J. Life Sci. Biomed. 6(2): 22-32, Mar 30, 2016  
JLSB  
© 2016, Scienceline Publication  
Journal of  
ISSN 2251-9939  
Life Science and Biomedicine  
A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are  
Strong to Support the Breeding Programs?  
  
Getinet Mekuriaw1,2,3,4 , Solomon Gizaw2, Tadelle Dessie2, Okeyo Mwai5, Appolinaire Djikeng4 and  
Kassahun Tesfaye1  
1Addis Ababa University, Department of Microbial, Cellular and Molecular Biotechnology, Addis Ababa, Ethiopia  
2International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia  
3Department of Animal Production and Technology; Biotechnology Research Institute, Bahir Dar University, Ethiopia  
4Biosciences for eastern and central Africa (BecA), Nairobi, Kenya  
5International Livestock Research Institute (ILRI), Nairobi, Kenya  
 yafetgetinet@gmail.com  
ABSTRACT: Genetic characterization requires knowledge of genetic variation that can be effectively measured  
within and between populations. It is considered as an important tool for sustainable management or  
conservation of a particular population. Presence of limited diversity may hamper the possibility of  
populations to adapt the local environment in the long term, but loss of genetic diversity can also more  
immediately lead to decrease fitness within populations. In this paper, genetic diversity of more than 120  
domestic goat populations found in various parts of the world has been summarized. The paper is limited only  
to the diversity study conducted by microsatellite loci. In all the goat populations reviewed, the within  
population genetic diversity is extremely higher than between population variation which might be due to the  
uncontrolled and random mating practiced among the breeding flock. However, the technical as well as  
statistical data management deficiencies, like selection of microsatellites and other sampling biases, observed  
in the reports could have their own influences on the limited and weak variations obtained within and among  
populations. The genetic distance among populations is very narrow especially populations found within  
states. In general, goats are the most transported animals during the lengthy commercial and exploratory  
journeys took place in the old world long time ago. This contributed the goat to have narrow genetic  
differentiation compared to other ruminant livestock. The technical fissures observed in the past efforts on  
identification and structure analyses of the goat populations might also demand further works to design  
appropriate conservation and breeding management programs.  
Keywords: Domestic goat, Genetic distance, Heterozygosity, Microsatellite marker, Polymorphic information  
content  
INTRODUCTION  
Genetic diversity has been shaped by past population processes and will also affect the sustainability of  
species and populations in the future [1]. Maintenance of genetic diversity in livestock species requires adequate  
implementation of conservation priorities and sustainable management programs [2]. It is also a key to the long-  
term survival of most species [3] and widely used to categorize animals in the world [4]. However, isolation-by-  
distance [5], historical and geological factors [6], physical barriers [7,8] and ecological factors through  
morphological adaptation to local conditions [9] are some of the factors which are suspected in disrupting  
patterns of genetic structure and gene flow of a given population. Especially in domestic animals, the gene flow  
disruption is overseen more by human intervention than by physical barriers [10].  
Farm animal genetic diversity is required to meet current production needs in various environments, to  
allow sustained genetic improvement, and to facilitate rapid adaptation to changing breeding objective and serves  
as a tool for animal breeding and selection [11- 13]. However, classifying the genetic diversity based on historical,  
anthropological and morphological evidences [14] as well as their geographical origin are not satisfactory and  
enough for the purpose of conservation and utilization of these resources. In addition, phenotypic  
characterization provides a crude estimate of the average of the functional variants of genes carried by a given  
individual or population, and the appropriateness of phenotypic traits to study the genetic variation between  
populations is very limited [15]. Hence, comprehensive knowledge of the existing genetic variability is the first  
step for the conservation and exploitation of domestic animal diversity [16].  
To cite this paper: Mekuriaw G, Gizaw S, Dessie T, Mwai O, DjikengA and Tesfaye K. 2016. A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
22  
Goats are considered the most prolific ruminant among all domesticated ruminants especially under harsh  
climatic conditions [17]. The high versatility, moderate size and hardy nature of goats made them ideal as a food  
resource in the lengthy commercial and exploratory journeys that took place in the old world a long time ago [18].  
