Genetic characterization of Tanzanian indigenous chickens in relation to the worldwide spectrum of chicken diversity
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Date
2014
Authors
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Publisher
Georg-August-Universitiit Gottingen
Abstract
Poultry production is the most dynamic sector that signified the rapid growth of all meat sectors
during the last decades (FAO. 2010). The global growth of poultry industry reflects an increase of
world meat demand and consumption (de Haan cl al.. 2001; Delego, 2003; Delgado el al., 2008;
Narrod ci al.. 2008; Trost le and Seeley. 2013; FAO 2014). Among the poultry species, chickens are
the humankind’s most common and widespread birds. Chicken meat represents 88% of poultry meat
output (Global Poultry Trends. 2014). Although the demand of chicken products has increased
tremendously due to not only the fast growth of world population but also the increase of per capita
global consumption of meal, nearly one third of chicken breeds are reported to be at risk of
extinction (Pym. 2010). This is alarming and thereby calls for an assessment of the existing genetic
resources, because many of the varieties which arc at risk may have trails that can be valuable in
future environmental challenges and marketing demands. Genetic variability in chickens is the best
insurance for the adaptation and sustainable production for the future unpredictable needs (Simianer
and Meyer. 2003). One of the important elements concerning sustainable use of animal genetic
resources is to ensure that locally adapted populations remain a functional part of production
systems.
Indigenous chickens are among the essential local assets of poor people living mainly in rural areas
in Africa, and who make up between 65% and 80% of the total population in sub-Saharan Africa
(Ndegwa et al, 2000). In sub-Saharan z\frica. 85% of all households keep chicken under free-range
system, with women owning 70% of these birds (Sonaiya et al., 2004; Abubakar et al.. 2007). In
Tanzania, which is one of the countries in Sub-Saharan Africa about 80% of the human population
lives in the rural area where majority of the indigenous chicken arc kept. Since village chickens play
numerous important roles in the rural households and village social welfares in Tanzania, efforts
towards populations’ characterizations, improvements, proper utilisation and conservation of the
existing chicken genetic resources should be made.
'The general objective of this study is to assess the genetic characterization of Tanzanian indigenous
chickens in relation to the worldwide spectrum of chicken diversity. The specific objectives were to:
(>) Investigate the maternal lineages and genetic diversity of Tanzanian indigenous chicken
(ii) Investigate the genealogical patterns of chicken breeds sampled in Europe
(Hi) Evaluate global diversity and genetic contributions of chicken populations from African,
Asian and European regions
Key words: Farm animal genetic resources. Global chicken diversity. Chicken population structure.
Genetic contribution, Tanzanian indigenous chickens, Microsatellite markers.
Mitochondrial DNA. Nucleotide diversity. Haplotype diversity. Phenotypic traits
xvIn the first objective of this study (Chapter 2), the genetic diversity and maternal lineages of five
Tanzanian indigenous chickens (Chiny'wekwe. Kuchi. Moroyoro-mcdium, Pemba and Unyuja) were
examined. Phenotypic measurements and blood samples were collected in 1% individual chickens
from eight regions of Eastern Zone. Central Zone. Lake Zone and Zanzibar islands. A principal
component analysis of morphological measurements distinguished individuals most by body sizes
and body weight. Moroyoro Medium, Pemba and Unyuja were grouped together, while Chiny'wekwe
stood out because of their disproportionate short shanks and ulna bones. Kuchi formed an
independent group owing to their comparably long body sizes. Individual chickens were genolyped
at 29 microsatellile loci. 28 of them taken from the 30 that have been suggested for biodiversity
studies in chickens. From molecular genetic marker analyses, the expected (0.62±0.028) and
observed (0.62±0.017) heterozygosity estimates in Tanzanian indigenous chickens, were more or less
similar with other African chicken populations. Genetical differentiation between Tanzanian chicken
ecotypes (F\r 0.048) was found to be smaller than between commercial chicken lines. Both
STRUCTURE analysis and phylogenetic neighbour-net revealed three clusters of Tanzanian chicken
populations. These clusters comprised i) Moroyoro-mcdium and Chiny ’uv.(uv from Eastern and
Central Zones ii) Unyuja and Pemba from Zanzibar Islands and iii) Kuchi from Lake Zone regions,
which formed an independent cluster. Sequence polymorphism of D-loop region was analyzed to
disclose the likely maternal origin of Tanzanian chickens. According to Liu et al., (2006) reference
mtDNA haplotypes, the Tanzanian chickens that were sampled encompass two haplogroups of
different genealogical origin. The haplotype network analysis indicates that Tanzanian chickens
probably originated from the Indian subcontinent and from Southeast Asia.
