Last update: February 8, 2013 07:33:19 AM E-mail Print





M.A. Snyman#1, E. van Marle-Köster2, S.O. Qwabe1,2 & C. Visser2

1Grootfontein Agricultural Development Institute, Private Bag X529, Middelburg (EC), 5900 2Department of Animal & Wildlife Sciences, Faculty of Natural & Agricultural Sciences,

University of Pretoria, Pretoria, 0002

#E-mail: Gretha Snyman



Genetic and phenotypic characterisation is essential for the conservation and utilisation of farm animal genetic resources, especially indigenous types that are often disregarded due to perceived lower production potential compared to commercial breeds. Indigenous breeds such as the Namaqua Afrikaner are particularly vulnerable as selection for improvement in production and uncontrolled mating strategies may lead to genetic dilution and even loss of genetic variation within these breeds, leading to their eventual extinction (Shrestha, 2005; Scherf et al., 2006). Genetic characterisation of endangered farm animal genetic resources such as the Namaqua Afrikaner sheep is an important step in a conservation program. In order to ensure proper conservation and utilisation of farm animal genetic resource, it is essential to evaluate the genetic diversity that exists within and between breeds. Several South African sheep and goat breeds have been characterised on a molecular level. These include studies on a number of sheep breeds by Buduram (2004), on three commercial and three indigenous goat populations by Visser et al. (2004), on Nguni sheep by Kunene et al. (2009) and on Angora goats by Visser & van Marle-Köster (2009).


The Namaqua Afrikaner sheep breed is part of the Grootfontein Agricultural Development Institute’s Biological Reserve for Small Stock (GADI-Biobank), which was established with the aim of promoting and facilitating the improvement and conservation of South African sheep and goat breeds (Snyman, 2011). The breed characterisation was the outcome of two workshops on the conservation of indigenous livestock. The first was a workshop hosted by the Northern Cape Department of Agriculture and Land Reform during May 2007 at the Vaalharts Experimental Station, focusing on the endangered Namaqua Afrikaner sheep breed followed by a second workshop, during November 2007 in Pretoria, where it was decided to perform a genetic and phenotypic characterisation of the three Namaqua Afrikaner flocks that were part of the GADI-Biobank at that stage.



The genetic and phenotypic characterisation were carried out using animals of two Namaqua Afrikaner flocks maintained at the Carnarvon and Karakul Experimental Stations of the Northern Cape Department of Agriculture, Land Reform and Rural Development and a third Namaqua Afrikaner flock kept by a private owner on his farm Welgeluk in the Carnarvon district. These flocks are part of the GADI-Biobank.


The three Namaqua Afrikaner sheep populations were characterised using a set of 20 microsatellite markers recommended by the International Society of Animal Genetics (ISAG) to determine genetic variation and genetic differentiation within the breed. Production and morphometric data of the Namaqua Afrikaner flock at the Carnarvon Experimental Station were included to describe the phenotypic characteristics of the breed.



Namaqua Afrikaner flock at Carnarvon Experimental Station (CES)

The Department of Agriculture bought one of the last purebred Namaqua Afrikaner flocks from Mr P.J. Maas from Namies, Springbok, during 1966 and since then this flock has been kept at the Carnarvon Experimental Station. Currently the flock comprises 120 ewes.


The flock is run continuously on the veld and no supplementary feeding is given at any time. A system of one breeding season per year has been followed since 1966, with a 34-day mating period during April. The lambs are weaned at four months of age. All lambs are retained until the age of 18 months, when ewe and ram replacements are picked at random. No selection for any specific production or reproduction traits is carried out. However, animals with physical deformities and which do not conform to the general breed appearance are culled. Ewes are replaced at a rate of 20%, while all rams are replaced annually.


In an effort to keep the inbreeding level as low as possible the ewes in the flock are divided into three groups. Young ewes from the same group replace the old ewes. The rams are used on a rotational basis between the groups (cyclic mating). Four rams per group are used in a group mating system, where each group of rams is run with their group of 35 to 40 ewes (Snyman et al., 1993). No outside rams have been introduced to the Carnarvon Namaqua Afrikaner flock since 1980.


