Genetic diversity and structure of native Egyptian cattle populations and French-Egyptian Cross via DNA-microsatellite

Eslam Faid-Allah, E. Ghoneim, A. R. Elbetagy, M. El-Dabour


This study investigates genetic diversity and structure of native Egyptian cattle populations, called Baladi, as Saidi from Southern Egypt, Menufi from Mid-Delta and their F1 crosses with the French Tarentaise breed using DNA Microsatellite markers. A total of unrelated 97 individuals were genotyped utilizing eight SSR primers (ETH10, ETH225, BM1818, BM1824, BM2113, SPS115, TGLA53 and TGLA126). All utilized SSR were found to be polymorphic. The highest and lowest numbers of alleles detected were 16 and 6 at TGLA53 and SPS115 loci, respectively. Baladi-Tarentaise crosses (Bal-Tar) had the highest number of alleles over all. The PIC values of 7 loci were higher than 0.5, indicating high allelic variation of utilized markers. Estimated PIC values were up to 0.898, 0.866 and 0.873 for TGLA53 genotyped in Saidi, Menufi and Bal-Tar, respectively. Hobs values were lower than the expected ones in the native populations accompanied with positive values for Fis and significant deviation from HWE indicating inbreeding trend in native populations. Structure analysis indicated three ancestral genetic backgrounds. The native populations share two main backgrounds in almost equal percentages, while the Bal-Tar had the third one. The three populations showed low percentage of admixture. The studied Mediterranean cattle populations that belong to Egypt and France seem to have differentiated from each other with only little genetic exchange between the geographically isolated populations so local cattle is very similar.


Cattle; Genetic Diversity; DNA Microsatellite.

Full Text:



Acosta AC, Uffo O, Sanz A, Ronda R, Osta R, Rodellar C, Martin-Burriel I, Zaragoza P. 2013. Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci. J Anim Breed Genet. 130:79–86.

Agung PP, Saputra F, Septian WA, Lusiana-Moch-Zein SA, Sulandari S, Anwar S, Wulandari AS, Said S, Tappa B. 2016. Study of genetic diversity among Simmental cross cattle in West Sumatra based on microsatellite markers. Asian-Australas J Anim Sci. 29:176–183.

Beja-Pereira A, Alexandrino P, Bessa I, Carretero Y, Dunner S, Ferrand N, Jordana J, Laloe D, Moazami-Goudarzi K, Sanchez A, Canon J. 2003. Genetic characterization of southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites. J Hered. 94:243–250.

Bishop M, Kappes S. 1994. A genetic linkage map for cattle. Genetics. 136:619–639.

Botstein D, White R, Skolnick M, Davis R. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet. 32:314–331.

Chaudhari M, Parmar S, Joshi C, Bhong C, Fatima S, Thakur M, Thakur S. 2009. Molecular characterization of Kenkatha and Gaolao (Bos indicus) cattle breeds using microsatellite markers. Anim Biodivers Conserv. 32:71–76.

Cymbron T, Freeman A, Malheiro M, Vigne J, Bradley D. 2005. Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations. Proc R Soc B. 272:1837–1843.

Dadi H, Tibbo M, Takahashi Y, Nomura K, Hanada H, Amano T. 2008. Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations. Anim Genet. 39:425–431.

DeAtley K, Rincon G, Farber C, Medrano P, Luna-Nevarez J, Enns R, Van Leeuwen D, Silver G, Thomas M. 2011. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus- and Brahman-influenced cattle. J Anim Sci. 89:2031–2041.

[FAO] Food and Agriculture Organization of the United Nations. 1993. Breed database, Map Manager. [accessed 21st November 2017].

Georges M, Massey J. 1992. Polymorphic DNA markers in Bovidae.

Goudet J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices version 2.9.3 [Internet]. [cited 2017 Oct 12]. Available from:

Hassanane M, El-Ashmaoui H, Abd El-Baset S, Mabrouk M, Abdel-Hameid Z. 2006. Preliminary results on genetic diversity in Egyptian cattle using microsatellite markers. Egypt J Anim Prod. 43:11–24.

Joshi N, Mclaughlin E, Philips R. 1957. Types and breeds of African cattle. Rome (Ital): Food and Agriculture Organization of the United Nations.