In the second study (Chapter 3). sequencing data of455bp fragment size of the control region (D-
loop) in the mitochondrial genome was studied in 1256 individuals collected from 55 European
chicken breeds. The 55 chicken breeds studied were categorized into six groups according to their
historical background; Mediterranean type. East European type, Northwest European type, breeds
based on introgression of Asian breeds into European breeds during their foundation 100 to 150
years ago (Intermediate types and Game birds), and breeds with recent Asian origin (Asian type).
Median-joining networks were constructed to establish the evolutionary relationships based on the
classification of haplotypes given by Liu et al. (2006) nomenclature. From the Median-joining
network, haplogroup E was the predominant clade among the European chicken breeds. Genetic
variation was assessed within breed categories using DnaSP v.5.10.01 program. Wide ranges of
haplotype diversity and nucleotide diversity in European chickens (0.442 < II < 0.761 and 0.0030 < it
< 0.0104 respectively) suggest that European breeds have relative high genetic variation between
them. High average haplotype number, haplotype diversity and nucleotide diversity were observed
for Asian type breeds followed by intermediate type. East European and Northwest European breeds
have lower haplotype and nucleotide diversity compared to Mediterranean type, intermediate type.
Game bird, and Asian type breeds. This study revealed that haplogroup of Clade E are predominant
xviin European breeds, and might have their roots mainly from the Indian subcontinent and some shown
to have traces from East Asia.
In the third study (Chapter 4). global genetic diversity and genetic contributions of chicken
populations from African. Asian and European regions were investigated by using multilocus
microsatellitc genotypes. A total of 3314 individuals from 113 chicken populations, which were
sampled in different geographical regions, climatic conditions and population management were
assessed using 29 autosomal microsatellitc loci for estimating diversity and genetic contributions.
The set of populations studied included 101 local populations with the breed history from three
continents of Africa. Asia and Europe. Three populations of red and nine commercial purebred lines
were included and used as reference populations in the analyses. The mean number of alleles per
locus and population was higher in African (5.2010.17) and Asian chickens (5.1210.16), than in
European breeds (3.2010.11) and commercial lines (3.2810.26). Higher estimates of expected
hetcrozAgosily were calculated for African (0.60410.016) and Asian (0.60310.015) chickens
compared to European (0.45510.011) and commercial (0.45310.026) breeds. Traditional farming
system in Africa of free-range management may have contributed to this higher genetic variation
within the population. African and Asian chickens showed lower genetic differentiation (l-\r
0.10810.004 and 0.12010.005, respectively) compared to European and commercial breeds
(0.32010.011 and 0.32710.022, respectively). The wider variation in diversity between European
chicken populations is to some degree related to a varying degree of population sizes and isolation.
NcighbourNet phylogenetic network based on a kinship distances of 113 chicken populations
revealed two main clusters of Asian and Northwestern European breeds at opposite ends of
geographical representation. African populations were clustered with breeds from Eastern Europe,
and Mediterranean regions. Broilers and Brown egg layers in between of these two main clusters.
Among the commercial breeds. White egg layers were clustered with Northwestern European
chickens. Red junglcfowl populations provide a high contribution (0.019) in the optimal core set,
followed by Asian chicken populations (0.0115). On average, European chicken population
contributed least to the core set (0.007), whereas the average contributions of commercial line
(0.009) is very similar to that of African chicken populations (0.009). Higher genetic differentiation
and low genetic contributions have been observed in European breeds.
In general. Tanzania chickens are as highly diverse as other African chicken ecotypes. In terms of
genetic compositions. Tanzania village chickens have the admixture of genetic material that is found
in Asian and European chicken populations. However, the current efforts for improving productivity
and disease resistance of Tanzania village chickens should go along with conservation efforts and
Smallholder farmers’ empowerment in rural areas in operating small-scale chicken breeding while
retaining the diversity would help in implementing the conservation of chicken genetic resources.
This study can potentially contribute to generating information on population structure and genetic
diversity of the Tanzanian indigenous chickens, with regard to the appropriate utilization and
conservation efforts of the existing chicken genetic resources.
Description
PhD Thesis
Keywords
Genetic characterization, Tanzanian indigenous Chickens, Indigenous Chickens, Chicken diversity