Namaqua Afrikaner flock at Karakul Experimental Station (KES)

In March 1985, 30 ewes and five rams from the Carnarvon Namaqua Afrikaner flock were transferred to the Tarka Conservation area near Hofmeyr in the Eastern Cape Province. Their numbers were allowed to increase to approximately 100 breeding ewes. In 1991 this flock was transferred to the Grootfontein Agricultural Development Institute. While the animals were at Tarka and Grootfontein, a free mating system was followed, where the rams were run with the ewes throughout the year. No supplementary feeding was given or any drenching and inoculation program followed. Once a year, replacement rams and ewes were picked at random and the surplus culled. Old ewes were culled when they had virtually no teeth left and started losing condition as a result.


In August 1995, the flock was transferred to the Karakul Experimental Station near Upington, where it is still maintained. The ewe flock comprises 120 ewes, that are kept on the veld continuously, and no supplementary feeding is given at any time. A system of one breeding season per year has been followed since 1997, with a 34-day mating period during September. The same general management and mating program as the one in the Carnarvon flock is followed in this flock. No outside rams have been introduced to this flock since 1985.


Namaqua Afrikaner flock of Mr Johann van der Merwe at Welgeluk, Carnarvon (WGK)

At Welgeluk farm multi-sire mating was used in the past, where rams and ewes were run together. The animals were not subjected to any selection pressure or intentional inbreeding. Mr Van der Merwe has however changed to cyclic mating in order to decrease the inbreeding level. During 1994 and 1995 Mr Van der Merwe purchased some Namaqua Afrikaner ewes and rams from the Carnarvon Experimental Station flock. He had also acquired some animals from other private farmers. The ewe flock comprises 100 ewes, which are run on the veld continuously and no supplementary feeding is given at any time (Personal communication: Mr Johann van der Merwe, Private Bag X529, Middelburg, 5900).


Genetic characterisation

A total of 144 blood samples from animals from the three participating flocks were used (48 animals from each flock, consisting of 10 rams and 38 ewes each). As full pedigrees were not available, and to include animals that had as little relationship as possible, samples were taken from animals in different cyclic mating groups and born in different years at the Carnarvon and Karakul experimental stations. Random sampling, within age groups, was conducted on the animals of the Welgeluk flock.


The blood samples were obtained from the GADI-Biobank and DNA was extracted from whole blood using the Roche kit for mammalian blood at the GADI DNA laboratory. The DNA was quantified using a spectrophotometer (Nanodrop ND-1000) at the Department of Genetics, University of Pretoria. DNA samples were amplified with 20 microsatellite markers recommended by ISAG. Markers were selected on the basis of amplification success fragment sizes and polymorphicity.  Polymerase chain reaction (PCR) and genotyping were done at the Animal Breeding and Genetics laboratory of the Department of Animal and Wildlife Sciences, University of Pretoria. Ms Toolkit (Park, 2001) was used to calculate parameters for genetic diversity and population structure was inferred using Structure (Pritchard et al., 2000).


Phenotypic characterisation

Production and reproduction data collected since 1982 on the animals in the Namaqua Afrikaner flock at the Carnarvon Experimental Station were used for this part of the study. Data collected on 2668 lambs, born from 1993 until 2009, were used for the evaluation of body weight. The following traits were analysed: birth weight, 42-day body weight, 120-day weaning weight, five to twelve month body weight. Data of 386 lambs born from 2007 to 2009 were used for the description of the following morphometric traits at 14 months of age: wither height (cm), body length (cm), heart girth (cm), cannon bone length (cm), colour pattern (any colour on body), colour of the head (brown or black), tail circumference at the root of the tail (cm), tail length (cm), twist of tail (none, to the right, to the left) and horned or polled.


The body weight and body measurements data were analysed with least-squares means procedure (Littell et al., 1991; SAS, 2009) fitting a general linear model. The following fixed effects were included in the linear model fitted to the data, namely year of birth, sex and birth status of the lamb, age of dam, cyclic mating group and all significant two-factor interactions.


