1School of Life Sciences, The University of Nottingham, University Park, Nottingham. NG7 2RD, United Kingdom
2Department of Animal Breeding and Genetics, Federal University of Agriculture, P. M. B. 2240, Abeokuta, Nigeria
Raman A. Lawal1, Ayotunde. O. Adebambo2, Takele T. Desta1, David Wragg1, Olivier Hanotte1
Introduction
Archaeological evidence shows that chicken, which millions of subsistence farmers depend on, likely entered the African
continent first through the North of Africa, and subsequently dispersed towards Eastern and Western Africa1,2. It is
assumed that this geographical dispersion pattern may have caused variation in the genetic structure of the village
chicken. This study examines the differentiation that may have taken place between and within Ethiopian and Nigerian
village chicken populations.
Methodology
A total of 52 samples from 14 populations of village chickens across Ethiopia (East Africa) and Nigeria (West Africa) were
genotyped using the high density (580K) Axiom® genome-wide chicken genotyping array3. Quality control include SNP
(Single Nucleotide Polymorphism) call rate of > 0.95, P < 0.001 for Hardy and Weinberg Equilibrium (HWE), and maf
(minor allele frequency) > 0.05. Principal component analysis (PCA4) was performed in R5 of GenABEL6 and Adegenet7
libraries using custom script, genetic relationships using MEGA 5.28 and admixture analysis using R5, distruct9 and GSview
version 5.010. The Fst and heterozygosities (Ho and He) of the population were calculated also in R5 using custom scripts.
Results and Discussion
Figure 1 PCA of Ethiopian - Nigerian population
Sampling area
The PCA results are presented in figure 1. 1st and 2nd PC
explains together about 50% of total variance. Both
separate the Nigerian and Ethiopian chicken with more
genetic variations across Ethiopian chicken. A group of 3
Ethiopian and one Nigerian chicken occupied an
intermediate position (C2) and 3 Nigerian chicken were
separated from the others (C1). Relationship tree (figure
3) largely support the PCA results (C1 and C2).
Incomplete genetic differentiation (Fst = 0.053) was
observed between the two countries despite the presence
of large geographical distances. Admixture (k = 2)
clearly separate Ethiopian and Nigerian populations
(figure 2). At advance level of k there is more diversity
within Ethiopian population than in Nigerian population.
Nigerian village chicken11
Figure 3 Genetic relationship tree (Neighbour Joining) of Ethiopian – Nigerian
chicken population
Ethiopia village chicken
(1) MacDonald KC .1992. J. of Arch. Sci., 19, 303–318. (2) Blench R, MacDonald KC. 2000. Origins & Development of African Livestock. (3) Kranis A.
et al., 2013 BMC Genomics 14:59 (4) Dray, S. and Dufour, A.B. 2007. J. Stat. Softw. 22(4), 1–20. (5) R Development Core Team, 2012. R Version
2.15.1 (6)Aulchenko, Y. S. et al., 2007. Bioinformatics,1294–1296 (7) Jombart T and Ahmed I (2011). d oi:10.1093/bioinformatics/btr521
Bioinformatics. (8) Saitou N. and Nei M. 1987. Mol. Bio and Evol. 4:406-425. (9) Rosenberg N. A. 2004. Molecular Ecology Notes 4:137-138.
(10) http://pages.cs.wisc.edu (11) www.bellanaija.com
References
Acknowledgment
This project was supported by The University of Nottingham Vice chancellor’s
Scholarship (International)
Sampling location in
blue circle
Population Ho ± SD He ± SD Inbreeding (Fis)
Nigeria 0.318 ± 0.035 0.353 ± 3.33e-05 0.101 ± 0.099
Ethiopia 0.299 ± 0.035 0.345 ± 4.20e-05 0.133 ± 0.102
Table 1 Mean and SD of Heterozygosity across loci within population
K
=
2
K
=
3
K
=
4
K
=
5
K
=
6
K
=
7
K
=
8
Figure 2 Genetic admixture observed in the sampled
of African village chicken population
Conclusions
1. Despite large geographical distance between the two populations, incomplete
genetic differentiation was observed between countries perhaps reflecting a
legacy of common ancestry and recent arrival of chicken on the studied
geographic areas
2. Alternatively, common commercial introgression may have happen in some birds
in Nigeria and Ethiopia
3. Higher proportion of molecular variations observed within Ethiopian population
support level of differentiation observed between population within country
4. Further studies with more locations and birds may further clarify these issues
Jarso chicken (Ethiopia)
with villager
Genetic differentiation of Ethiopian
and Nigerian village chicken
Corresponding author: Raman Lawal (plxral@nottingham.ac.uk)
C1
C2
PC1 (49.52)
P
C
2
(
5
.6
5
)
C1
C2
Ethiopian chicken
Nigerian chicken
2.0