J. Anim. Breed. Genet.

ISSN 0931-2668

ORIGINAL ARTICLE

Genetic diversity in Egyptian and Italian goat breeds measured

with microsatellite polymorphism
S.H. Agha1, F. Pilla2, S. Galal1, I. Shaat3, M. D’Andrea2, S. Reale2, A.Z.A. Abdelsalam4 & M.H. Li5*
1 Department of Animal Production, Faculty of Agriculture, Ain Shams University, Shubra Alkhaima, Cairo, Egypt
2 Department of Animal, Agricultural and Environmental Sciences, Faculty of Agriculture, Molise University, Campobosso, Italy
3 Department of Sheep and Goat Research, Animal Production Research Institute, Agriculture Research Center, Dokki, Cairo, Egypt
4 Department of Genetics, Faculty of Agriculture, Ain Shams University, Shubra Alkhaima, Cairo, Egypt
5 Biotechnology and Food Research, MTT Agrifood Research Finland, Jokioinen, Finland
* present address: Ecological Genetics Research Unit, Department of Biological and Environment Sciences, PO Box 65, FIN-00014 University of
Helsinki, Finland

Keywords
Barki; Egyptian Baladi; genetic diversity;
Maltese and Montefalcone goat;
microsatellites; polymorphism; Zaraibi.
Correspondence
Ihab Shaat, Department of Sheep and Goat
Research, Animal Production Research
Institute, Agriculture Research Center,
Nadi El-Said Street, 12311, Dokki, Cairo, Egypt.
Tel: +202 3337 1994; Fax: +202 3760 0598;
E-mail: shaat@hotmail.com
Received: 30 July 2007;
accepted: 14 January 2008
Summary
Seven microsatellite markers were used to study genetic diversity of
three Egyptian (Egyptian Baladi, Barki and Zaraibi) and two Italian
(Maltese and Montefalcone) goat breeds. The microsatellites showed a
high polymorphic information content (PIC) of more than 0.5 in most
of the locus–breed combinations and indicated that the loci were useful
in assessing within- and between-breed variability of domestic goat (Ca-
pra hircus). The expected heterozygosity of the breeds varied from 0.670
to 0.792. In the geographically wider distributed Egyptian Baladi breed
there were indications for deviations from random breeding. Analysis of
genetic distances and population structure grouped the three Egyptian
goat breeds together, and separated them from the two Italian breeds.
The studied Mediterranean breeds sampled from African and European
populations seem to have differentiated from each other with only little
genetic exchange between the geographically isolated populations.

of local breeds, in which the Zaraibi breed has been a

Introduction
In Egypt, goats are an important source of meat.
They are distributed across the country, especially
dense in the Nile valley and delta and with lower
concentration in the north-western coastal region
and at oases (Galal et al. 2005). In the Nile valley
goats are usually found in small holdings as mixed
flocks with sheep and other farm animals like cattle
and buffaloes, while in the north-western Mediterra-
nean coast (Figure 1) they are in large herds mixed
with sheep. Most of the livestock breeds in Egypt lack
molecular characterization required for establishing
adequate utilization of genetic variation in develop-
ing animal production. Goat genetic improvement
schemes in Egypt have involved crossbreeding trials
with examples Damascus goats and the development
recent target of joint work with the Food and Agri-
culture Organization of the United Nations (FAO).
Animals were purchased from farmers and markets
in different governorates to establish a research herd
and a selection programme for a breed where special
attention was paid to avoidance of inbreeding.
The goat is among the earliest livestock species to
have been domesticated approximately 9000 BP in
Southeast Asia along the present Iran–Iraq borders
(Mason 1981). Goats are spread over a wide range
of habitats with a substantial concentration in the
tropics and dry zones in developing countries (Galal
2005; FAOSTAT 2006). Therefore, they are expected
to show a large amount of genetic diversity in adapt-
ing to the varying ecosystems. So far, the goat diver-
sity studies based on microsatellites have been

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194 Journal compilation ª 2008 Blackwell Verlag, Berlin • J. Anim. Breed. Genet. 125 (2008) 194–200

