Animal Genetic Resources, 2012, 50, 13–20. © Food and Agriculture Organization of the United Nations, 2012
doi:10.1017/S2078633612000070
Genetic diversity analysis of the mitochondrial
D-loop of Nigerian indigenous sheep
B.O. Agaviezor1,2,3, M.A. Adefenwa3,4, S.O. Peters1,3, A. Yakubu5, O.A. Adebambo1, M.O. Ozoje1,
C.O.N. Ikeobi1, B.M. Ilori1, M. Wheto1, O.O. Ajayi1, S.A. Amusan1, M. Okpeku6, M. De Donato3
and I.G. Imumorin3
Department of Animal Breeding and Genetics, Federal University of Technology, Abeokuta, Nigeria, Nigeria; 2Department of Animal
Science and Fisheries, University of Port Harcourt, Port Harcourt, Nigeria; 3Department of Animal Science, Cornell University,
Ithaca, NY 14853, USA; 4Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria; 5Department of Animal
Science, Nasarawa State University, Keffi, Shabu-Lafia Campus, Lafia, Nigeria; 6Department of Livestock Production, Niger Delta
University, Amasomma, Bayelsa State, Nigeria
1
Summary
Indigenous livestock resources are strategic in the socio-economics of rural agricultural systems to ensure food security in resourcepoor countries. Therefore, better understanding of genetic variation holds the key to future utilization through conservation. We report
the first analysis of genetic diversity of Nigerian sheep based on the D-loop region of the Ovis aries mitochondrial genome using 1 179
bases between sites 15 437 and 16 616 base pairs. A sample of 290 animals made up of Balami, West African Dwarf (WAD), Uda and
Yankasa breeds were randomly collected from across Nigeria. Ninety-six haplotypes were observed with a high mean haplotype diversity of 0.899 ± 0.148. Gene diversity was highest in Uda (0.921 ± 0.021) and lowest in WAD (0.852 ± 0.061). Population specific FST
indices varied from 0.00133 in Uda to 0.00335 in WAD. Yankasa had the highest number of polymorphic sites (201), while the least
was in Uda (96). Analysis of molecular variance revealed that 0.23 percent of the variation is found among populations compared with
99.77 percent variation found within populations. The phylogenetic tree indicates that the mitochondrial lineages of these sheep breeds
originated from a common source consistent with first divergence of Yankasa followed by WAD, while Balami and Uda remain more
closely related. These results suggest that evolutionary divergence of Nigerian sheep breeds based on mitochondrial DNA D-loop
sequence may be coincident with geographical distribution in Nigeria and suggest significant interbreeding. This could have implications for managing improvement and conservation strategies and long-term conservation of Nigerian indigenous sheep.
Keywords: mitochondrial DNA, genetic distance, genetic diversity, Nigerian sheep
Résumé
Les ressources des animaux d’élevage indigènes représentent une valeur stratégique dans la socio-économie des systèmes agricoles
ruraux qui permettrait de garantir la sécurité alimentaire dans les pays pauvres en ressources. Par conséquent, l’utilisation future de
ces ressources par le biais de la conservation dépend d’une meilleure compréhension de la variation génétique. Nous signalons la
première analyse de la diversité génétique des moutons nigériens basée sur la région de la boucle D du génome mitochondrial
d’Ovis aries en utilisant 1 179 bases entre les sites 15 437 et 16 616 paires de bases. Des échantillons de 290 animaux provenant
des races Balami, West African Dwarf, Uda et Yankasa ont été collectés au hasard dans tout le Nigéria. On a observé 96 haplotypes
avec une moyenne élevée de diversité d’haplotype de 0,899 ± 0,148. On a relevé la diversité génétique la plus élevée chez les moutons
Uda (0,921 ± 0,021) et la plus faible chez les moutons West African Dwarf (0,852 ± 0,061). Les indices spécifiques de population FST
variaient entre 0,00133 pour les Uda et 0,00335 pour les West African Dwarf. Les moutons Yankasa présentaient le nombre le plus
élevé de sites polymorphiques (201) tandis que le plus bas a été repéré chez les Uda (96). L’analyse de la variance moléculaire a
indiqué que 0,23 pour cent de la variation se trouve parmi les populations tandis que 99,7 pour cent se situe au sein des populations.
