Genetic Diversity and Population Structure of Local Chicken in Burkina Faso

S. Pindé; R. W.  Ouédraogo; A. S. R.  Tapsoba; E. A. W.  Pilabré; S. E. Sawadogo; F. G. Traoré; S. Ba; M. Sanou; H. H. Tamboura; A. Traoré; K. Periasamy; J. Simporé

doi:10.5398/tasj.2026.49.6.544

S. Pindé ⁽¹⁾ , R. W. Ouédraogo ⁽¹⁾ , A. S. R. Tapsoba ⁽¹⁾ , E. A. W. Pilabré ⁽¹⁾ , S. E. Sawadogo ⁽¹⁾ , F. G. Traoré ⁽¹⁾ , S. Ba ⁽¹⁾ , M. Sanou ⁽¹⁾ , H. H. Tamboura ⁽¹⁾ , A. Traoré ⁽¹⁾ , K. Periasamy ⁽²⁾ , J. Simporé ⁽³⁾

(1) Laboratoire de Biologie et Santé Animales (LaBioSA), Institut de l’Environnement et de Recherches Agricoles (INERA), Burkina Faso,

(2) International Atomic Energy Agency (IAEA)-Animal Production and Health Laboratory, Austria,

(3) Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE), Université Joseph KI-ZERBO (UJKZ), Burkina Faso

https://doi.org/10.5398/tasj.2026.49.6.544

Issue
Vol. 49 No. 6 (2026): Tropical Animal Science Journal (Issue in progress)

Submitted
April 1, 2026

Accepted
July 14, 2026

Published
September 3, 2026

Keywords:

diversity, structure, microsatellite, chickens, Burkina Faso

PDF XML

Abstract

Poultry farming plays a vital role in rural livelihoods and is a primary source of animal protein in Burkina Faso. However, the increasing introduction of fast-growing exotic breeds threatens the genetic integrity of local chicken populations. This study aimed to assess the genetic diversity and structure of local chickens using 27 microsatellite markers, of which 23 were selected and 19 polymorphic markers were retained for analysis. A total of 116 individuals from local populations were genotyped, along with 20 individuals of the exotic broiler breed Cobb 500 for comparison. Genetic diversity, Hardy-Weinberg equilibrium, genetic distances, and population structure were evaluated using Bayesian and multivariate approaches. Results showed that 19 loci were polymorphic, revealing high allelic diversity with 117 alleles and a mean of 6.16 alleles per locus. The overall heterozygosity deficit (FIS) was low (0.04). Genetic differentiation among all populations was moderate (FST = 0.10), with higher differentiation between local populations and the exotic breed (FST = 0.19) and very low differentiation among local subpopulations (maximum FST = 0.04). Phylogenetic and Bayesian analyses indicated high admixture among local chickens, suggesting a largely homogeneous genetic structure, although the Sahelian population appeared slightly distinct. Evidence of introgression from exotic breeds was also observed, particularly in the Sudanian and Sudano-Sahelian zones. In conclusion, the local chickens of Burkina Faso form a single, weakly structured genetic pool characterized by high allelic diversity and a low heterozygosity deficit.

Full text article

Generated from XML file

References

Ajibike, A. B., Adeniyi, O. A., Ilori, B. M., Durosaro, S. O., Osinbowale, D. A., Adeleye, O. O., & Adebambo, A. O. (2022). Genetic diversity and population structure of Nigerian indigenous chicken populations inferred from microsatellite markers. Agriculturae Conspectus Scientificus, 87(1), 61–67. https://hrcak.srce.hr/file/397844

Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314-331. https://pmc.ncbi.nlm.nih.gov/articles/PMC1686077/

Dieringer, D., & Schlotterer, C. (2003). MICROSATELLITE ANALYZER (MSA): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167-169. https://doi.org/10.1046/j.1471-8286.2003.00351.x

Earl, D. A. & VonHoldt, B. M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361. https://doi.org/10.1007/s12686-011-9548-7

Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology, 14(8), 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

Fathi, M. M., Al-Homidan, I., Motawei, M. I., Abou-Emera, O. K., & El-Zarei, M. F. (2017). Evaluation of genetic diversity of Saudi native chicken populations using microsatellite markers. Poultry Science, 96(3), 530–536. https://doi.org/10.3382/ps/pew357

Felsenstein, J. (1989). PHYLIP : Phylogeny Inference Package (Version 3.2). Cladistics 5, 164-166.

Gheyas, A. A., Vallejo-Trujillo, A., Kebede, A., Lozano-Jaramillo, M., Dessie, T., Smith, J., & Hanotte, O. (2021). Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens. Molecular Biology and Evolution, 38(10), 4268–4285. https://doi.org/10.1093/molbev/msab156

Goudet, J. (2002). FSTAT version (2.9.3.2). A computer program to calculate F-Statistics. Journal of Heredity 86(6), 485-486.

