Genome screening for specific microsatellite markers in Nigerian ethnic populations

Abstract

Background: DNA markers are very effective for distinguishing among individuals. The abundance and high variability of microsatellites in diverse genomes are useful tools for identification, linkage analysis, forensic investigations and phylogeny reconstruction. This study analyzed microsatellites in three Nigerian ethnic groups in order to detect unique microsatellites for estimation of ethnic affiliation.

Materials and methods: Five hundred and sixty adult Nigerians of Hausa (175), Igbo (163) and Yoruba (222) extraction participated in the study. Deoxyribonucleic acid (DNA) was extracted from dry blood spots on filter paper and microsatellites loci were amplified by Inter Simple Sequence Repeat (ISSR) primers. Amplicon bands were scored for distinct microsatellite alleles. The result was analyzed for phylogeny, cluster analysis, genetic distance, and genetic identity. Sequencing was performed on microsatellite loci within ethnic clusters.

Results: The phylogenetic tree and the principal coordinate analysis of amplified loci revealed clustering of the three ethnic populations with a 2% molecular variance. Pairwise population matrix of Nei genetic distance was 0.032 between Hausa and Igbo, 0.027 between Igbo and Yoruba, and 0.024 between Hausa and Yoruba. Fixation index was 0.022 for Hausa and Igbo, 0.020 for Igbo and Yoruba, and 0.019 for Hausa and Yoruba. Nei genetic identity was 0.969 between Hausa and Igbo, 0.973 between Igbo and Yoruba, and 0.977 between Hausa and Yoruba. Allelic sequencing revealed 1484 microsatellites, 2.8% (41) of which were specific for the ethnic groups either trimeric, tetrameric, pentameric or hexameric.

Conclusion: Findings of this study are suggestive of microsatellites being able to confirm the identity of ethnic populations despite close genetic distance.

Keywords: Genome screening, microsatellite markers, Nigerian populations.

Abstrait
Contexte : les marqueurs ADN sont très efficaces pour distinguer les individus. L’abondance et la grande variabilité des microsatellites dans divers génomes sont des outils utiles pour l’identification, l’analyse de liaison, les enquêtes forensiques et la reconstruction de la phylogénie. Cette étude a analysé des microsatellites dans trois groupes ethniques nigérians afin de détecter des microsatellites uniques pour l’estimation de l’appartenance ethnique.

Matériel et méthodes : Cinq cent soixante Nigérians adultes d’extraction haoussa (175), Igbo (163) et yoruba (222) ont participé à l’étude. L’acide désoxyribonucléique (ADN) a été extrait de taches de sang sec sur papier filtre et les locus de microsatellites ont été amplifiés par des amorces Inter Simple Séquence Répéter (ISSR). Les bandes d’ amplicon ont été évaluées pour les allèles microsatellites distincts. Le résultat a été analysé pour la phylogénie, l’analyse des groupes, la distance génétique et l’identité génétique. Le séquençage a été effectué sur des loci microsatellites au sein de groupes ethniques.

Résultats: L’arbre phylogénétique et l’analyse des coordonnées principales des locus amplifiés ont révélé un regroupement des trois populations ethniques avec une variance moléculaire de 2%. La matrice de population par paires de la distance génétique Nei était de 0,032 entre Haoussa et Igbo, 0,027 entre Igbo et Yoruba et 0,024 entre Haoussa et Yoruba. L’indice de fixation était de 0,022 pour haoussa et Igbo, de 0,020 pour Igbo et yoruba et de 0,019 pour haoussa et yoruba. L’ identité génétique Nei était de 0,969 entre Haoussa et Igbo, 0,973 entre Igbo et Yoruba et 0,977 entre Haoussa et Yoruba. Le séquençage allélique a révélé 1484 microsatellites, dont 2,8% (41) étaient spécifiques des groupes ethniques trimériques, tétramériques, pentamériques ou hexamèriques.

Conclusion: Les résultats de cette étude suggèrent que les microsatellites sont capables de confirmer l’identité des populations ethniques malgré une distance génétique proche.

Mots clés: Dépistage du génome, marqueurs microsatellites, populations nigérianes.

Correspondence: Prof. M.T. Shokunbi, Department of Anatomy, College of Medicine, University of Ibadan, Ibadan, Nigeria. E-mail: temitayoshokunbi@yahoo.com

pdf

References

Campbell, MC and Tishkoff SA. African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annual review of Genomics and Human Genetics 2008; 9: 403-433.

Jeffreys AJ, Royle NJ, Wilson V and Wong Z. Spontaneous mutation rates to new length alleles at tandem-repetitive hypervariable loci in human DNA. Nature1988; 332(6161), 278.