L’arbre phylogénétique indique que les lignées mitochondriales de ces races de moutons proviennent d’une source commune cohérente
avec la première divergence des Yankasa suivie par les West African Dwarf, tandis que les races Balami et Uda restent plus étroitement
apparentées. Ces résultats semblent indiquer que la divergence évolutive des races de moutons indigènes basée sur la séquence de la
boucle D d’ADN mitochondrial pourrait coïncider avec la distribution géographique au Nigéria et suggérer un croisement considérable.
Cette conclusion pourrait avoir des retombées dans la gestion des stratégies d’amélioration et de conservation et dans la conservation à
long terme des moutons indigènes du Nigéria.
Mots-clés: DNA mitochondrial, distance génétique, diversité génétique, moutons nigériens
Resumen
Los recursos ganaderos autóctonos son de carácter estratégico en los aspectos socioeconómicos de los sistemas agrícolas para garantizar la seguridad alimentaria en los países de escasos recursos. Por lo tanto, conocer mejor la importancia de la variabilidad genética es
vital para su futura utilización, por medio de la conservación. Se presenta el primer análisis de la diversidad genética en ovejas de
Correspondence to: Dr Ikhide G. Imumorin, Department of Animal Science, Cornell
University, 267 Morrison Hall, Ithaca, NY 14853, USA. email: igi2@cornell.edu
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B.O. Agaviezor et al.
Nigeria basado en la región de control (D-loop) del Ovis aries del genoma mitocondrial, utilizando 1.179 bases entre las posiciones
15.437 y 16.616 de pares de bases. Una muestra de 290 animales, compuesta por las razas Balami, West African Dwarf (WAD), Uda y
Yankasa, fue tomada al azar de toda Nigeria. Se observaron noventa y seis (96) haplotipos, con una alta diversidad media en cuanto a
éstos de 0,899 ± 0,148. La diversidad genética fue mayor en la raza Uda (0,921 ± 0,021) y menor en la raza WAD (0,852 ± 0,061). Los
índices de población específicos FST variaron de 0.00133 en la raza Uda a 0,00335 en la raza WAD. La raza Yankasa presentó el mayor
número de posiciones polimórficas (201), mientras que el menor lo mostró la raza Uda (96). Análisis de la varianza molecular reveló
que 0,23% de la variación se encuentra entre las poblaciones, en comparación con el 99,77% de variación que se encuentra dentro de
las poblaciones. El árbol filogenético indica que los linajes mitocondriales de las razas ovinas partieron de un origen común en conformidad con la primera divergencia de la raza Yankasa, seguida por WAD, mientras que las razas Balami y Uda se encuentran más
estrechamente relacionadas. Estos resultados demuestran que la divergencia evolutiva de las poblaciones ovinas de Nigeria, basados en
el ADN mitocondrial de la región control, puede coincidir con la distribución geográfica en Nigeria e indican una tasa importante de
cruzamiento entre ellas. Esto podría tener ventajas desde el punto de vista de la gestión de la mejora y las estrategias de conservación y
preservación a largo plazo de las ovejas autóctonas de Nigeria.
Palabras clave: ADN mitocondrial, distancia genética, diversidad genética, oveja nigeriana
Submitted 1 November 2011; accepted 24 January 2012
Introduction
Animal genetic resources are defined as animal species
that are used, or may be used for the production of food
and fibre (FAO, 2007). Livestock currently contribute
about 30 percent of agricultural gross domestic product
in developing countries, with a projected increase to
about 40 percent by 2030. The World Bank has estimated
that it will be necessary to increase meat production by
about 80 percent between 2000 and 2030 (FAO, 2011).