Today, there are >1,000 goat breeds (www.fao.org/corp/statistics/en/), and recently >861.9 million goats are  
kept around the world with the respective continental share in Million: Asia (514.4), Africa (291.1), South  
America (21.4), Europe (18.0), Central America (9.0), Caribbean (3.9), Northern America (3.0) and Oceania (0.9)  
[19]. The existence of such a large gene pool is important for the potential future breed preservation and for the  
development of a sustainable animal production system [2].  
The absence of well-managed conservation genetics programs and the uncontrolled introgression between  
indigenous as well as foreign breeds are seriously threatening the future of many populations in various parts of  
the world [20]. The high gene flow and the admixture of the breeds can result low level of genetic differentiation  
[21]. This has also an implication of the presence of terrible risk that most breeds may perish before they have  
been exclusively recognized and exploited. Microsatellite marker is the main molecular markers employed to  
identify and characterize genetic diversity of domestic goats found in various corners of the world by various  
scholars. However, following financial and other reasons, most of the efforts conducted may not be as supportive  
as expected in revealing the required information for designing appropriate and sustainable goat breeding  
programs. Therefore, given the limited number of efforts conducted on domestic goats, strength and gaps (with  
emphasis) of past efforts have been summarized and possible ‘the way forward’ is suggested in this paper.  
GENETIC DIVERSITY AND POLYMORPHIC INFORMATION CONTENT  
Genetic diversity refers to the total number of genetic characteristics in the genetic makeup of a species  
that serves as a way for populations to adapt to changing environments. It represents diversity within a  
population [22] and it is distinguished from genetic variability, which describes the tendency of genetic  
characteristics to vary. With more variation, it is more likely that some individuals in a population will possess  
variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce  
offsprings bearing that allele. The population will continue for more generations because of the success of these  
individuals (http://genetics.nbii.gov/GeneticDiversity.html).  
Choosing the appropriate breed or population for conservation is one of the most important problems in  
the conservation of genetic diversity in domestic animals. Some of the parameters which can help the study of  
genetic diversity within a population are expected heterozygosity estimates and allelic distribution; and they are  
believed as they are good indicators of genetic polymorphisms within a population [22-24]. On the other hand,  
the precision of estimated genetic diversity is a function of the number of loci analyzed, the heterozygosity of  
these loci and the number of animals sampled in each population [25].  
Estimation of heterozygosities  
Estimations of expected and observed heterozygosities are measures of genetic variability within a given  
population [23]. The expected heterozygosity is the proportion of heterozygotes expected in a population;  
whereas, observed heterozygosity is the percentage of loci heterozygous per individual or the number of  
individuals heterozygous per locus [26].  
As it is indicated in the table, several reports confirmed the status of genetic variability of different goat  
populations (Table 1) and genetic diversity (HE and HO) estimates observed in goat of Sri Lanka, Australia, Korean,  
Botswana and in some Indian and Brazilian goat populations were below 0.5. This is because of maintaining  
microsatellite loci which had registered heterozygosity estimates below 0.5 in the respective breeds during the  
analysis. Literatures suggest that heterozygosity estimates having greater than 0.5 heterozygosity estimates are  
believed to be appropriate for genetic diversity study [44, 45]. Similarly, some of the estimated values were also  
closer to the margin. These low estimates imply that there might have been high selection pressure, small  
population size, minimal or null immigration of new genetic materials into the populations. Similar low genetic  
diversity estimates were reported for Argentinean and Chilean goat populations despite the small sample sizes  
used in the analysis [18].  