S. H. Agha et al.
Figure 1 Geographical distribution of the studied goat breeds.
carried out on Swiss (Saitbekova et al. 1999) and
Asian breeds (Barker et al. 2001; Ganai & Ydav 2001;
Li et al. 2002; Li & Valentini 2004). Only recently,
some attention has been paid to Mediterranean
breeds (Iamartino et al. 2005; Cañon et al. 2006),
although the area around the Mediterranean Sea
has approximately 16% of the total goat breeds in
the FAO list (http://www.fao.org/dad-is/), and for
example, Italy is an important reservoir of goat
diversity harbouring the second largest number (50)
of goat breeds after China (http://www.fao.org/dad-
is/). There were very few studies done on the molec-
ular genetic variation of African goat populations.
Cañon et al. (2006) included Middle East goat popu-
lation, however, in their study there were no breeds
from the African continent, with the closest being
two populations (Beeshi, Najrani) from Saudi Arabia.
Thus, there is a need to extend the diversity studies
to cover also African goat populations and find their
position in the global goat diversity. The information
on molecular genetic variation could help in under-
standing the relationship and diversity within and
among the local Egyptian and Mediterranean breeds
(Galal et al. 2005). The genetic distance measure-
ment between the breeds can also be used to quan-
tify genetic similarities between the breeds and even
to proxy the expected heterosis gained in crossing
the breeds (Toro & Mäki-Tanila 2007).
Employment of microsatellites is one of the most
powerful means for studying the genetic diversity
ª 2008 The Authors
Journal compilation ª 2008 Blackwell Verlag, Berlin • J. Anim. Breed. Genet. 125 (2008) 194–200
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Genetic diversity in Egyptian and Italian goat breeds
because of their high degree of polymorphism, ran-
dom distribution across the genome and neutrality
with respect to selection. Many bovine microsatellite
markers have been used for genetic analysis in sheep
and goats (Bruford & Wayne 1993). The objectives
of the present study were to investigate the poly-
morphism in a set of microsatellites and to quantify
the genetic diversity of three Egyptian and two Ital-
ian goat breeds. The three Egyptian breeds serve as
part of a first attempt to describe the characteristics
of molecular genetic variation in Egyptian goat pop-
ulations in relation to breeds from the north shore
of the Mediterranean. The two Italian breeds have
been studied and documented by Iamartino et al.
(2005).
Materials and methods
Animals
Egyptian animals were sampled from three research
stations where breed status is well known and the
pedigree information has been maintained over sev-
eral generations. The pedigree information was used
to sample animals, which were unrelated. The sta-
tions belong to the Animal Production Research
Institute (APRI) of Agriculture Research Center at
the Egyptian Ministry of Agriculture. The breeds
were Egyptian Baladi at Sakha station in the Nile
delta, Zaraibi at El-Serw station in the north-eastern
Egypt in the Nile delta, and Barki at Borg El-Arab
station in the north-western coastal Mediterranean
region of Egypt (Figure 1). Forty seven blood sam-
ples of Egyptian goats (Egyptian Baladi, 21; Barki,
14; and Zaraibi, 12) were collected using vactutainer
tubes via the jugular vein. There were DNA samples
available from the Italian goats, which were repre-
sented by 50 animals from Maltese breed and 29
from Montefalcone breed (Figure 1).
Molecular analysis
Seven microsatellites (INRA005, ILSTS019, SRCRSP5,
ILSTS087, CSRD247, HSC, INRA063) were used
(Table 1). The markers were chosen on the basis of
polymorphism, allele size range and ability to coam-
plify in PCR reactions in the earlier study on the
Italian breeds (Iamartino et al. 2005), which included
the breeds of Montefalcone and Maltese at the listed
markers except HSC. Genotypes of the other micro-
satellites in the Italian breeds were obtained from
the previous study of Iamartino et al. (2005). Four of
the markers (SRCRSP5, ILSTS087, CSRD247, INRA063)
appeared in the list of markers recommended by the
195
 14390388, 2008, 3, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/j.1439-0388.2008.00730.x by Egyptian National Sti. Network (Enstinet), Wiley Online Library on [23/07/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Genetic diversity in Egyptian and Italian goat breeds S. H. Agha et al.

Table 1 Number of alleles (bold), polymor-

Breed phic information content and the size (bp)
Egyptian and frequency (%) of private alleles (italics) of
Microsatellite Baladi Barki Zaraibi Maltese Montefalcone All References the microsatellites in the Egyptian and Italian
goat breeds
INRA005 4 4 3 4 4 4 Vaiman et al. (1992)
0.604 0.541 0.511 0.394 0.607
ILSTS019 7 6 4 6 6 8 Kemp et al. (1995)
0.797 0.617 0.221 0.703 0.619
SRCRSP5 8 6 6 11 6 12 Arevalo et al. (1994)
0.762 0.697 0.672 0.691 0.608
177:8.33 163:1.06
HSC 13 7 9 10 10 16 de Gortari et al. (1997)
0.874 0.714 0.844 0.794 0.781
268:5.88 300:2.04
296:2.94
ILSTS087 9 5 7 8 8 11 Kemp et al. (1995)
0.764 0.597 0.770 0.791 0.587
155:17.78
CSRD247 7 7 4 8 8 10 Kemp et al. (1995)
0.788 0.758 0.694 0.669 0.734
INRA063 5 4 4 4 5 5 Vaiman et al. (1994)
0.578 0.651 0.482 0.631 0.590
All 53 39 37 51 47 66