Sheep are very important in the socio-economic lives of
the people of Nigeria (Abdullahi, 2002). However, their
potential value is not realized because of low productivity
resulting from high mortality and poor performance among
others. Geographical isolation, natural and artificial selection for physical or productive characters, genetic drift,
mutations and interpopulation gene flows have altered
gene frequencies over many generations (Pariset et al.,
2011), and this could affect fitness and adaptive potentials
of animals (Luikart and Allendorf, 1996). The current loss
of genetic resources concerns not only the extinction of
traditional breeds, but also the loss of genetic diversity
within breeds (Taberlet et al., 2011). In terms of biodiversity, conservation and utilization, these genetic resources
require further identification and evaluation to assess
their potential contribution to food and agricultural production in the future.
The initial step in characterization is identification of distinct populations using information on their geographic
and ecological isolation, traditional nomenclatures (traditionally recognized populations), phenotypic distinctness
and the level of genetic differentiation among the populations (Gizaw et al., 2011). Since the beginning of the
1990s, molecular data have become more relevant to the
characterization of genetic diversity (Groeneveld et al.,
2010), and the identification of genetically distinct breeds
is commonly based on these state-of-the-art techniques
(Gizaw et al., 2011). Mitochondrial DNA (mtDNA)
diversity is a useful molecular tool in establishing phylogenetic relationships among breeds and at species level
(Tanaka et al., 2011; Zhao et al., 2011). According to
Ajmone-Marsan and The GLOBALDIV Consortium
(2010), studies of mtDNA, microsatellite DNA profiling
and Y-chromosomes have revealed many details about
the process of domestication, diversity retained by breeds
and the relationships between breeds.
Although a preliminary study of natural genetic variation
among Nigerian sheep breeds using microsatellite markers
was reported by Adebambo et al. (2004), the full extent of
molecular variation and diversity remain largely unknown,
and studies based on other molecular markers capable of
unraveling phylogenetic history and development to better
understand the genetic structure of the Nigerian sheep
population are scarce. As part of efforts to better understand the genetics of Nigerian sheep for improvement
and conservation goals, we report the first study undertaken to assess population structure and genetic diversity
of Nigerian sheep using D-loop sequence of the ovine
mitochondrial genome.
Materials and methods
Study area and study population
This study was carried out using samples collected across all
over Nigeria. Nigeria is located in West Africa on the Gulf
of Guinea between latitude 10° north of the equator and
longitude 8° east of Greenwich Meridian with a total area
of 923 768 km2. Nigeria is bounded by Niger, Benin and
Cameroon Republics on the North, West and East, respectively (Figure 1). The five agro-ecological zones include
Sahel and Sudan Savannah, Guinea Savannah, derived
Guinea Savannah and Rainforest/Mangrove swamp. For
the purposes of sampling, Sahel and Sudan savannas were
combined into Sahelo-Sudan; derived Guinea and Guinea
Genetic diversity analysis of Nigerian indigenous sheep
Figure 1. Map of Nigeria showing sampled locations.
savannas were combined into Guinea savanna and sampling
was carried out from three main agro-ecological zones of
Sahelo-Sudan Savannah, Guinea Savannah and Rainforest/
Mangrove swamp.
Two hundred and ninety sheep were sampled from the
three main agro-ecological zones of Nigeria comprising
98 Balami, 43 Uda, 110 Yankasa and 39 West African
Dwarf (WAD) breeds. Approximately 5 ml of blood was
collected into heparinized tubes from the jugular vein of
the sheep, stored on ice before transfer to the laboratory
for analysis.
