Skip to main content
SpringerLink
Log in

Genetic Variation at 15 Autosomal STR Loci Among Seven Egyptian Populations

  • Original Article
  • Published:
Biochemical Genetics Aims and scope Submit manuscript

Abstract

Egypt is a transcontinental country containing substantial ethnic, cultural, and linguistic diversity among its people. This study was conducted to investigate the genetic variation at 15 AmpFlSTR Identifiler short tandem repeat (STR) loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA, within and between seven Egyptian populations. Samples of 814 unrelated individuals from Northern Coast, Delta, Greater Cairo, Canal governorates, Northern Upper Egypt, Southern Upper Egypt, and Sinai were investigated. All loci were highly polymorphic in all sample populations. The data were analyzed to give information on allele frequencies and other population statistical parameters. After applying Bonferroni correction, the agreement with Hardy–Weinberg equilibrium (HWE) was confirmed for all loci (exact test), and for all loci with the exception of D3S1358, D19S433, and D18S51 (X2 test). The levels of genetic differentiation and the genetic relationships among populations were evaluated by coefficient of genetic differentiation (FST), AMOVA, and genetic distance of Nei. The most differentiated populations were found between Sinai and Southern Upper Egypt. These two populations showed the lowest within-population variation, whereas the population of Greater Cairo showed the highest within-population variation as indicated by the fixation index FIS. The varying levels of genetic relatedness among the populations in relation to their geographical distribution were analyzed using Mantel test. The results demonstrated that the effectiveness of STR markers enhances their value for identifying the genetic variation within and between Egyptian populations.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Ahmed SM (2017) Consanguineous marriage among Egyptian youth: secondary analysis of survey of young people in Egypt, 2014. EJCM 35:85–94

    Google Scholar 

  • Babiker HM, Schlebusch CM, Hassan HY, Jakobsson M (2011) Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci. Invest Genet 2:1–13

    Article  Google Scholar 

  • Barbarii LE, Rolf B, Constantinescu C, Hohoff C, Calistru P, Dermengiu D (2004) Allele frequencies of 13 short tandem repeat (STR) loci in the Romanian population. Forensic Sci Int 141:171–174

    Article  PubMed  CAS  Google Scholar 

  • Barni F, Berti A, Pianese A, Boccellino A, Miller MP, Caperna A, Lago G (2007) Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region. Forensic Sci Int 167:87–92

    Article  PubMed  CAS  Google Scholar 

  • Bassiouney R (2015) Language and identity in modern Egypt. Edinburgh University Press, Edinburgh

    Google Scholar 

  • Bentayebi K, Abada F, Ihzmad H, Amzazi S (2014) Genetic ancestry of a Moroccan population as inferred from autosomal STRs. Meta Gene 2:427–438

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Borosky A, Toscanini U, Gómez AA, Parolín ML, Basso N, Vullo C (2014) Forensic population data for 20 STR loci in Argentina. Forensic Sci Int Genet 13:e20–e21

    Article  PubMed  CAS  Google Scholar 

  • Bostein D, White RL, Skolnick M, Davis RW (1980) Construction of genetic linkage maps in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–331

    Google Scholar 

  • Butler JM (2006) Genetics and genomics of core STR loci used in human identity testing. J Forensic Sci 51:253–265

    Article  PubMed  CAS  Google Scholar 

  • Chan KM, Chiu CT, Tsui P, Wong DM, Fung WK (2005) Population data for the identifier™ 15 STR loci in Hong Kong Chinese. Forensic Sci Int 152:307–309

    Article  PubMed  CAS  Google Scholar 

  • Cifuentes L, Jorquera H, Acuña M, Ordóñez J, Sierra AL (2008) Allele frequencies for 12 autosomal short tandem repeat loci in two Bolivian populations. Genet Mol Res 7:271–275

    Article  PubMed  CAS  Google Scholar 

  • Collin H, Burri R, Comtesse F, Fumagalli L (2013) Combining molecular evolution and environmental genomics to unravel adaptive processes of MHC class IIB diversity in European minnows (Phoxinus phoxinus). Ecol Evol 3:2568–2585

    Article  PubMed  PubMed Central  Google Scholar 

  • Drobnic K, Bakal N, Marjanovic D (2005) Allele frequencies for the 15 short tandem repeat loci in Slovenian population. J Forensic Sci 50:1–3

