three Genetic Distances. Molecular Ecology, 11, 1263-1273.
[32] Pearse, D.E. and Crandall, K.A. (2004) Beyond FST: Analysis of Population Genetic Data for Conservation. Conservation Genetics, 5, 585-602.
[33] Balloux, F. and Lugon-Moulin, L. (2002) The Estimation of Population Differentiation with Microsatellite Markers. Molecular Ecology, 11, 155-165.
[34] Hedrick, P.W. (2005) A Standardized Genetic Differentiation Measure. Evolution, 59, 1633-1638.
[35] Nei, M. and Roychoudhury, A.K. (1974) Sampling Variances of Heterozygosity and Genetic Distance. Genetics, 76, 379-390.
[36] Ruane, J. (1999) A Critical Review of the Value of Genetic Distance Studies in Conservation of Animal Genetic Resources. Animal Breeding and Genetics, 116, 317-323.
[37] Nei, M. (1972) Genetic Distance between Populations. American Naturalist, 106, 283-292.
[38] Nei, M., Tajima, F. and Tateno, Y. (1983) Accuracy of Estimated Phylogenetic Trees from Molecular Data. Journal of Molecular Evolution, 19, 153-170.
[39] Weir, B.S. and Cockerham, C.C. (1984) Estimating F-Statistics for the Analysis of Population Structure. Evolution, 38, 1358-1370.
[40] Laval, G., San Cristobal, M. and Chevalet, C. (2001) Measuring Genetic Distances between Breeds: Use of Some Distances in Various Short Term Evolution Models. Genetics Selection Evolution, 34, 481-507.
[41] Felsenstein, J. (1981) Evolutionary Trees from DNA Sequences: A Maximum Likelihood Approach. Journal of Molecular Evolution, 17, 368-376.
[42] Nei, M. and Kumar, S. (2000) Molecular Evolution and Phylogenetics. Oxford University Press, Inc., New York.
[43] Thorne, J.L., Kishino, H. and Felsenstein, J. (1991) An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences. Journal of Molecular Evolution, 33, 114-124.
[44] Suhr, D.D. (2005) Principal Component Analysis vs. Exploratory Factor Analysis. SUGI 30 Proceedings, 203-230.
[45] Price, A.L., Patterson, N.J., Plenge, R.M., Weinblatt, M.E., Shadick, N.A. and Reich, D. (2006) Principal Components Analysis Corrects for Stratification in Genome-Wide Association Studies. Nature Genetics, 38, 904-909.
[46] Raymond, M. and Rousset, F. (1995) GENEPOP (Version 1.2): Population Genetics Software for Exact Tests and Ecumenicism. Journal of Heredity, 86, 248-249.
[47] Rousset, F. (2008) GENEPOP’007: A Complete Reimplementation of the GENEPOP Software for Windows and Linux. Molecular Ecology Resources, 8, 103-106.

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