DNA extraction, polymerase chain reaction
amplification and sequencing
DNA was extracted from 50–100 µl of whole blood using
the ZymoBeadTM Genomic DNA Kit (Zymo Research
Corp. Irvine, CA, USA) according to the manufacturer’s recommendations. Quantification of DNA yield and assessment
of quality were done using the Nanodrop ND-100
Spectrophotometer (Thermo Scientific, Wilmington, DE,
USA). The DNA was amplified via polymerase chain reaction (PCR) in a MyCyclerTM Thermal Cycler (Biorad,
Hercules, CA, USA) using primers designed from published
ovine sequences (Genbank Accession Number AF010406)
(Hiendleder et al., 1998): tRNA-proline (5-CAGTGCCTT
GCTTTGGTTAAGC-3) and tRNA-phenylalanine (5-CA
CCATCAACCC CAAAGCTGAAG-3). The total volume
of 20 µl amplification reactions contained 20–50 ng template
DNA, 2.0 µl each of forward and reverse primers, and 16 µl
nuclease-free water in a BIONEER AccuPower® TLA PCR
Premix (containing NTPs, MgCl2 and DNA polymerase)
(BIONEER Corporation, Alameda, CA, USA). PCR used
the following protocol: initial denaturation at 94°C for 5
min, 35 cycles of amplification at 94°C for 30 s, annealing
at 62°C for 30 s, extension at 72°C for 1 min, final extension
at 72°C for 5 min and held at 4°C until analysis. Ten microlitres of the PCR product were separated in a 1.5 percent
agarose gel prestained with 0.5 µg/ml ethidium bromide.
Electrophoresis was carried out at room temperature for 40
min at 100 V using a Bio-Rad Power PacTM electrophoresis
apparatus (Biorad). The resulting amplified bands were visualized with UV light and photographed using the
AlphalmagerTM 2200 electrophoresis documentation and
analysis system (Cell Biosciences, CA, USA), and were
scored using GENEMate Quanti-Marker 100 bp DNA ladder
(BioExpress, UT, USA). Amplified PCR products were
sequenced with the Applied Biosystems Automated 3730
DNA Analyzer (Applied Biosytems, Foster City, CA, USA)
using the Big Dye Terminator chemistry and AmpliTaq-FS
DNA polymerase. Sequencing reactions used tRNA-proline
primer (5-CAGTGCCTTGCTTTGGTTAAGC-3).
Statistical analysis
Sequence alignment of the 1 179 bp PCR-amplified fragment
(after excluding the 75 nt tandem-repeat elements) was done
using DNA alignment software (Fluxus Technology, http://
www.fluxus-engineering.com/). A pair-wise distance matrix
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B.O. Agaviezor et al.
Table 1. Standard diversity indices for mtDNA analysis of Nigerian sheep breeds.
Indices
Balami
Number of gene copies
98
Number of haplotypes (h)
49
Number of loci
297
Number of polymorphic sites (S)
195
Sum of square frequency
0.0889
Hyplotype diversity (Hd)
0.9205 ± 0.0219
Mismatch observed mean
13.175
Mismatch observed variance
690.468
Parameters of the spatial expansion assuming constant deme size
Tau
19.213
Theta
5.784
M
0.425
between mtDNA sequences were computed using the nucleotide p-distance (Nei and Kumar, 2000), and a neighbourjoining (NJ) tree constructed on the basis of these distances
using the MEGA 3.0 software (Kumar, Tamura and Nei,
2004). A median joining network (Bandelt, Forster and
Rohl, 1999) was drawn from haplotypes using the program
Network 4.1.0.9 (www.fluxus-engineering.com). Indices of
sequence variation and haplotype structure were calculated
using the DnaSP 4.00 program (Rozas et al., 2003) including
nucleotide diversity (π), number of haplotypes (nh), haplotype
diversity (Hd) and number of polymorphic sites (S). An analysis of molecular variance (AMOVA) was computed to test significant differences in mitochondrial diversity between
Nigerian sheep breeds using ARLEQUIN 3.01 (Excoffier,
Laval and Schneider, 2005).
Results
Table 1 shows values for standard diversity indices for the
study of mtDNA of the Nigerian sheep. A total of 96 haplotypes were observed among the populations. Haplotypes
2, 3, 9, 12, 13, 14, 15, 16, 17, 18, 22, 23, 25, 31, 34, 36, 37
and 63 were shared among the different populations with
haplotypes 2, 9, 12 and 15, common to all the populations.
However, haplotype 2 had the highest distribution among
the four populations studied (Tables 2 and 3). Number of
polymorphic sites varied across the populations with the
highest value in Yankasa (201) and the lowest in Uda
(96). Gene diversity was high in all the populations.