Whereas the remaining estimates conclude that the studied populations have substantial and high amount  
of within population genetic diversity. This might be due to low selection pressure, large population size and  
immigration of new genetic materials [41]. High value of average expected heterozygosity within the populations  
could also be attributed to the large allele numbers detected in the tested loci [46]. In most of the above diversity  
estimates, the observed heterozygosity (HO) and expected heterozygosity (HE) estimates for each locus and goat  
population are closer to each other indicating no overall loss in heterozygosity (allele fixation) [40]. However, few  
To cite this paper: Mekuriaw G, Gizaw S, Dessie T, Mwai O, DjikengA and Tesfaye K. 2016. A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
23  
of the microsatellites studied by various scholars (e.g. [41]) had higher observed heterozygosity than expected  
heterozygosity estimates that probably indicate the existence of sampling bias [45].  
Table 1. Estimation of genetic heterozygosity of indigenous goats  
Breed  
Country  
Sri Lanka-Australian  
Korean  
India  
Swiss3-24  
C. Islands  
--  
HE  
0.45-0.49  
0.38  
0.54-0.79  
0.66  
HO  
--  
0.36  
0.505  
--  
--  
--  
0.56  
0.78  
No.MS  
22  
Author  
[27]  
[28]  
[29-32]  
[13]  
[33]  
[34]  
[35]  
[36]  
[37]  
[38,39]  
[40]  
[39]  
[2]  
[41]  
Sri Lanka and Australian goats (12)  
Korean goats  
9
Indian goat populations  
Swiss goats (11)  
17- 25  
47  
Canary Island goats  
Kalahari Red goats  
Sub-Saharan breeds  
Spanish Guadrrama goat  
Croatian spotted goat  
Chinese ten goat populations  
Brazilian goats and herds  
Guinea Bissau goat  
Iranian goat populations  
Ardi  
0.62  
0.63  
0.54  
0.81  
27  
8
11  
10  
20  
14  
11  
14  
*
Spain  
Croatia  
China  
Brazil  
W. Africa  
Iran  
0.77  
0.76  
0.54-0.64  
0.50-0.70  
0.60  
0.65-0.80  
0.68  
0.55-0.62  
0.61-0.70  
0.61  
--  
0.55  
13  
11  
17  
S.Arabia  
China  
Twelve Chinese breeds  
0.61- 0.78  
0.60 - 0.78  
[16]  
Three Egyptian and two Italian goat  
breeds  
Egypt and Italy  
0.67- 0.79  
--  
7
[42]  
Tswana goat  
Ethiopian goat populations  
Botswana  
Ethiopia  
0.16  
0.55-0.69  
0.12  
0.52-0.68  
12  
15  
[43]  
[22,24]  
MS=Microsatellite;* Uganda (4), Tanzania (5), Kenya (2), Mozambique (2), Nigeria (3), Mali (1) and Guinea Bissau (1)  
On the other side, heterozygosity estimates of nine domestic Swiss goat herds were higher than Wild Ibex  
goats and Bezoar goats with the mean HE ranging from 0.51 to 0.58 for domestic herds and from 0.17 to 0.19 for  
the wild species [47]. The lowest heterozygosity, the lowest genetic variation within the population, estimates are  
comparable with the mean observed (HO=0.12±0.16) and expected heterozygosity (HE=0.16±0.20) values of  
Tswana goat population [43] which is because of the effects of inbreeding and selective breeding in small and  
closed population. This idea is supported by Caňón et al. [48] who stated the positive correlation (r = 0.35) of  
population size with heterozygosity estimates. Low amounts of genetic diversity increase the vulnerability of  
populations to catastrophic events such as disease outbreaks that indicates high levels of inbreeding with its  
associated problems of expression of deleterious alleles or loss of over-dominance [2]. It can also destroy local  
adaptations and break up co-adapted gene complexes ultimately leading to the probability of population or  
species extinction [2].  