The data used for the calculation of the reproductive performance of the Carnarvon Namaqua flock consisted of 2925 individual ewe records, which were collected over a 27-year period from 1982 to 2009.  The available data for each ewe for each lambing season included identity of ewe and lamb/s, birth date, birth weight, sex, birth status and 120-day weaning weight of each lamb. From these data, the annual total weight of lamb weaned for each ewe joined, as well as the total weight of lamb weaned by each ewe over her lifetime in the flock were calculated. For the analyses of variance for body weight of ewes, total weight of lamb produced per ewe per year, number of lambs born and number of lambs weaned per ewe per year, fixed effects for year and age of the ewe were included in the models. Least-squares means for these traits were obtained with the PROC GLM-procedure of SAS (Littell et al., 1991; SAS, 2009). Fixed effects included for lifetime reproduction were year of birth of the ewe and number of lambing opportunities.



Genetic characterisation

Each of the 20 microsatellite markers used in this study gives information regarding the variation that is present at a specific locus. The more alleles present in the population at a specific locus, the higher the level of genetic diversity. Although a range of alleles could be present in the population for each locus, a given individual can only carry two of these at a specific locus. The animal can carry either two similar alleles (homozygous individual) or two different ones (heterozygous individual). If a range of alleles is present at a locus in the population, it indicates higher levels of molecular variation and a higher probability that genetic diversity could be maintained.


The number of alleles detected in all three populations, unique alleles to each population and those alleles that were found to be present the least and the most frequent in each population are summarised in Table 1. The frequencies of each of the least and most frequent alleles are indicated in brackets.


A total number of 98 different alleles were detected for the 20 microsatellite markers that were genotyped in 144 individuals. The number of alleles observed across microsatellite markers varied from two to eight. The mean number of alleles detected across the populations was 5.0 over all loci. The Welgeluk (WGK) population had the highest mean number of alleles (4.2), followed by the Carnarvon Experimental Station (CES) population (3.8) and the Karakul Experimental Station (KES) population (3.6). Alleles unique to certain populations were also observed (Table 1). The WGK population had the highest number of unique alleles; a total of ten alleles were observed only in this population with frequencies ranging between 0.01 and 0.19. Five unique alleles were observed in the KES population with frequencies between 0.01 and 0.16. The CES population had only four unique alleles with allele frequencies ranging from 0.02 to 0.13. Although low frequencies for these unique alleles were observed, they can be used to distinguish between the three Namaqua Afrikaner populations.


Table 1. The number of alleles detected in all three populations, and those alleles that were found to be present the least and the most frequent in each population at each locus (frequency)


n a

Alleles detected b, d

Most frequent alleles

Least frequent alleles









72, 78, 80, 90, 96, 106

72 (0.42)



96 (0.42)



106 (0.02)





214, 218, 232, 236, 238, 244, 246

214 (0.73)

214 (0.55)

214 (0.94)

244 (0.01)

232 (0.02)

218, 244, 246 (0.01)



128, 130

130 (0.69)



130 (0.94)

128 (0.31)






108, 110, 112, 116, 118, 122

116 (0.58)

122 (0.44)

116 (0.71)

108 (0.03)

118 (0.03)

118, 112 (0.01)



144, 146

144 (0.87)



144 (1.0)

146 (0.12)





212, 216, 218, 222, 224

218 (0.46)

218 (0.47)

216 (0.68)

212 (0.02)

212 (0.045)





113, 119

113 (0.72)

113 (0.51)

113 (0.89)

119 (0.27)

119 (0.48)





181, 183



181 (0.94)

181 (0.61)

183 (0.31)

183 (0.05)





125, 127, 129, 131, 133, 135, 145, 147

129 (0.37)

129 (0.61)

129 (0.38)

145 (0.04)

131 (0.01)





157, 159, 167, 171, 181, 183,  189

167 (0.33)

157 (0.40)

171 (0.64)

181, 183 (0.03)

167 (0.04)





121, 123, 125, 131, 133

121 (0.64)

121 (0.45)

123 (0.59)

131 (0.01)

133 (0.03)





216, 220, 222, 226, 228, 230, 238, 242

226 (0.39)

228 (0.42)

226 (0.36)

220 (0.01)