Habimana, R., Okeno, T. O., Ngeno, K., Mboumba, S., Assami, P., Gbotto, A. A., Keambou, C. T., Nishimwe, K., Mahoro, J., & Yao, N. (2020). Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS ONE, 15(4), e0225084. https://doi.org/10.1371/journal.pone.0225084

Hall, S. J. G. (2022). Genetic differentiation among livestock breeds-values for Fst. Animals, 12(9), 1115. https://doi.org/10.3390/ani12091115

Hailu, A., Kyallo, M., Yohannes, T., Sendeku, W., Getu, A., Dagnachew, S., Dejen, M., Wolde, Y., Engdaw, F., Kidane, A., Dessie, T., Tarekegn, G. M., Githae, D., & Pelle, R. (2020). Genetic diversity and population structure of indigenous chicken ecotypes (Gallus gallus domesticus) in Ethiopia using LEI0258 microsatellite. International Journal of Poultry Science, 19(3), 102–110. https://doi.org/10.3923/ijps.2020.102.110

Kalinowski, S. T., Taper, M. L., & Marshall, T. C. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16(5), 1099-1106. https://doi.org/10.1111/j.1365-294X.2007.03089.x

Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096

Lawal, R. A., Al-Atiyat, R. M., Aljumaah, R. S., Silva, P., Mwacharo, J. M., & Hanotte, O. (2018). Whole-genome resequencing of red junglefowl and indigenous village chicken reveal new insights on the genome dynamics of the species. Frontiers in Genetics, 9, article 264. https://doi.org/10.3389/fgene.2018.00264

Lawal, R. A., & Hanotte, O. (2021). Domestic chicken diversity: Origin, distribution, and adaptation. Animal Genetics, 52(4), 385–394. https://doi.org/10.1111/age.13091

Leroy, G., Baumung, R., Boettcher, P., Besbes, B., From, T., & Hoffmann, I. (2018). Animal genetic resources diversity and ecosystem services. Global Food Security, 17, 84-91. https://doi.org/10.1016/j.gfs.2018.04.003

Long, A., Qing, Y., Gu, T., Zhu, Q., Liu, Y., Wang, Y., Yin, H., Shu, G., Zhang, Y., Lai, S., & Zhao, X. (2017). Genetic variation of nine chicken breeds collected from different altitudes revealed by microsatellites. The Journal of Poultry Science, 54(1), 18–25. https://doi.org/10.2141/jpsa.0160033

Manjula, P., Kim, M., Cho, S., Seo, D., & Lee, J. H. (2021). High levels of genetic variation in MHC-linked microsatellite markers from native chicken breeds. Genes, 12(2), 240. https://doi.org/10.3390/genes12020240

Mogano, R. R., Mpofu, T. J., Mtileni, B., & Hadebe, K. (2024). The risk status, signatures of adaptation, and environmental suitability of village-based indigenous chickens from certain regions of Limpopo and KwaZulu-Natal provinces of South Africa. Frontiers in Genetics, 15, article 1450939. https://doi.org/10.3389/fgene.2024.1450939

MRAH/DGESS. (2023). Annuaire statistique du Ministère des Ressources Animales et Halieutiques. Burkina Faso.

Mwambene, P. L., Kyallo, M., Machuka, E., Githae, D., & Pelle, R. (2019). Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing. Poultry Science, 98(7), 2734–2746. https://doi.org/10.3382/ps/pez043

Nematbakhsh, S., Pei Pei, C., Nordin, N., Selamat, J., Idris, L. H., & Abdull Razis, A. F. (2024). Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches. Poultry Science, 103(10), 104128. https://doi.org/10.1016/j.psj.2024.104128

Nxumalo, N., Ceccobelli, S., Cardinali, I., Lancioni, H., Lasagna, E., & Kunene, N. W. (2020). Genetic diversity, population structure and ancestral origin of KwaZulu-Natal native chicken ecotypes using microsatellite and mitochondrial DNA markers. Italian Journal of Animal Science, 19(1), 1275–1288. https://doi.org/10.1080/1828051X.2020.1838350

Okumu, O. N., Ngeranwa, J. J. N., Binepal, Y. S., Kahi, A. K., Bramwel, W. W., Ateya, L. O., & Wekesa, F. C. (2017). Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers. Journal of Genetic Engineering and Biotechnology, 15(2), 489–495. https://doi.org/10.1016/j.jgeb.2017.04.007

Oosterhout, C. V., Hutchinson, W. F., Wills, D. P. M., & Shipley, P. (2004). Program Note: Microchecker: Software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4(3), 535-538. https://doi.org/10.1111/j.1471-8286.2004.00684.x

Pindé, S., Tapsoba, A. S. R., Traoré, F., Ouédraogo, R., Ba, S., Sanou, M., Traoré, A., Tamboura, H. H., & Simporé, J. (2020). Caractérisation et typologie des systèmes d’élevage de la poule locale du Burkina Faso. Journal of Animal & Plant Sciences, 46(2), 8212-8225. https://doi.org/10.35759/JAnmPlSci.v46-2.6