Estimation of allelic distribution and locus variability  
The allelic distribution is the other measure of genetic variability in a given population [23, 43]. The  
primary disadvantage of using allelic richness, i.e. the corrected mean number of alleles reflected in the  
standardized sample size [49], as a measure of genetic diversity is that it is highly dependent on sample size: large  
samples are expected to contain more alleles than small samples [50]. Similarly, more alleles are expected to be  
found in a region sampled many times than in a region sampled few times. Private allelic richness has the same  
problem: large samples are expected to have more private alleles than small ones. On the other hand, intensive  
sampling of genetically similar populations may reduce the number of private alleles to any population.  
Therefore, a region that has been sampled intensively may appear to have fewer private alleles than a region  
sampled less intensively. These problems have a straightforward statistical solution: rarefaction can be used to  
compensate for differences in sample size and number [50]. The mean number of alleles and expected  
heterozygosities are very accurate indicators of the genetic polymorphism within a population [41]. Mean  
observed alleles (na) that explain high level of polymorphism of the studied microsatellites were reported for  
several goat populations (Table 2).  
Though the mean number of alleles (MNAs) indicated in table 2 showed the suggested minimum estimates,  
except some Ethiopian, Brazilian, Egyptian, Italian and Iran goat populations, comparatively the average as well as  
the range of alleles estimated were the highest estimation (14.9 mean number of alleles with a range of five to 43  
alleles per locus for 45 breeds) for the 45 goat populations studied in the Mediterranean regions [48] (Table 2). In  
addition to this, all the microsatellites (30 microsatellites, which is the maximum coverage) were covered during  
the study. One of the reasons for the lowest estimates of MNA per locus, in many of the studies, might be because  
To cite this paper: Mekuriaw G, Gizaw S, Dessie T, Mwai O, DjikengA and Tesfaye K. 2016. A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
24  
of using very few bucks, e.g. 3-5 bucks per year for Tswana goat for 16 years of almost closed breeding program at  
BCA farm [43]; and it might also be because of directional selection for parasite resistance/tolerance coupled with  
increased productivity [51] that possibly accumulates inbreeding. Similarly, among the 26 loci of twelve Chinese  
goat populations, 17 were polymorphic and the number of alleles varied between 4 (ILSTS005) and 19 (BM2113);  
the remaining nine loci (excluded from the analysis) tested had less than four alleles or non-specific PCR products  
[16]. The later screening procedure was not undertaken by many of the authors. For studies like genetic distance,  
microsatellite loci should have no fewer than four alleles to reduce the standard errors of distance estimates [25].  
For the other goat populations relatively encouraging estimates of MNA were reported. However, though  
those reports explain the existence of high polymorphism, the average number of alleles depends on sample size,  
number of observed alleles tends to increase with increasing population size and the number of sires used in a  
breeding program. This is because of the presence of unique alleles in populations which occur at very low  
frequencies [41, 43].  
In general, heterozygosity deficiency may be resulted because of the presence of a null allele which is the  
allele that fails to multiply during PCR using a given microsatellite primer due to a mutation at the primer site [25,  
53], small sample size where rare genotypes are likely to be included in the samples [2], Wahlund effect, that is  
presence of fewer heterozygotes in population than predicted on account of population subdivision and decrease  
in heterozygosity because of increased consanguinity (inbreeding) [11]. Higher heterozygosity provides better  
assignment performance [54] and the loss of alleles is probably the consequence of repeated founder effects  
during migration events [55].  
Estimation of polymorphic information content (PIC)  
Literatures state that the polymorphic information content (PIC) values depict the suitability of the  
markers and their primers used in the study for analyzing the genetic variability of a given population. Hence,  
microsatellite markers having greater than 0.5 PIC value are considered as highly informative and highly  
polymorphic [56, 57]. Therefore, highly polymorphic markers were employed for the goat populations indicated  
in Table 2.  