226 (0.04)





121, 123, 127

121 (0.91)

121 (0.71)



127 (0.02)

123 (0.27)





164, 166, 172, 182

164 (0.51)

164 (0.41)

166 (0.53)

182 (0.02)

172 (0.24)

125, 127 (0.01)



114, 120, 122, 126, 134

134 (0.42)

134 (0.40)

134 (0.50)

114 (0.09)

120 (0.14)





144, 148, 150, 164

148 (0.52)

148 (0.76)

148 (0.72)

164 (0.21)

144 (0.01)





134, 138, 140, 141, 142

140 (0.61)

140 (0.97)

142 (0.47)

134 (0.02)

138 (0.02)





141, 151, 153, 155, 157, 159

155 (0.69)

155 (0.59)

155 (0.71)

141 (0.02)

151, 153 (0.02)

141, 151 (0.01)



198, 202, 206, 210, 212, 214, 216

206 (0.26)

206 (0.63)

216 (0.34)

210 (0.15)

216 (0.08)

202, 214 (0.01)



169, 171, 172, 173

171 (0.62)

171 (0.59)

171 (0.51)

172 (0.09)

172 (0.01)



a n: number of alleles detected at each locus for all animals

b Alleles detected: e.g. 72 indicates the length of the allele in terms of number of base pairs that the allele consists of

c CES: Carnarvon Experimental Station; KES: Karakul Experimental Station; WGK: Welgeluk

d Alleles unique to: CES - italic and bold; KES - bold; WGK - bold and underlined



The heterozygosity at each locus was estimated to determine the level of genetic variation within the populations. The observed heterozygosity for individual loci ranged from 0.0 for SRCRSP05, CSSM47 and TTH225 in KES and in WGK to 0.913 for INRA23 in CES. The average observed heterozygosity for CES, KES and WGK was 0.551, 0.456 and 0.462 respectively.


The mean estimates of F-statistics obtained over loci were: FIS = 0.019 ± 0.019 (within-population inbreeding estimate), FST = 0.105 ± 0.013 (estimate of population differentiation) and FIT = 0.123 ± 0.025 (overall global deficit of heterozygotes across populations). The average FIS value across the three populations was low positive, which indicates a low level of inbreeding. The average genetic differentiation between all populations (FST) indicates that 10.5% of genetic diversity can be explained by the genetic differentiation among the populations, while the remaining 89.5% can be explained by differences among individuals within the populations. The overall global deficit of heterozygotes across populations (FIT) indicates a 12.3% decrease in the amount of heterozygosity due to inbreeding.


Analyses of molecular variance (AMOVA) were performed to further explain the partitioning of the level of genetic variation of the Namaqua Afrikaner sheep populations. The results obtained by AMOVA analyses were similar to those revealed by the FST estimate, which illustrated that 89.5% of genetic diversity occurred within populations and 10.5% between the populations (Table 2).


Table 2. AMOVA analyses for the three Namaqua Afrikaner sheep populations

Source of variation

Sum of squares

Variance components

Percentage variation


Among populations





Within populations











A breed with constant gene and genotype frequencies is said to be in Hardy-Weinberg equilibrium (HWE). The test of genotype frequencies for deviation from HWE at each locus over all populations revealed that 80% of the loci agreed with Hardy-Weinberg expectations (P<0.05). Only four loci (SRSRSP05, ETH225, TGLA53 and BMI824) did not show adherence to HWE.


The genetic relationship between populations can be measured by determining the genetic distance between populations. This distance between two populations provides a good estimate of how divergent they are genetically. Allele frequencies were used to determine genetic distances between the three Namaqua Afrikaner sheep populations. The genetic distance estimates ranged from 0.0621 between CES and WGK to 0.1596 between KES and WGK (Table 3). The smallest genetic distance was observed between CES and WGK and the largest genetic distance was observed between KES and WGK. 