Guidelines for Development of National Farm Ani-
mal Genetic Resources Management Plans of the
FAO (Measurement of Domestic Animal Diversity,
MoDAD; http://www.fao.org/dad-is/). DNA was
extracted from blood using standard phenol-chloro-
form extraction method (Sambrook et al. 1989). PCR
reactions were performed in a final volume of 10 ll
containing 200 lM dNTPs, 0.1 ll of a 5 U ⁄ ll of
Ampli-Taq (Applied Biosystems, Foster City, CA,
USA), 1.5 mM MgCl2, 1 · PCR buffer, 5–25 lM of
each primer and 20–50 ng of genomic DNA. Ampli-
fied fragments were separated by capillary electro-
phoresis using an ABI PRISM310 automatic
sequencer (Applied Biosystems, Foster City, CA,
USA). Fluorescently-labelled fragments were
detected and sized using GeneMapper (version 3.7)
(Applied Biosystems).
Statistical analysis
Frequencies and number of alleles for each locus,
private alleles in each population, observed and
expected heterozygosity, Wright’s statistics FIS and
FST were estimated using fstat (version 2.9.3.2)
(Goudet 2002). GENEPOP (version 3.4) (Raymond &
Rousset 1995) was used to estimate Hardy–Weinberg
equilibrium (HWE) over loci within each population.
The polymorphic information content (PIC) value
was calculated according to Botstein et al. (1980).
Nei’s (1987) standard genetic distances among
populations were computed by popgene (version
1.31) (Yeh et al. 1999). A pairwise matrix of the
genetic distances was then used to obtain a neigh-
bour-joining (NJ) tree (Saitou & Nei 1987), which
was visualized using the software TreeView (Page
1996). Bootstraps of 1000 replicates were performed
in order to test the robustness of tree topology using
the dispan program (Ota 1993).
The population structure was evaluated based on
a Bayesian clustering analysis by employing the
structure program (Pritchard et al. 2000). This
method uses multilocus genotypes to infer for all the
individuals and populations the fractions in their
genetic ancestry that belong to a given number (k)
of clusters. A Monte Carlo Markov chain was run
for k = 2, 3, 4 or 5 with a burn-in period of 20 000
and a run length of 20 000 iterations. A default set-
ting assuming an admixture model with correlated
allele frequencies was used in all runs. The graphical
display of the structure results was generated using
distruct software (Rosenberg 2004).
Results and discussion
Variation at microsatellite markers
Microsatellites used in the present study were poly-
morphic in all the breeds (Table 1). The highest
number of alleles (16) was at HSC and the lowest (4)
at INRA005. Egyptian Baladi had the highest number
of alleles at the loci, which may be due to genetic

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196 Journal compilation ª 2008 Blackwell Verlag, Berlin • J. Anim. Breed. Genet. 125 (2008) 194–200
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S. H. Agha et al. Genetic diversity in Egyptian and Italian goat breeds