In contrast to this, lower PIC values of microsatellites (for instance Korean goats PIC = 0.35, [28]; for  
Egyptian and Italian goats of few loci PIC=0.221, 0.482 & 0.389 [42] and for India goat having 28% of the loci <0.5  
PIC [58]) which were expected to be excluded were included in the analysis. In fact, the PIC is determined by  
heterozygosity and number of alleles [41] and this makes microsatellite markers the choice for genetic  
characterization and diversity studies. In particular, the high PIC values of a particular marker suggest its  
usefulness for genetic polymorphism and linkage mapping studies in goats and 60% of microsatellite loci had  
significant hardy-Weinberg equilibrium (HWE).  
Level of inbreeding (FIS)  
FIS is a measurement of the reduction in heterozygosity of an individual as a result of non-random mating  
within its subpopulation [59]. It is an average increase of homozygous loci by decreasing the heterozygous loci  
with the same proportion [43]. It is less suited to reflect historical processes because it has a different, more rapid  
dynamic than does gene diversity [59]. A high positive FIS indicates a high degree of homozygosity and vice versa  
[45]. Inbreeding coefficients is estimated for populations which show significant deviation from the HWE [26].  
This indirectly implies that inbreeding coefficient (FIS) [59] is significant for significant HWE estimation; but it  
may not work for all loci of a population.  
Based on this background, moderate and high level of inbreeding coefficients were reported by various  
scholars for different goat populations; for instance, for Marwari (FIS=0.26; [32]), Jamunapari (FIS=0.19; [66]),  
Mehsana (FIS=0.16; [60]) and Kutchi (FIS=0.23; [31]) breeds of India, Ardi goat breed (FIS =0.18 with only 50% of  
the markers under HWE; [41]) of Saudi Arabia, Tswana goat breed (FIS =0.12; [43]) of Botswana are some of the  
reports having high level of inbreeding. However, particularly for Tswana goat breed, the FIS estimate ranged from  
-0.2340 (INRA006) indicating low levels of inbreeding at that marker locus to 0.8772 (MCM527) depicting high  
levels of inbreeding. This might be because of the small population size, closed breeding system and very limited  
number of breeding bucks used for many consecutive years in the farm [43]. The lowest heterozygosity and MNA  
estimates indicated in table1 and 2 above strengthen this rationale. However, tolerable mean value of FIS (0.03)  
with the range of -0.223 to 0.220 was obtained for 17 microsatellites (with 12 MNA per locus and a range of 0.586  
to 0.790 HE estimates) of 12 Chinese indigenous goat populations [16].  
The moderate level of inbreeding may be a result of moderate levels of mating between closely related  
individuals under field conditions and may be the uncontrolled and unplanned mating that caused high level of  
To cite this paper: Mekuriaw G, Gizaw S, Dessie T, Mwai O, DjikengA and Tesfaye K. 2016. A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
25  
inbreeding. On the contrary, very low inbreeding value (FIS=0.10) were reported within 45 rare breeds of 15  
European and Middle Eastern countries [48] compared with the above reports and the discrepancy between the  
observed and expected heterozygosities and the difference between the observed and effective number of alleles  
could confirm the existence of inbreeding [48]. Still the level of inbreeding estimates in all the 45 breeds studied  
except the two populations (St. Gallen Booted goat breed of Switzerland, FIS = 0.048 and Thuringian forest goat  
breed of Germany FIS =0.049) are not tolerable because the estimated values obtained were higher than 0.05.  
Table 2. Estimated mean number of alleles and polymorphic information content  
Country  
origin/Region  
MNA per  
breed  
MNA per  
MS  
PIC per  
locus  
MS  
(No.)  