Kesvulu P, Rao G, Ahmed A, Gupta B. 2009. Molecular genetic characterization of Punganur cattle. Indian J Vet Anim Sci Res. 5:179–185.

Luo Y, Wang Z, Li J, Zhang G, Chen Y. 2006. Genetic variation and genetic relationship among 13 Chinese and introduced cattle breeds using microsatellite DNA markers. Biodiv Sci. 14:498–516.

MacHugh D, Shriver M, Loftus R, Cunnigham P, Bradley D. 1997. Microsatellite DNA variation and the evolution, domestication and phylogeography of Taurine and Zebu cattle (Bos taurus and Bos indicus). Genetics. 146:1071–1086.

Maudet C, Luikart G, Taberlet P. 2002. Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. J Anim Sci. 80:942–950.

MoDAD. 2004. Secondary guidelines for development of national farm animal genetic resources management plans, measurement of domestic animal diversity: Recommended microsatellite markers [Internet]. [cited 2017 Aug 19]. Available from:

Molina-Flores B, Landi V, Martínez A, Delgado J, Galal S, Abdelaziz A. 2011. Caracterización de la raza vacuna Baladi del Alto Egipto mediante microsatélites. AIDA.

Moore S, Byrne K. 1993. Dinucleotide polymorphism at the bovine calmodulin independent adenylcyclase locus. Anim Genet. 24:150–159.

Nei M. 1987. Molecular evolutionary genetics. [New York (USA)]: Columbia University Press.

Ota T. 1993. DISPAN: Genetic distance and phylogenetic analysis software. Pennsylvania (USA): Institute of Molecular Evolutionary Genetics, Pennsylvania State University.

Padilla J, Sansinforiano E, Parejo J, Rabasco A, Martínez-Trancón M. 2009. Inference of admixture in the endangered Blanca Cacereña bovine breed by microsatellite analyses. Livest Sci. 122:314–322.

Pham L, Do D, Binh N, Nam L, Ba N, Thuy T, Hoan T, Cuong V, Kadarmideen H. 2013. Assessment of genetic diversity and population structure of Vietnamese indigenous cattle populations by microsatellites. Livest Sci. 155:17–22.

Pritchard J, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945–959.

Qiu Z. 2007. Studies on genetic diversity and correla¬tion between microsatellite markers and growth traits in Xiangxi Yellow cattle. Changsha (China): Hunan Agricultural University.

Rambaut A. 2012. FigTree (ver.1.4) released 8th, Institute of Evolutionary Biology. Edinburgh (UK): Edinburgh University.

Raymond M, Rousset F. 1995. GENEPOP (ver. 1.2) population genetics software for exact tests and ecumenicism. J Hered. 86:248–249.

Saitou N, Nei M. 1987. The Neighbor-Joining Method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406–425.

Steffen P, Eggen A. 1993. Isolation and mapping of polymorphic microsatellites in cattle. Anim Genet. 24:121–124.

Suh S, Kim Y, Cho C, Byun M, Choi S, Ko Y, Lee C, Jung K, Bae K, Kim J. 2014. Assessment of genetic diversity, relationships and structure among Korean native cattle breeds using microsatellite markers. Asian-Australas J Anim Sci. 27:1548–1553.

Sun W, Chen H, Lei C, Lei X, Zhang Y. 2007. Study on population genetic charac¬teristics of Qinchuan cows using microsatellite markers. J Genet Genomics. 34:17–25.

Toldo S, Fries R. 1993. Physically mapped, cosmid-derived microsatellite markers as anchor loci on bovine chromosomes. Mamm Genome. 4:720–727.

Vaiman D, Mercier D, Moazami-Goudarzi K. 1994. A set of 99 cattle microsatellites: characterization, synteny mapping and polymorphism. Mamm Genome. 5:288–297.

Yeh F, Yang R, Boyle T. 1999. POPGENE (ver.1.31): A Microsoft Windows-based freeware for population genetic analysis. Edmonton (Canada): Alberta University & the Centre for International Forestry Research.


  • There are currently no refbacks.

Copyright (c)  2018 Indonesian Journal of Animal and Veterinary Sciences

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.