Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

Richard Habimana; Tobias Otieno Okeno; Kiplangat Ngeno; Sylvere Mboumba; Pauline Assami; Anique Ahou Gbotto; Christian Tiambo Keambou; Kizito Nishimwe; Janvier Mahoro; Nasser Yao

doi:10.1371/journal.pone.0225084

Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers

PLoS One. 2020 Apr 2;15(4):e0225084. doi: 10.1371/journal.pone.0225084. eCollection 2020.

Authors

Affiliations

¹ Animal Science and Veterinary Medicine, University of Rwanda, College of Agriculture, Nyagatare, Rwanda.
² Department of Animal Science, Animal Breeding and Genomics Group, Egerton University, Nakuru, Kenya.
³ Faculty of Agronomy and Biotechnologies, Masuku University of Science and Techniques, Franceville, Gabon.
⁴ Biosciences eastern and central Africa, International Livestock Research Institute Hub, Nairobi, Kenya.
⁵ Laboratoire de genomique Fonctionnelle et Amélioration Génétique Université Nangui Abrogoua, Abidjan, Cote d'Ivoire.
⁶ Faculty of Agriculture and Veterinary medicine, University of Buea, Buea, Cameroon.

Abstract

Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chickens were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. One hundred eighty-six (186) distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant (p<0.05) in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Alleles
Animals
Breeding*
Chickens / genetics*
Genetic Variation / genetics*
Genotype
Humans
Microsatellite Repeats / genetics
Population Surveillance*
Rwanda

Grants and funding

This study was part of PhD research of the first author and he is thankful to the financial and technical support from BecA-ILRI Hub through Africa Biosciences Challenge Fund (ABCF) programmes. The ABCF Programmes is funded by the Australian Department for Foreign Affairs and Trade (DFAT) through the BecA-CSIRO partnership; the Syngenta Foundation for Sustainable Agriculture (SFSA); the Bill & Melinda Gates Foundation (BMGF); the UK Department for International Development (DFID) and the Swedish International Development Cooperation Agency (SIDA). This material is also based upon work supported by the United States Agency for International Development, as part of the Feed the Future initiative, under the CGIAR Fund, award number BFS-G-11-00002, and the predecessor fund the Food Security and Crisis Mitigation II grant, award number EEM-G-00-04-00013. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.