exchange between the widely distributed Egyptian nitude as the average expected heterozygosity of
Baladi goats and other goat populations in the Nile 0.68 in the Brown Short Haired goat reported by
valley and delta region. Maltese breed also possessed Jandurová et al. (2004). In Chinese goats the
a high number of alleles. The breed originates on expected genetic heterozygosity varied from 0.611 to
the island of Malta and has probably been crossed 0.784 (Li et al. 2002). Our diversity results are within
with North-African goat populations (Iamartino et al. the ranges found in a study on the goat breeds in
2005). Barki & Zaraibi breeds had smaller numbers Europe and in Saudi Arabia (Cañon et al. 2006).
of alleles. The home tracts of these two breeds are in In assessing diversity estimates from different studies,
more restricted areas. All the markers were highly it should be mentioned that the values are not
informative in the studied breeds (PIC > 0.50), directly comparable, as different microsatellites have
except ILSTS019 in Zaraibi (PIC = 0.221), INRA005 in been used. There were three common microsatellites
Maltese (PIC = 0.394), and INRA063 in Zaraibi with Cañon et al. (2006), two with Li et al. (2002)
(PIC = 0.482). Microsatellites with high PIC are use- and none with Jandurová et al. (2004). Hence the
ful in genetic diversity studies. comparisons have only suggestive indications.
In this study private alleles were found in Egyp- The high genetic diversity observed in a breed
tian Baladi, Zaraibi and Maltese (Table 1). However, could be explained by overlapping generations, mix-
Iamartino et al. (2005) found private alleles in both ing of populations from different geographical loca-
Maltese and Montefalcone breeds. There are several tions, natural selection favouring heterozygosity or
reasons for the existence of private alleles, like subdivision accompanied by genetic drift (Toro &
multi-origin of the breeds, little subsequent genetic Mäki-Tanila 2007). The effect of these factors is
exchange between them or genetic drift. The highest more pronounced when the effective population size
frequency of a private allele was 0.178 at ILSTS087 is very large. The expected heterozygosity was the
(155 bp) in Maltese, so that genetic drift may highest (0.792) in Egyptian Baladi. A wide distribu-
explain the observed differentiation between the tion of this breed across the country increases the
breeds. The small size of population samples pre- likelihood for the enrichment of different alleles
vents us from making any definite explanations for in the geographically widely scattered population.
the observed values. The Egyptian breeds are very close to the domestica-
tion centre of goats in the near East (Zeder & Hesse
2000) and therefore, they are expected to have
Within breed variation
maintained relatively high genetic diversity.
Genetic variability within the breeds is relatively Mean observed heterozygosity was lower than the
high, as evidenced by the high mean expected het- expected in all the studied breeds, and deviation
erozygosity (0.722) (Table 2). It is of a similar mag- from HWE was significant in all of them (Table 2).
Heterozygosity deficit within a population, as mea-
Table 2 Number of animals (n), mean observed number (na) (and SD)
sured by Wright’s FIS, was positive in all the breeds
of alleles, mean (and SE) of observed (Hobs) and expected when averaged across the loci, and ranged from
heterozygosity (Hexp), the exact test for Hardy-Weinberg equilibrium 0.057 in Montefalcone to 0.168 in Egyptian Baladi
(HWE) and Wright’s FIS in Egyptian and Italian goat breeds (Table 2). The Egyptian breeds had higher FIS values
than the Italian breeds did. The variation at the mi-
Breed n na Hobs Hexp HWE test1 FIS2
crosatellite markers indicated deviations from ran-
Egyptian Baladi 21 7.6 0.662 0.792 0.0028 0.168* dom mating in the three sampled Egyptian breeds,
(2.9) (0.040) (0.034) although measures are practiced to avoid inbreeding,
Barki 14 5.6 0.660 0.724 0.0064 0.091NS like restricting the use of same sires, exchanging
(1.3) (0.051) (0.028)
sires between the stations and adding new ‘blood’
Zaraibi 12 5.3 0.612 0.670 0.3202 0.094NS
(2.1) (0.054) (0.085)
from outside the stations.
Maltese 50 7.2 0.685 0.724 0.0016 0.068NS
(2.8) (0.026) (0.053)
Genetic differentiation among breeds
Montefalcone 29 6.7 0.660 0.701 0.1157 0.057NS
(2.1) (0.033) (0.025) Pairwise genetic differentiations quantified by FST
All 126 6.5 0.654 0.722 – 0.096NS estimates ranged from 0.042 between Egyptian Bala-
(2.2) (0.041) (0.045)
di and Barki to 0.149 between Zaraibi and Montefal-
1
All the test values were highly significant, p < 0.001. cone, and similarly Nei’s (1987) standard genetic
2
NS = not significant, p ‡ 0.05; *Significant, p < 0.05. distance varied between 0.160 and 0.493 (Table 3).

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Journal compilation ª 2008 Blackwell Verlag, Berlin • J. Anim. Breed. Genet. 125 (2008) 194–200 197
 14390388, 2008, 3, Downloaded from https://onlinelibrary.wiley.com/doi/10.1111/j.1439-0388.2008.00730.x by Egyptian National Sti. Network (Enstinet), Wiley Online Library on [23/07/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License
Genetic diversity in Egyptian and Italian goat breeds S. H. Agha et al.