    Article  Google Scholar 

  • Eltouhamy I (2015) Language attitudes towards dialects of Arabic in Egypt. MA Thesis, The American University in Cairo, Egypt

  • Excoffier L, Laval G, Schneider S (2005) Arlequin Ver. 3.1.1: an integrated software package for population genetics data analysis. Evol Bioinform Online 1:147–150

    Article  Google Scholar 

  • Gary JO, Gamal-Eldin S (1982) Cairene Egyptian colloquial Arabic. Lingua Descriptive Studies, Vol. 6, North-Holland, Amsterdam

  • Goudet J (2002) FSTAT computer package for PCs. Institute of Ecology, UNIL, Lausanne

    Google Scholar 

  • Hadi I, Abdullah M, Jaber A, Yoke C (2014) Genetic variation of twenty autosomal STR loci and evaluate the importance of these loci for forensic genetic purposes. Afr J Biotechnol 13:1210–1218

    Article  CAS  Google Scholar 

  • Haeri N (1997) The sociolinguistic market of Cairo. Paul Kegan International, London

    Google Scholar 

  • Halima MSHA, Bernal LP, Sharif FA (2009) Genetic variation of 15 autosomal short tandem repeat (STR) loci in the Palestinian population of Gaza Strip. Leg Med (Tokyo) 11:203–204

    Article  CAS  Google Scholar 

  • Jeran N, Havas D, Ivanovic V, Rudan B (2007) Genetic diversity of 15 STR loci in a population of Montenegro. Coll Antropol 3:847–852

    Google Scholar 

  • Jong R (2000) A grammar of the Bedouin Dialects of the Northern Sinai Littoral: bridging the linguistic gap between the eastern and western Arab world. Brill, Leiden

    Google Scholar 

  • Jong R (2011) A grammar of the Bedouin Dialects of Central and Southern Sinai. Brill, Leiden

    Book  Google Scholar 

  • Keita SO, Boyce AJ (2005) Genetics, Egypt, and history: interpreting geographical patterns of Y chromosome variation. Hist Afr 32:221–246

    Article  Google Scholar 

  • Khodjet-el-khil H, Fadhlaoui-Zid K, Gusmao L, Alves C, Benammar-Elgaaied A, Amorism A (2012) Allele frequencies for 15 autosomal STR markers in the Libyan population. Ann Hum Biol 39:80–83

    Article  PubMed  Google Scholar 

  • Kimura M, Crow JF (1964) The number of alleles that can be maintained in a finite population. Genetics 49:725–738

    PubMed  PubMed Central  CAS  Google Scholar 

  • Krings M, Salem AE, Bauer K, Geisert H, Malek AK, Chaix L, Simon C, Welsby D, Di Rienzo A, Utermann G, Sajantila A, Paabo S, Stoneking M (1999) mtDNA analysis of Nile River Valley populations: a genetic corridor or a barrier to migration. Am J Hum Genet 64:1166–1176

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Levene H (1949) On a matching problem in genetics. Ann Math Stat 20:91–94

    Article  Google Scholar 

  • Marsot A (2007) A history of Egypt from the Arab conquest to the present. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Midant-Reynes B (2000) The prehistory of Egypt: from the first Egyptians to the first Pharaohs. Blackwell, Oxford

    Google Scholar 

  • Mortera J, Vecchiotti C, Zoppis S, Merigioli S (2016) Paternity testing that involves a DNA mixture. Forensic Sci Int Genet 23:50–54

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Article  Google Scholar 

  • Nishio T (1994) The Arabic Dialect of Qifṭ (Upper Egypt): grammar and classified vocabulary. Asian & African Lexicon 27, Institute for the Study of Languages and Cultures of Asia and Africa, Tokyo

  • Omran GA, Rutty GN, Jobling MA (2009) Genetic variation of 15 autosomal STR loci in Upper (Southern) Egyptians. Forensic Sci Int Genet 3:e39–e44

    Article  PubMed  CAS  Google Scholar 

  • Osman AE, Alsafar H, Tay GK, Theyab J, Mubasher M, Eltayeb-El Sheikh N, AlHarthi H, Crawford MH, El Ghazali G (2015) Autosomal short tandem repeat (STR) variation based on 15 loci in a population from the central region (Riyadh Province) of Saudi Arabia. J Forensic Res 6:267–271

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Rouchdy A (1991) Nubians and the Nubian language in contemporary Egypt: a case of cultural and linguistic contacts. Brill, Leiden