Table 3. Genetic distance between the three Namaqua Afrikaner populations











The structure software program (Pritchard et al., 2000) was used to assign individual animals into their specific populations. Three distinct clusters were identified for this population of animals. Table 4 presents the proportion of individuals of each of the populations in the three most likely clusters inferred by the structure program, and this corresponded to the three different populations included in the study. Nearly 86% of the CES population was assigned to Cluster 1, whereas approximately 89% of the KES animals were assigned to Cluster 2. The WGK animals were mainly assigned to Cluster 3 (81%) with a smaller component assigned to Cluster 1 (15%).


Table 4. Proportion of membership of the Namaqua Afrikaner sheep population in each of the three clusters inferred in the structure program


Inferred Cluster

Number of animals 




















Phenotypic characterisation

The reproductive performance of the Namaqua Afrikaner ewe flock from 1982 to 2011 is presented in Table 5.


Table 5. Body weight (± s.e.) and reproductive performance (CV%) of Namaqua Afrikaner ewes since 1982 in the Carnarvon flock



Body weight before mating (kg)

50.2 ± 0.6

Body weight after weaning (kg)

50.2 ± 0.9


Total weight of lamb weaned / year (kg)

33.7  (42.7)

Number of lambs born / year

1.38 (40.7)

Number of lambs weaned / year

1.24 (44.5)

Number of lifetime lambing opportunities


Total weight of lamb weaned / lifetime (kg)

110.6 (38.1)

Number of lambs born / lifetime

4.45 (36.1)

Number of lambs weaned / lifetime

4.01 (39.1)


Least-squares means for body weight of ram and ewe lambs from birth until 12-months of age from 1993 to 2010 are presented in Table 6. From Table 6 it is evident that ram lambs were heavier than ewe lambs at birth and remained heavier throughout their lives.


Table 6. Body weight of ram and ewe lambs (± s.e.) since 1993 in the Carnarvon Namaqua Afrikaner flock




Birth weight (kg)

4.1 ± 0.1

3.9 ± 0.1

42-day body weight (kg)

13.0 ± 0.3

12.0 ± 0.4

120-day weaning weight (kg)

25.1 ± 0.6

22.7 ± 0.7

5-month body weight (kg)

30.0 ± 0.7

26.7 ± 0.8

6-month body weight (kg)

36.9 ± 0.7

31.9 ± 0.7

7-month body weight (kg)

43.1 ± 0.7

36.5 ± 0.7

8-month body weight (kg)

41.7 ± 0.7

36.1 ± 0.8

9-month body weight (kg)

43.0 ± 0.7

38.0 ± 0.8

10-month body weight (kg)

44.3 ± 0.8

38.2 ± 0.8

11-month body weight (kg)

45.2 ± 0.8

40.9 ± 0.8

12-month body weight (kg)

49.1 ± 0.7

43.3 ± 0.8

 All values differed significantly (P<0.001) between sexes



The description of the morphometric traits recorded on the 2007 to 2010-born lambs is presented in Table 7.


Table 7. Morphometric traits (± s.e.) at 14 months of age of the 2007- to 2010-born Namaqua Afrikaner ewe and ram lambs in the Carnarvon flock




Body length (cm)

70.5a ± 0.5

67.9a ± 0.5

Wither height (cm)

73.0a ± 3.3

67.8a ± 3.3

Heart girth circumference (cm)

101.3a ± 0.9

95.1a ± 1.0

Cannon bone length (cm)

17.3a ± 0.3

17.1a ± 0.3

Tail circumference at base (cm)

47.1a ± 0.6

35.8a ± 0.6

Tail length (cm)

41.5a ± 0.6

39.6a ± 0.6

Testis circumference (cm)

32.2 ± 0.4


Teat length left (mm)


20.4 ± 0.7

Teat length right (mm)


19.1 ± 0.7


Percentage of animals

Tail twist: To Left



Tail twist: To Right



Tail no twist - straight



Colour of the head: Black



Colour of the head: Brown



Colour on body: Yes



Colour on body: No









a Values with the same superscripts differ significantly (P<0.05) between sexes


The morphometric traits indicated that rams had larger body dimensions than ewes, as is evident from the higher body length, wither height, heart girth circumference and cannon bone length. Rams also had longer and thicker tails than ewes (P<0.001). In the majority of the animals, the tails twisted to the left, while more animals had black heads than brown heads. All males were horned and the majority of females also had horns (84%). The majority of the animals had no colour on the body. This could be expected, as it was one of the criteria on which surplus young animals were culled.