Table 3 Estimated pairwise FST as a measure of genetic differentia- Zaraibi goats are Nile valley and delta breeds (Fig-
tion (above diagonal) and Nei’s (1987) standard genetic distance ure 1). There is only weak differentiation among the
(below diagonal) among Egyptian and Italian goat breeds
Egyptian breeds, while the phylogenetic tree shows
Population Egyptian a clearer differentiation between the Egyptian and
Baladi Barki Zaraibi Maltese Montefalcone the Italian breeds (Figure 2).
Bayesian analysis of the data with a structure pro-
Egyptian Baladi – 0.042NS 0.051* 0.077** 0.067**
Barki 0.160 – 0.061NS 0.080** 0.095**
gram (Pritchard et al. 2000) showed that the samples
Zaraibi 0.163 0.172 – 0.114** 0.149** had the highest estimated likelihood at k = 3 and
Maltese 0.291 0.265 0.367 – 0.103** running the program at k = 4 did not detect any
Montefalcone 0.223 0.303 0.493 0.338 – additional cluster (Figure 3). Thus, three genetic
clusters were identified, that is, two monophyletic
NS = not significant, p ‡ 0.05; *significant, p < 0.05; **highly signifi-
cant, p < 0.01.
clusters coinciding with the two Italian breeds and a
cluster of the three Egyptian breeds. Genetic cluster-
ing of the populations is consistent with the phylo-
genetic dendrogram (Figure 2). Our results indicated
that genetic components of the three Egyptian goat
breeds are quite similar, which can be due to little
genetic divergence among them after their immigra-
tion into Egypt out of the domestication centre in
Figure 2 Neighbour-joining tree with 1000 bootstraps on Nei’s (1987)
the Near East. This speculation was also seen as a
standard genetic distances. Bootstrap values are reported as percent- higher level of genetic diversity in the three breeds.
ages.

Conclusions
Genetic differentiation (FST) between Egyptian
breeds is very small, reflecting a high genetic similar- The Egyptian goat breeds, especially the Egyptian
ity among these breeds, while they are differentiated Baladi breed with a wider distribution across the Nile
from the Italian ones. The Italian breeds are geneti- valley and delta, is possessing high genetic variabil-
cally diverged from each other (Table 3). When the ity. The study is indicating that the analyzed Medi-
breed relationships are visualized with the dendro- terranean goat breeds have been genetically
gram (Figure 2), Egyptian Baladi and Zaraibi are differentiated in line with their geographical separa-
together with Barki deviating from the pair – still tions. Most likely there has been only little genetic
with a low bootstrap value (48%). The Barki goat is exchange between the goat populations in the
a desert breed that lives in the north-western coastal region. This study is the first attempt to characterize
region of Egypt, while both Egyptian Baladi and the molecular genetic variability of the Egyptian goat
Egyptian baladi

Egyptian baladi
Montefalcone

Montefalcone
Maltese

Maltese
Zaraibi

Zaraibi
Barki

Barki

Figure 3 The clustering outcomes for all

samples at k = 3 and k = 4. The length of
the segment in white, light grey, dark grey,
or black shows the individual’s estimated
proportion of membership in that cluster.
Black lines separate the individuals of differ-
k=3 k=4 ent breeds. Populations are labelled above.

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198 Journal compilation ª 2008 Blackwell Verlag, Berlin • J. Anim. Breed. Genet. 125 (2008) 194–200

S. H. Agha et al.
populations. There is a need for a more thorough
analysis of the goat genetic diversity in the region by
including more breeds, larger sample sizes and addi-
tional molecular markers.
In terms of improving the efficiency of Egyptian
goat production, we have observed that the popula-
tions have a similar amount of genetic variation as
other goat breeds, when extrapolated from the infor-
mation on microsatellite markers. The Nile val-
ley ⁄ delta breeds are distinct from the desert breed
and would all deserve an independent improvement
schemes. The Egyptian breeds are exhibiting a gen-
erally high prolificacy and therefore there is no need
to make any efforts to bring additional or compensa-
tory gains in such a low-heritability trait (which
would need more time to change through within-
population selection) via a crossbreeding pro-
gramme, as such a program brings along the risk of
losing other well identified and beneficial character-
istics in well established breeds.
Acknowledgements
A part of this work was prepared through a scholar-
ship from the Framework of the Individual Mobility
Grant of Education and Training Programs and
Actions (TEMPUS), European Commission. Special
thanks are due to Ms. Asmaa Aboshady and Ms.
Hend Abo-Elazm for helping in running the labora-
tory work. Dr Ahmad EL-Beltagi’s help in the statis-
tical analysis is acknowledged. We would also like to
thank the two anonymous referees and the editor
for very useful comments on the earlier versions of
the manuscript.
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