Values ranged from 0.9601 ± 0.0170 in Uda to 0.8522 ±
0.0611 in WAD. A variation in mismatch observed mean
was noticed in this study, with WAD having the highest
value of 18.214.
Uda
WAD
Yankasa
43
27
297
96
0.0622
0.9601 ± 0.0170
11.218
150.985
39
15
297
190
0.1772
0.8522 ± 0.0611
18.214
2078.648
110
39
297
201
0.1425
0.8654 ± 0.0288
10.764
642.036
0.689
6.267
938.614
0.945
1.481
8.815
0.594
2.288
1166.750
Parameters of spatial expansion assuming constant deme
size is shown in Table 1. Tau ranged from 0.594 in
Yankasa to 19.213 in Balami. However, Uda had the highest value of 6.267 for Theta, with the lowest value seen in
WAD. Higher variation in M was also observed with
values ranging from 0.425 in Balami to 9338.613 in
Uda. The AMOVA is shown in Table 4. The AMOVA
analysis revealed that 0.23 percent of the variation is
found among populations compared with 99.77 percent
variation found within populations. Population-specific
FST indices are presented in Table 5. FST values are very
low and range from 0.00133 in Uda to 0.00335 in
WAD. The fixation index FST is 0.00226.
The estimation of population size change for Nigerian sheep
breeds using pair-wise comparison is shown in Figure 2. In
all the populations, a sharp variation for both observed and
expected pair-wise differences was observed. The fluctuation was highest among Uda. Figure 3 shows the median
joining network for the haplotypes observed among
Nigerian sheep. The network shows a grouping of the haplotypes into two haplogroups. The unweighted pair group
method analysis (UPGMA) tree of Nigerian sheep
mtDNA sequences is shown in Figure 4. The tree shows
that all the breeds originated from a common source.
However, Yankasa diverged first. This was followed by
WAD and lastly Balami and Uda, although separated but
are more genetically closely related.
Discussion
Variation among all the standard diversity indices was
observed across the four Nigerian sheep breeds studied.
Table 2. Haplotypes shared among populations.
Uda
WAD
Yankasa
Balami
Uda
WAD
14 (2, 3, 9, 12, 14, 15, 17, 18, 22, 23, 25, 34, 36, 37)
5 (2, 9, 12, 14, 15)
14 (1, 2, 3, 9, 12, 13, 14, 15, 16, 18, 21, 31, 34, 37)
5 (2, 9, 12, 14, 15)
9 (2, 3, 9, 12, 15, 18, 34, 37)
6 (2, 9, 12, 14, 15, 63)
Genetic diversity analysis of Nigerian indigenous sheep
Table 3. Distribution of haplotypes among the populations
studied.
Haplotype
1, 13
2
3
4–8, 10–11, 19–20, 24, 26–30, 32–
33, 35, 38–49
9
12
13
14
15
16
17, 20, 25, 36
18
21
22
34
37
50–62
63
64–72
73–77, 79–89, 91–96
78
90
Balami
Uda
WAD
Yankasa
1
26
1
1
0
7
1
0
0
11
0
0
1
38
2
0
6
5
2
3
4
2
1
4
5
1
1
1
0
0
0
0
0
0
3
4
0
1
3
0
1
2
0
2
2
1
1
0
0
0
0
0
3
2
0
1
2
0
0
0
0
0
0
0
0
1
1
0
0
0
11
3
1
3
5
4
0
4
6
0
2
1
0
1
0
1
3
2
Table 4. AMOVA analysis.
Among
population
Within
population
Total
Df
Sum of
squares
3
Population
Balami
Uda
WAD
Yankasa
FST
0.00180
0.00133
0.00335
0.00274
Fixation index FST: 0.00226.