Korpelainen H, Kostamo K and Virtanen V. Microsattelites marker identification using genome screening and restriction-ligation. BioTechniques 2007; 42(4):479-486.

Ellegren H. Microsatellites: Simple Sequences with complex evolution. Nature Reviews Genetics 2004; 5: 435- 445.

Weissenbach J, Gyapay G, Dib C, et al. Second-generation linkage map of the human genome. Nature 1992; 359: 794–801.

Broman KW, Murray JC, Sheffield VC, White RL and Weber JL. Comprehensive human genetic maps: individual and sex-specific variation in recombination. American Journal Human Genetics 1998; 63, 861–869.

Kashyap VK, Ashma R, Gaikwad S, Sarkar BN and Trivedi R. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: Analysis based on 15 microsatellite markers. Journal of Genetics 2004; 83(1): 49-63.

Kopelman NM, Stone L, Wang C, et al. Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations. BMC Genetics 2009; 10:80.

Babiker HMA, Schlebusch CM, Hassan HY and Jakobsson M. Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci. Investigative Genetics 2011; 2:12.

Pemberton TJ, DeGiorgio M, and Rosenberg NA. Population structure in a comprehensive genomic data set on human microsatellite variation. G3: Genes, Genomes, Genetics 2013; 3(5), 891-907.

Camacho-Mejorado R, Noris G, Santana C, et al Interethnic variation of the MMP-9 microsatellite in Amerindian and Mexican Mestizo populations: considerations for genetic association studies. Genetics and Molecular Research 2015; 14(1), 2929-2939.

Algee-Hewitt BF, Edge MD, Kim J, Li JZ and Rosenberg NA. Individual identifiability predicts population identifiability in forensic microsatellite markers. Current Biology 2016; 26(7), 935-942.

Agbo BU, Ebuehi OAT and de Osuntoki AA. Genetic Variations at 15 Forensically Relevant Microsatellite Loci (STRs) in the Three Major Ethno-Linguistic Population Groups in Nigeria. The FASEB Journal 2017; 31(1_supplement), 591-610.

He G, Wang Z, Wang M, et al. Genetic variations and forensic characteristics of Han Chinese population residing in the Pearl River Delta revealed by 23 autosomal STRs. Molecular biology reports 2018; 45(5), 1125-1133.

Bashalkhanov S, Pandey M and Rajora OP. A simple method for estimating genetic diversity in large populations from finite sample sizes. BMC genetics 2009; 10(1): 84.

Paetkau D. Calvert W, Stirling I, Strobeck C. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 1995; 4(3): 347–354.

Rannala B and Mountain JL. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA 1997; 94: 9197– 9201.

Neel JV. “Private” genetic variants and the frequency of mutation among South American Indians. Proceedings of National Academy Science 1973; 70(12):3311–3315.

Reed TE. Number of gene loci required for accurate estimation of ancestral population proportions in individual human hybrids. Nature 1973; 244:575-576.

Chakraborty R, Fornage M, Gueguen R and Boerwinkle E. Population genetics of hypervariable loci: analysis of PCR based VNTR polymorphism within a population. In DNA fingerprinting: approaches and applications 1991; (pp. 127-143). Birkhäuser Basel.

Chakraborty R, Kamboh MI, Nwankwo M and Ferrell RE. Caucasian genes in American blacks: new data. American Journal of Human Genetics 1992; 50(1):145–155.

Stephens JC, Briscoe D, O’Brien SJ. Mapping by admixture linkage disequilibrium in human populations: limits and guidelines. American Journal Human Genetics 1994; 55(4):809–824.

Shriver MD, Smith MW, Jin L, et al. Ethnic-affiliation estimation by use of population-specific DNA markers. American journal of human genetics 1997; 60(4), 957.

Sun H, Zhou C, Huang X, et al. Correlation between the linguistic affinity and genetic diversity of Chinese ethnic groups. Journal of human genetics 2013; 58(10): 686-693.

Otitie O. Nigeria’s Identifiable Ethnic Groups. https://www.onlinenigeria. com/tribes/tribes.asp. Extracted on 20/9/2016.

Edwards AL, Hammond H.A, Jin L, Caskey CT and Chakraborty R. Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. Genomics 1992; 12(2): 241-253.

Norrgard K. Forensics, DNA fingerprinting, and CODIS. Nature Education 2008; 1(1):35.

Madden T. The BLAST sequence analysis tool 2013.

Coordinators NR. Database resources of the national center for biotechnology information. Nucleic acids research 2015; 43(Database issue), D6.

Tishkoff SA, Reed FA, Friedlaender FR, et al. The Genetic Structure and History of Africans and Afrcan Americans. Science 2009; 324(5930): 1035-1044.