Breed  
Author  
Egyptian and Italian goat breeds (5) Italy  
6.48  
6.33-9.7  
6.7  
3.8-9.8  
4-24  
2.4-5.2  
0.22 -0.87  
0.08-0.90 [23,40,59,60]  
0.54-0.81  
[42]  
7
17-25  
9
Indian goat breeds (10) f  
India  
Taleshi goat  
Iran  
[61]  
Iranian goat breeds (6)  
Croatian spotted goat  
Iran  
Croatia  
6.46 -8.15  
8.1  
0.71-0.86  
0.74  
[2,62]  
[37]  
13  
20  
8.1  
Ardi goat  
Saudi Arabia  
6.64  
0.63  
[41]  
Brazilian goat breed (3)  
Brazil  
3.5 -7.2  
3-11  
NA  
[40]  
11  
Namibian goat breeds (4)  
Kalahari Red goat  
Tete goat  
Namibia  
4.67 – 6.00  
[63]  
[34]  
[64]  
[64]  
18  
18  
South Africa  
Mozambique  
Mozambique  
Mediterranean  
regions  
7.77  
5.58  
6.94  
7.77  
NA  
NA  
Pafuri goat  
45 breeds  
5.2-9.1  
5-43  
[48]  
30  
Chinese goat populations (22)  
Tswana goat  
Indigenous goat populations (17)  
Key:- MS=Microsatellite  
China  
Botswana  
Ethiopia  
5.24 -9.1  
4-19  
1.83  
2.06-23  
0.62-0.88  
0.58  
[16,65]  
[43]  
[22,24]  
17-20  
12  
15  
5.13 -6.73  
NA  
From thirty microsatellites used, twenty-four of them were in H–W equilibrium (p>0.05) and is more than  
90% of the total 45 populations of European and Middle East goats studied [48]. However, small number of loci  
which were in Hardy-Weinberg Equilibrium: only seven loci (ILSTS011, SPS113, ILSTS029, SRCRSP3, MAF70,  
ILSTS005 and OarAE54) i.e., only 50% of the total fourteen microsatellite markers, showed Hardy Weinberg  
Equilibrium (HWE) (p>0.05) in Ardi goat population of Saudi Arabia [41]. Similarly, only 55% of the total  
microsatellites used showed HWE (P>0.05) in Alpine Saanen and Moxotó dairy goat populations in Brazil [40].  
Such findings indicate the presence of effect of selection or uncontrolled breeding practice in the study  
populations [41]. Huge deviation from HWE (16 out of 20 loci), i.e. only 20% showed HWE (P>0.05), was  
observed on Kanniadu goats of India [67]; the possible reasons for the deviations pointed out were existence of  
"null" alleles, high mutation rate and size of homoplasy of microsatellite loci, besides the small study population.  
On the other hand, four out of the 12 loci (SRCRSP5, MCM527, ILST087 and INRA006) that differed significantly  
from the Hardy-Weinberg equilibrium (HWE) were observed indicating subjection of, particularly, those loci to  
systematic selection and dispersive forces such as genetic drift and inbreeding [43]. In this study, five out of the  
total 12 loci were monomorphic (fixed allele) that could be linked to genes responsible for parasitic resistance,  
and this goes in line with the study made by Beh et al. [68].  
The large proportion of loci without of HWE might be because of those loci being under within major  
histocompatibility complex [69] and under strong natural selection pressure [70]; or it might be because of the  
presence of null or non-amplified alleles, allele grouping defects, a sampling structure effect, selection against  
heterozygotes or inbreeding [40]. In other study, it is also stated that deviations from Hardy-Weinberg  
equilibrium could also be due to a variety of causes including: excess of heterozygote individuals than  
homozygote individuals [71] in contrast Mahmoudi et al. [2] who stated heterozygosis deficiency is one of the  
parameters underlying departure from HWE), migration, high mutation rate at microsatellite loci and artificial  
selection .  
GENETIC DISTANCE AMONG POPULATIONS  
The simplest parameters for assessing diversity among breeds are the genetic differentiation or fixation  
indices. Several estimators have been proposed (e.g. FST and GST), the most widely used being FST [72], which  
measure the degree of genetic differentiation of subpopulations through calculation of the standardized variances  
To cite this paper: Mekuriaw G, Gizaw S, Dessie T, Mwai O, DjikengA and Tesfaye K. 2016. A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
26  
in allele frequencies among populations. Statistical significance can be calculated for the FST values between pairs  
of populations [73] to test the null hypothesis of lack of genetic differentiation between populations and,  
therefore, partitioning of genetic diversity [74]. Hierarchical analysis of molecular variance (AMOVA) can be  
performed to assess the distribution of diversity within and among groups of population [75].  