Genetic diversity is defined as the variety of alleles and genotypes present in a population and this is reflected in morphological, physiological and behavioural differences between individuals and populations. In the present study, genetic diversity was measured in terms of various statistical parameters. The mean number of alleles across the populations was relatively low (5.0). This value was similar to the value reported by Buduram (2004) on a study with SA indigenous sheep populations, which varied from 4.3 for Blinkhaar Ronderib Afrikaner to 4.9 for Namaqua Afrikaner sheep.


The level of genetic diversity obtained in this study was low to moderate. CES (55%) had the highest level of genetic diversity when compared to KES (48%) and WGK (46%). The genetic variation obtained in the present study was similar to the values reported by Buduram (2004) for Namaqua Afrikaner (49%) and Blinkhaar Ronderib Afrikaner sheep (52%), but lower than the values obtained for Pedi (67%), Damara (58%), Zulu (65%), Swazi (69%) and SA Mutton Merino (70%) sheep.  The present genetic diversity estimates were also lower than the values obtained for Muzzafarnagri indigenous sheep (69%) by Arora & Bhatia (2004), Red Madras sheep (78%) by Selvam et al. (2009), Red Maasia-Mutara (61%) and Maasia-Olmagogo sheep (58%) by Muigai et al. (2009) and Ganjam sheep (68%) by Arora et al. (2010).


Low to moderate levels of genetic diversity was expected in the current populations as they have been closed for more than fifteen years. Reed (2007) mentioned that the loss of genetic diversity is of particular concern, especially with regard to the conservation of endangered species of animals because it can compromise the future ability of the animals to survive in extreme and changing environmental conditions. Introducing outside rams into these conserved Namaqua populations may increase the genetic variation. However, as there are not many purebred Namaqua Afrikaner flocks left, it is risky to introduce rams from flocks with an unknown breeding history. Breeding of the purebred Namaqua Afrikaner sheep with rams of uncertain descendency should be avoided at all cost to prevent further dilution of the breed that could contribute to its extinction.


In this study, 80% of the loci were in HWE. These results reflected that the Namaqua Afrikaner sheep populations under investigation were not subjected to any evolutionary forces such as selection, migration, mutation and genetic drift and hence were able to maintain their relative allele frequencies. This is true because no selection and migration of any sort have taken place in these populations for the past fifteen years. The number of loci in HWE in the present study was similar to the number obtained by Martinez et al. (2004) for Blanca goats.


The overall inbreeding coefficient (FIS) across all populations was low positive, which indicate a low level of inbreeding. Some level of inbreeding can be expected to occur in populations that are closed. These results reflected the good management practice that the Namaqua Afrikaner populations have been subjected to with the use of cyclic mating. Dixit et al. (2010) and Dalvit et al. (2008) reported a high level of inbreeding in the indigenous Southern India goats and endangered Alpine sheep breed respectively.  


Using both AMOVA analysis and FST estimate it was shown that the genetic differentiation among the three populations was 10.5%, indicating that genetic variation was mainly present within populations. FST values up to 0.05 indicate negligible genetic differentiation, whereas >0.25 means large genetic differentiation amongst populations (Hartl, 1980). The present study reported a moderate level of differentiation among the populations. These values were higher than the values reported by Zhong et al. (2010) in ten Chinese indigenous sheep breeds (4.8%) and Nahas et al. (2008) in different sheep breeds (3.7%), but similar to the values reported by Dixit et al. (2010) among Southern India indigenous goat breeds (14%).  The fact that no selection for or against any specific production trait has been carried out in the flocks, might have contributed to the genetic variation within the flocks in the current populations.


The unbiased genetic distance estimates revealed a close relationship between CES and WGK. The close relationship between CES and WGK may be explained by the fact that the owner of WGK bought some of his animals from CES in 1994 and 1995. It was interesting to discover that the KES population was clearly distinct from the CES population, despite the fact that the animals in KES originated from CES 27 years previously.