The highest number of polymorphic sites in Yankasa could
be attributed to the fact that it is the most populous sheep
breed in Nigeria spread across different agro-ecological
zones of the country (Adebambo et al., 2004). The mismatch distribution analyses and the genetic diversity analyses suggest that these breeds must have undergone
relatively recent population expansion (Qing et al.,
2009). The values of haplotype and nucleotide diversities
observed in this study are a little higher than haplotype
diversity of 0.792 ± 0.37 and nucleotide diversity of
0.00392 ± 0.00046 observed by Wang et al. (2006) from
analysis of mtDNA variation and matrilineal structure in
blue sheep populations of Helan Mountain, China.
However, the values of haplotype diversity are comparable
to 0.857 ± 0.137 to 1.000 ± 0.052 reported by Sulaiman,
Wu and Zhao (2011). Mohammadhashemi et al. (2010)
also reported that sequence analysis of the mtDNA from
Moghani breed with another Iranian sheep showed high
genetic diversity with some Iranian sheep breeds. Pariset
et al. (2011) observed that mtDNA analysis showed higher
levels of sheep nucleotide diversity in the South-East,
which was congruent with the proximity to the
Source of
variation
Table 5. Population specific FST indices.
Variance
components
Percentage of
variation
1.543
0.00102
0.23
286
123.900
0.48910
99.77
289
125.443
0.44993
domestication centre. In a related study in goats,
Benjelloun et al. (2011) reported very high haplotype
diversity obtained for the Moroccan goats, and this,
according to the same authors, could have resulted from
the capture of a large part of the wild diversity during
domestication.
The AMOVA showed that 0.23 percent of the genetic variation among Nigerian sheep breeds is attributed to among
populations compared with 99.77 percent due to variation
within populations. A higher variation within than among
Nigerian sheep breeds suggests high levels of femalemediated gene flow (Tserenbataa et al., 2004). More so,
the results of pair-wise computations and AMOVA indicates that some breeds are differentiated relative to a random collection of genotypes and reflect differences in
the spatial distribution of genetic variation (Wang et al.,
2006). Similar to these findings, Pariset et al. (2011)
reported that the major mitochondrial variation was distributed within breeds (95.04 percent), while it was lower
among regions (0.90 percent) and among breeds within
regions (4.06 percent).
The genetic differentiation fixation index (FST) among the
Nigerian sheep breeds was low. The highest FST value in
Nigerian WAD sheep could be the results of its presence
only in the southern part of the country. Reduced differentiation could be attributed to shrinkage of grazing area,
indiscriminate cross-breeding/intermixing between breeds
and lack of appropriate breeding and management policies.
Although there are no strict breeding rules, geographical
isolation between the investigated sheep from different
regions has probably led to the moderate level of differentiation among them since genetic drift and natural selection
are two main factors that give rise to genetic differentiation
among populations (Qing et al., 2009). The observed FST
values indicate significant inbreeding from subdivision of
the breeds. The degree of subdivision suggests gene flow
between the breeds (Kantanen et al., 1995). If gene flow is
greater than one, it could play a uniform action of resisting
the action of genetic drift and preventing differentiation
between populations (Qing et al., 2009). According to
Gizaw et al. (2011), an important characteristic to note in
genetic diversity in livestock populations is that the variation
within a population is much larger than that between the
populations. This is well exemplified in the study of
Ethiopian sheep where the diversity between Ethiopian
sheep populations accounted for only 4.6 percent of the
overall genetic diversity (global FST value = 0.046 ±
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B.O. Agaviezor et al.
0.004), the rest being accounted for by within-population
variation. The variation in the number of haplotypes and
gene copies analysed contributes to unravelling genetic
diversity among Nigerian sheep breeds. Despite the high
haplotype diversity observed in Uda, the higher number of
polymorphic sites in Yankasa compared with other breeds
is likely to have contributed to Yankasa’s adaptation ability.
Out of the 96 haplotypes observed in this study, only 5 haplotypes are common to all the breeds with haplotype 2 having the highest frequency. This probably points to the
existence of evolutionary relationship among them; and
equally suggests evidence linking the four Nigerian sheep
breeds to a common ancestor or a small number of founders.