    Book  Google Scholar 

  • Rousset F (2008) GENEPOP ‘007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Res 8:103–106

    Article  Google Scholar 

  • Shaw I (2004) Ancient Egypt: a very short introduction. Oxford University Press, New York

    Book  Google Scholar 

  • Shawky RM, El-Awady MY, Elsayed SM, Hamadan GE (2011) Consanguineous mating among Egyptian population. EJMHG 12:157–163

    Google Scholar 

  • Stanciu F, Stoian IM, Popescu OR (2009) Population data for 15 short tandem repeat loci from Wallachia region, South Romania. Croat Med J 50:321–325

    Article  PubMed  PubMed Central  Google Scholar 

  • Thomson JA, Pilotti V, Stevens P, Ayres KL, Debenham PG (1999) Validation of short tandem repeat analysis for the investigation of cases of disputed paternity. Forensic Sci Int 100:1–16

    Article  PubMed  CAS  Google Scholar 

  • Versteegh K (2001) The Arabic language. Edinburgh University Press, Edinburgh

    Google Scholar 

  • Weir BS (1990) Genetic data analysis: methods for discrete population genetic data. Sinauer Associates, Sunderland

    Google Scholar 

  • Weir BS (1996) The second national research council report on forensic DNA evidence. Am J Hum Genet 59:497–500

    PubMed  PubMed Central  CAS  Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    PubMed  CAS  Google Scholar 

  • White JM (2011) Everyday life in ancient Egypt. Dover Publications, New York

    Google Scholar 

  • Woidich M (1994) Cairo Arabic and the Egyptian dialects. In Caubet D, Vanhove M (eds) Actes des Premières Journees Internationales de Dialectologie Arabe de Paris. Paris, pp 493–507

  • Woidich M (1996) Rural Dialect of Egyptian Arabic: an overview. Égypte-monde arabe 27–28:325–354

    Article  Google Scholar 

  • Wright S (1951) The genetic structure of populations. Ann Eugen 15:323–354

    Article  PubMed  CAS  Google Scholar 

  • Wright S (1978) Evolution and the genetics of populations: variability within and among natural populations, vol 4. University of Chicago Press, Chicago

    Google Scholar 

  • Yao J, Wang LM, Gui J, Xing JX, Xuan JF, Wang BJ (2016) Population data of 15 autosomal STR loci in Chinese Han population from Liaoning Province, Northeast China. Forensic Sci Int Genet 23:e20–e21

    Article  PubMed  Google Scholar 

  • Yeh FC, Boyle T, Rongcai Y, Ye Z, Xian JM (1999) POPGENE, Version 1.31. A Microsoft Window based free ware for population genetic analysis. University of Alberta, Edmonton

Download references

Acknowledgements

The authors gratefully thank the volunteers whose cooperation made this study possible. The authors also would like to thank the Forensic Science Laboratory Unit, Police Academy, Cairo, Egypt, for the support during the investigation, also the Egyptian Ministry of Interior for its cooperation. The authors would like to express their deepest gratitude and thanks to Prof. Mohammed Saber, Cell Biology Department, National Research Center, Egypt, Dr. Sherif Abdel-Ghany, Faculty of Agriculture, Cairo University, Egypt, and Dr. Abdullah Agha, Faculty of Science, Taibah University, Saudi Arabia, for their kind support and suggestions.

Author information

Authors and Affiliations

  1. General Authority of Forensic Evidence, Police Academy, Cairo, Egypt

    Ahmed F. AbdEl-Hafez

  2. Department of Zoology, Faculty of Science, Ain Shams University, Cairo, Egypt

    Sherif H. El-Alfy, Hamdy H. Swelim & Nagwa H. A. Hassan

  3. Department of Biology, Faculty of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia

    Sherif H. El-Alfy

Authors
  1. Ahmed F. AbdEl-Hafez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sherif H. El-Alfy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hamdy H. Swelim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nagwa H. A. Hassan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ahmed F. AbdEl-Hafez.

Ethics declarations

Conflict of interest

The authors declare no conflict of interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

AbdEl-Hafez, A.F., El-Alfy, S.H., Swelim, H.H. et al. Genetic Variation at 15 Autosomal STR Loci Among Seven Egyptian Populations. Biochem Genet 57, 170–191 (2019). https://doi.org/10.1007/s10528-018-9879-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-018-9879-0

Keywords

Search

Navigation