In relative to other markers, microsatellite data are commonly used to assess genetic relationships between  
populations and individuals through the estimation of genetic distances [76-80]. The most commonly used  
measure of genetic distances is Nei’s standard genetic distance (DS) [81]. However, the modified Cavalli-Sforza  
distance (DA) is recommended for closely related populations where genetic drift is the main factor of genetic  
differentiation, as is often the case in livestock populations particularly in the developing world [82].  
Genetic relationship between populations is often visualized through the reconstruction of a phylogeny,  
most often using the neighbor joining (N-J) method [83]. However, a major drawback of phylogenetic tree  
reconstruction is that the evolution of lineages is assumed to be non-reticulated, i.e. lineages can diverge, but can  
never result from crosses between lineages. This assumption will rarely hold for livestock where new breeds  
often originate from cross-breeding between two or more ancestral breeds. The visualization of the evolution of  
breeds provided by phylogenetic reconstruction must, therefore, be interpreted cautiously.  
Multivariate analysis and more recently Bayesian clustering approaches have been suggested for admixture  
analysis of microsatellite data from different populations [84]. Probably the most comprehensive study of this  
type in livestock is a continent-wide study of African cattle [85], which reveal the genetic signatures of the origins,  
secondary movements, and differentiation of African cattle pastoralism.  
Based on comparison of genetic distances that measure genetic drift, with microsatellite data set, the  
Reynolds distances underestimate the divergence of eastern Mediterranean goat populations (Saudi Arabia,  
Turkey, Albania and Cyprus) with a high heterozygosity [48]. Model-based clustering [84] of the goat  
microsatellite genotypic values indicates that the most significant subdivision is at the level of breeds or groups of  
closely related breeds [48]. Analysis at lower K-values may indicate a subdivision of the goat population [86] that  
preceded breed formation.  
In relative to other reports, lower average values of FST for the four goat populations clusters (East  
Mediterranean: FST=0.033, Central Mediterranean: FST=0.040, West Mediterranean: FST=0.051 and Central-north  
European: FST=0.069) were obtained [48] than the values of 0.14 recorded for Asian goats [27], of 0.17 for Swiss  
goat populations [49] and of 0.10 for a set of Chinese goat populations [16]. Similar low estimate of mean  
differentiation among populations (FST = 0.0717) was also reported that indicates presence of mixing among  
population and the most variability occurs within a population [40]. This might be because of gene flow among  
most breeds has probably been restricted by geographical isolation rather than adherence to pedigree; i.e. a  
geographical restriction of genetic contacts of population may cause geographical clines or maintain clines that  
predate breed formation [48].  
FST values for each pair of the goat populations in Ethiopia varied from 0.001 to 0.040 [22]. The average FST  
values over all microsatellite loci was 0.026, indicating that a 2.6% of total genetic variation corresponded to  
differences among populations, whereas 97.4% was explained by difference among individuals. Similarly, it was  
also noted that 5% of the total variation occurred due to population subdivision, while the remaining 95% of the  
variation existed among individuals within the goat ecotypes [24].  
It was recommended that the highest genetic distance (FST) to be higher than 0.25, moderate to be between  
0.05 and 0.25 and the lowest estimate below 0.05 [46, 87]. In general, the genetic distance between populations  
obtained by many of the scholars [16, 21, 22, 24, 40] is almost negligible (<0.05) and/or moderate  
(0.05<FST<0.25) values. Some of the authors revealed significant genetic distance estimates among populations.  
This implies that, despite the limitations of sampling and other related statistical management limitations stated  
above there is relatively moderate genetic sub-differentiation among the goat populations. A fixation index (FST)  
of about 0.15 is considered to be an indication of significant differentiation among populations [88]. In line with  
this, as an indirect way to measure quantitative genetic diversity, a fixation index (FST) of about 0.25 total genetic  
variance could be explained among-breed genetic variance [49].  