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155, 945-959. https://doi.org/10.1093/genetics/155.2.945

Rashid, M. A., Manjula, P., Faruque, S., Bhuiyan, A. K. F. H., Seo, D., Alam, J., Lee, J. H., & Bhuiyan, M. S. A. (2020). Genetic diversity and population structure of indigenous chicken of Bangladesh using microsatellite markers. Asian-Australasian Journal of Animal Sciences, 33(11), 1732–1740. https://doi.org/10.5713/ajas.20.0189

Raymond, M., & Rousset, F. (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86(6), 248-249. https://doi.org/10.1093/oxfordjournals.jhered.a111573

Ren, T., Nunome, M., Suzuki, T., & Matsuda, Y. (2022). Genetic diversity and population genetic structure of Cambodian indigenous chickens. Animal Bioscience, 35(6), 826–837. https://doi.org/10.5713/ab.21.0351

Roh, H. J., Kim, S. C., Cho, C. Y., Lee, J., Jeon, D., Kim, D. K., Kim, K. W., Afrin, F., Ko, Y. G., Lee, J. H., Batsaikhan, S., Susanti, T., Hegay, S., Kongvongxay, S., Gorkhali, N. A., Nguyen Thi, L. A., Thao, T. T. T., & Manikku, L. (2020). Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers. Asian-Australasian Journal of Animal Sciences, 33(12), 1896–1904. https://doi.org/10.5713/ajas.19.0958

Samaraweera, A. M., Liyanage, R., Ibrahim, M. N., Okeyo, A. M., Han, J., & Silva, P. (2021). High genetic diversity but absence of population structure in local chickens of Sri Lanka inferred by microsatellite markers. Frontiers in Genetics, 12, article 723706. https://doi.org/10.3389/fgene.2021.723706

Sunde, J., Yıldırım, Y., Tibblin, P., & Forsman, A. (2020). Comparing the performance of microsatellites and RADseq in population genetic studies: Analysis of data for pike (Esox lucius) and a synthesis of previous studies. Frontiers in Genetics, 11, article 218. https://doi.org/10.3389/fgene.2020.00218

Tapsoba, A. S. R., Sawadogo, S. E., Yougbaré, B., Traoré, F. G., Béré, F., Sanou, M., Tamboura, H. H., Bayala, B., Pichler, R., Traoré, A., & Periasamy, K. (2024). Genetic diversity and population structure of taurine cattle using STR markers in Burkina Faso, West Africa. Tropical Animal Science Journal, 47(2), 131–140. https://doi.org/10.5398/tasj.2024.47.2.131

Traoré, F. G., Traoré, A., Bayala, B., Dayo, G. K., Tapsoba, A. S., Ssoudré, A., Sanou, M., Tindano, K., & Tamboura, H. H. (2018). Characterization and typology of Guinea fowl (Numida meleagris) farming Systems in Burkina Faso. International Journal of Advanced Research, 6(1), 6-21. https://doi.org/10.21474/IJAR01/6177

Wen, Z., Cai, X., Liu, Z., Tan, L., Kong, Y., Wang, Y., & Zhao, Y. (2025). Genomic analyses reveal a lack of widespread strong selection in indigenous chickens. Poultry Science, 104(5), 105081. https://doi.org/10.1016/j.psj.2025.105081

Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38(6), 1358-1370. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1984.tb05657.x

Wright, S. (1978). Evolution and the Genetics of Populations, Volume 4: Variability Within and Among Natural Populations. University of Chicago Press, USA.

Xu, D., Zhu, W., Wu, Y., Wei, S., Shu, G., Tian, Y., Du, X., Tang, J., Feng, Y., Wu, G., Han, X., & Zhao, X. (2023). Whole-genome sequencing revealed genetic diversity, structure and patterns of selection in Guizhou indigenous chickens. BMC Genomics, 24(1), 570. https://doi.org/10.1186/s12864-023-09621-w

Yacouba, Z., Isidore, H., Michel, K., Isidore, G. B., Boureima, T., Vinsoun, M., Maurice, K., Ousseni, B., Moussa, Z., Valerie, B.-Y. M. C., Romdhane, R., & Joseph, N. A. (2022). Genetic diversity and population structure of local chicken ecotypes in Burkina Faso using microsatellite markers. Genes, 13(9), 1523. https://doi.org/10.3390/genes13091523

Zhi, Y., Wang, D., Zhang, K., Wang, Y., Geng, W., Chen, B., Li, H., Li, Z., Tian, Y., Kang, X., & Liu, X. (2023). Genome-wide genetic structure of Henan indigenous chicken breeds. Animals 13(4), 753. https://doi.org/10.3390/ani13040753

Zhuang , Z., Zhao, L., Zong, W., Guo, Q., Li, X., Bi, Y., Wang, Z., Jiang, Y., Chen, G., Li, B., Chang, G., & Bai, H. (2023). Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis. Journal of Animal Science, 101, article skad182. https://doi.org/10.1093/jas/skad182