In a related study in buffalo, few haplotypes of South
Kanara and Toda were found to be quite distinct from the
commonly found haplotypes, indicating that these might
have been ancestral to all the present-day haplotypes
(Kathiravan et al., 2011). Relatively divergent haplotypes
within breeds and geographical locations suggests that
gene flow has occurred on a regional scale at some time
in the recent past and that the breeds have not been subdivided by long-term biogeographic barriers (Luikart and
Allendorf, 1996). Similar mean haplotype diversity of
0.945 and mean nucleotide diversity and 0.013 from genetic
diversity and structure of the West Balkan Pramenka sheep
types as revealed by microsatellite and mtDNA analyses
further support the results of this study (Cinkulov et al.,
2008). In a related study in goats, Vacca et al. (2010)
reported that the animals showed a high genetic haplotype
diversity, as 35 haplotypes were each represented by a
single sequence and only a few haplotypes were shared
among the animals, thereby lending credence to the findings
of Naderi et al. (2007) that it is common to find haplotypes
represented by one individual or shared by only a few subjects, because mtDNA variation is a more frequent component within breeds than between them. The significant
differentiation in the haplotype frequencies among
Nigerian sheep breeds suggest that little gene flow currently
exist among the breeds (Luikart and Allendorf, 1996).
Figure 2. Estimation of population size changes for Nigerian sheep breeds.
The median joining network separated the 96 haplotypes into
two major haplogroups. The UPGMA tree separated the four
Nigerian sheep breeds according to their geographical
locations and population sizes in the country. Balami and
Uda are northern breeds which are also fewer than WAD
which is a southern breed compared with Yankasa with a
wider geographical spread across the country. Evidence
from the phylogenetic tree supports first divergence of
Yankasa followed by WAD and later by Uda and Balami.
However, Zhao et al. (2011) reported that FS value was
−13.17574 (P = 0.00000) for haplogroup A in Chinese
large-fat-tailed sheep breeds, which suggested one expansion
event in this population’s demographic history. Analysis of
mismatch distribution also revealed an almost multi-modal
distribution of mtDNA D-loop for haplogroup B. FS value
was −6.39666 (P = 0.00000) for haplogroup B, which showed
no population expansion and relatively stable population size
because of no significant difference from neutrality.
Genetic diversity analysis of Nigerian indigenous sheep
Figure 3. A median joining network for the haplotypes observed among Nigerian sheep. Circles represent haplotypes and have a size proportional to frequency.
Mutational differences are shown on lines.
population sizes with a rough grouping of the northern
breeds (Balami and Uda) and the southern breeds (WAD
and Yankasa). The evolutionary divergence into distinct entities of Nigerian sheep breeds based on mtDNA D-loop
sequence appear to closely follow their geographical distribution in Nigeria, and this could have implications for management, improvement and conservation strategies in
Nigerian sheep.
Figure 4. UPGMA tree of Nigerian sheep mtDNA sequences.
The present information could be used to strengthen the
monitoring, characterization and conservation of animal
genetic resources towards the sustainable rearing of the
autochtonuous sheep breeds. However, further studies
involving the use of endogenous retroviruses (Chessa
et al., 2009) as a new class of genetic markers, combined
with existing knowledge from microsatellite (Agaviezor
et al. accepted. Adebambo et al., 2004) will help to unravel the history of domestication of Nigerian sheep.
Statement of Interest: The authors wish to state that there is
no conflict of interest as regards this manuscript.
Acknowledgements
Financial support from College of Agriculture and Life
Sciences, Cornell University through a partnership with
University of Agriculture, Abeokuta, Nigeria is gratefully
acknowledged. Special thanks to Prof. W. Ron Butler for
the opportunity given to the first two authors as visiting
graduate students at Cornell University.
Conclusions
Genetic diversity among Nigerian indigenous sheep breeds
is eroding due to indiscriminate cross-breeding/intermixing
between breeds, and lack of appropriate breeding and management policies. The highest number of polymorphic loci
in Yankasa compared with other breeds suggests wider genetic variation that can be exploited in its improvement. In
addition, the four Nigerian sheep breeds studied separated
genetically based on their geographical locations and
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