In the phylogeny tree analysis employing both the NJ and UPGMA trees might be good. However, it would  
have been more informative if the fitness of the trees were statistically tested. This limitation makes the result  
blurred and difficult to arrive at certain conclusion with either of the phylogenetic tree analyses. In addition,  
besides to the polymorphic nature of microsatellites there might be a chance to face monomorphic nature of  
them. Hence, this demands some techniques to isolate such loci. However, there is no clear methodology that  
describes whether such techniques were employed or not. Monomorphic microsatellite loci were obtained while  
studying the Indian domestic goat populations and dropped out from the analysis [30]. Probably, the minimum  
To cite this paper: Mekuriaw G, Gizaw S, Dessie T, Mwai O, DjikengA and Tesfaye K. 2016. A Review on Current Knowledge of Genetic Diversity of Domestic Goats  
(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
27  
estimates of MNA per locus obtained in the microsatellite loci genotyped might be an indication of absence of  
employing some screening techniques. Such limitations were seen in many of the studies.  
GAPS IDENTIFIED  
Apart from the least sample size used in some of the studies, e.g. Halima et al [24] who used eight animals  
to represent a population and which is quite far from FAO recommendation for SSR marker analysis [89], the  
number of samples used for a study was not equal which leads the genetic diversity parameters like HWE and  
MNA to be sensitive for biasness; or there is no any technique indicated in the papers which was employed to  
handle such a limitation [90]. Large samples are expected to have more alleles than small samples [91]; however,  
the degree of influence of small sample size is weak as compared with the size of number of markers to be used  
[90].  
In addition to the procedures to be followed in handling unequal sample size, selection of microsatellite loci  
which are efficient in polymorphism and techniques of screening monomorphic loci [93] and design of statistical  
genetic analysis in general are not clearly indicated in the papers and might bias the readers. This ultimately  
could have their own influence on implementation of further activities of improvement and conservation  
breeding programs. On the other hand, only very few or no microsatellite loci used in the analysis showed higher  
observed heterozygosity values than expected heterozygosity values [16, 22, 24, 39, 40]. This probably implies  
the existence of sampling bias [45]. In addition, some of the microsatellite loci (table 1) had shown HE and HO  
estimates of less than 0.5; however, it was suggested that such loci having values less than 0.5 are not  
appropriate for heterozygosity evaluation [44,45]. Similarly, the number of alleles found per locus is the other  
indicative in evaluating the efficiency of loci; hence, though it was not seen in some of the studies found in table 2,  
the number of alleles to be found per locus for remarkable genetic diversity of a population should be equal or  
greater than four [25, 92]. These all points remark as the microsatellites could be dropped out or could require to  
be prudent in selecting microsatellite. Apart from that it is important to note to be keen in selecting  
microsatellites to deliver strong recommendation that serves for effective sustainable conservation and breeding  
management strategies.  
CONCLUSIONS AND RECOMMENDATION  
Genetic diversity studies carried out on domestic goat at various parts of the world were compiled in this paper.  
More than 120 goat populations were included in the review. These all goat populations were studied with  
microsatellite markers. The results indicated that there is high within population genetic variations and very  
narrow population differentiation among the goat populations studied. On the other side, limited sample sizes  
which are not equal for the populations included in the respective studies, weak efficiency of the markers  
employed for the analysis (e.g. few numbers of alleles per marker, very low heterozygosity estimate per marker,  
etc) which lead to bias the parameters measured or absence of handling techniques to capture those limitations  
are observed in most of the studies. In general these all demand further works to support the goat breeding  
interventions.  
Competing Interests  
The authors have declared that there is no competing interest  
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(Capra hircus) Identified by Microsatellite Loci: How those Efforts are Strong to Support the Breeding Programs? J. Life Sci. Biomed. 6(2): 22-32.  
Journal homepage: www.jlsb.science-line.com  
32