Genetic disconnectedness in indigenous village chickens
Takele Taye Desta§, David Wragg, Joram Mwacharo, Olivier Hanotte
Centre for Genetics and Genomics, School of Biology, University of Nottingham, University Park, Nottingham, UK
§plxtd@nottingham.ac.uk
Introduction
Village chickens have been kept by smallholder farmers since the domestication of Gallus gallus. They are characterized by hypervariable phenomic landscape.
Specifically, high intra population phenotypic diversity has made largely impractical to assign these populations into clearly defined breeds. Dissecting the genetic
structure of admixed populations of this kind requires a large number of genetic markers. Exploring this genetic diversity is important for genetic improvement and
conservation management. Here we present the genetic structure of eight village chicken populations sampled from Africa, Asia and Latin America.
Study tools Genetic distances: Pairwise genetic distance was the lowest between
Indigenous chickens from Cambodia (n = 4), Sri Lanka (n = 4), Ethiopia (n = Madagascar and Cambodia populations (0.312), whereas it was the highest
23), Kenya (n = 25), Burkina Faso (n = 8), Botswana (n = 8), Madagascar (n between Burkina Faso and Sri Lanka populations (0.369). Within population
= 8) and Chile (n = 14) were genotyped using 60K Illumina SNP chip. Quality genetic distance was the lowest for Burkina Faso population (0.207) whereas
checks were performed in GenABEL1 and 47486 filtered SNPs were used in the highest was found in Sri Lanka population (0.331). Moderate and positive
downstream analysis. Population structure was assessed using STRUCTURE2 correlation was found at global level between genetic and geographic distances
and PCA3. Optimal K was identified using ΔK approach4 as implemented in (r = 0.47, P = 0.009, Fig. 3).
Structure Harvester5. Fixation indices were calculated in R6 using custom
scripts. Phylogenetic structure and genetic distances were computed using Y = 0.17 + 0.044x, R2 = 0.22
MEGA57.
Results and discussions
Ancestral population: The ΔK indicated eight ancestral populations. At K = 8,
a single predominant genetic background was observed in all populations
except Cambodia and Chile, and only two genetic backgrounds were found in
the former. The Kenyan population show two genetic groups. The Ethiopian and
Burkina Faso populations were differentiated from the remaining populations
from K = 2 and k = 3 onwards, respectively.
Burkina Faso
Madagascar
Cambodia
Botswana
Sri Lanka
Ethiopia
Kenya
Chile
K=9
Figure 3. Regression of genetic distance on geographic distance.
K=8
Phylogenetic tree: A neighbour-joining phylogenetic tree (Fig. 4) indicates
K=7 that, except Botswana and Sri Lanka chickens, chickens that sampled from the
same country were grouped into their original population group.
K=6
K=5
K=4
K=3
K=2
Figure 1. Proportions of admixtures observed in the sampled chicken
populations.
Population structure: PCA revealed three genetic groups (Fig. 2): (1)
Ethiopian, (2) Burkina Faso and (3) the remaining populations.
PC 2 = 5.6%
Indigenous hen Indigenous cock
Figure 4. Neighbour joining phylogenetic tree of sampled chicken populations.
Conclusions
1. The admixed nature of village chickens has confounded our ability to
observe the expected level of genetic differentiation and to uniquely cluster
each population even using large number of genetic markers.
Flock owners Scavenging flock
2. The moderate level of population stratification observed at global level might
PC 1 = 6.9% be the consequence of local founder events and management histories.
3. A geographically proportionate and larger sample sizes are required to refine
Figure 2. Cluster of populations found using PCA.
further the genetic structure of these populations.
This genetic stratification was possibly observed due to limited gene flow
Acknowledgements: This study was financed by BBSRC research grant
and/or chickens may have arrived in these regions through different routes
BB/H009051/1 and hosted by The University of Nottingham. CH4D project is
and/or at different time periods and/or they may derived from different
credited for the photographs.
populations and/or developed under different management histories.
Fixation indices: Pairwise FST values ranged from 0.025 (Kenya vs Botswana) Literatures cited
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(t47485 = 209.98, P < 0.0001)