The description of the population structure is important for the proper management of the population (Dalvit et al., 2008). The results from the assignment test suggested a true genetic structure with significant differentiation among all three Namaqua Afrikaner populations. The results supported the genetic distance estimates by confirming the differentiation of three clusters with relationships between the CES and WGK populations. Nearly 86% of the CES population was assigned in Cluster 1, whereas nearly 89% of the KES animals were assigned in Cluster 2. The WGK animals were divided between Cluster 3 and Cluster 1. Approximately 81% of the WGK population was assigned to Cluster 3 but 15% of this population was assigned in the same cluster as the CES population (Cluster 1), indicating a possible gene flow between the two populations and therefore a higher level of admixture. 


The reproductive performance level of the Namaqua Afrikaner sheep revealed that this breed compares favourably with other South African sheep breeds. The total weight of lambs weaned, number of lifetime lambs born and weaned and body weight and growth rate of lambs recorded for the Namaqua Afrikaner ewes compared favourably to the values obtained by van Wyk et al. (1993) for Dormer sheep, Snyman et al. (1995) and Snyman & Herselman (2005) for Afrino sheep, Snyman et al. (1997) and Olivier et al. (2002) for Merino sheep, Cloete et al. (2000) and Snyman & Olivier (2002) for Dorper sheep, as well as by Olivier et al. (2010) for Dohne Merino sheep.



This study combined phenotypic and genetic information on the Namaqua Afrikaner sheep breed in South Africa and it is hoped that the information obtained will contribute in developing proper strategies for the long-term genetic management, mating strategies, utilisation and conservation of this endangered, indigenous sheep breed.


Genetic diversity in the three flocks studied was low to moderate, which could be a cause for concern. Any immediate plans for the improvement of genetic diversity should, however, be approached with caution, as indiscriminate breeding of the existing purebred Namaqua flocks with rams from outside flocks with unknown history, is contraindicated. It is therefore recommended that the three flocks be kept intact as they are.


Since the start of this study, another two Namaqua Afrikaner flocks have been included in the conservation program under the “Maintenance of live herds” project. These flocks are also available for the cryopreservation and blood and DNA bank projects. One of the flocks is kept near Calvinia in the Northern Cape Province, and the other at Barkley-East in the Eastern Cape Province. The Barkley-East flock has genetic ties with the CES flock, as the owner bought some animals from the CES flock during 1994 to 1996, and again in 2010. It is recommended that the same set of microsatellites used in this study, be used to genetically characterise animals from these two new flocks, in order to determine their genetic diversity and distance from the three flocks already characterised. If the animals in these flocks are sufficiently diverse from the flocks used in this study, the possibility of introducing rams from these flocks into the CES or KES flocks could be considered in future.


With regard to the inbreeding estimates, the average FIS was low positive, indicating a low level of inbreeding across the three populations. Therefore it is suggested that the current system of cyclic mating should be continued. The inbreeding level should be evaluated every five years to determine any unfavourable change in inbreeding level early, so that appropriate steps could be taken to prevent further increases in inbreeding.


Results revealed that most of the genetic variation occurred within populations, rather than between populations. The lack of selection for or against any specific production traits, probably contributed to the genetic variation within the flocks. It is therefore proposed that the current system of random selection of replacement ewes and sires, where only animals with physical deformities and which do not conform to the general breed appearance are culled, should be continued.


The results on the three inferred clusters, which corresponds with the three flocks, as well as the genetic distance estimates between the flocks, indicate that all three the flocks should be maintained as part of the GADI-Biobank.


As far as the ex situ conservation of the breed is concerned, 307 embryos obtained from Namaqua Afrikaner ewes of the Carnarvon Experimental Station have already been cryopreserved and are kept in the GADI-Biobank. Keeping in mind the genetic distance between the CES and KES flocks, it is recommended that embryos from the KES flock should also be cryopreserved.


The conservation of farm animal genetic resource through utilisation is one way of ensuring that an indigenous breed is successfully conserved. The success of the indigenous Nguni cattle is an excellent example. This cattle breed has a breeders’ association and are being farmed with commercially. The phenotypic production and reproduction performance of the Namaqua Afrikaner sheep indicated that their growth rate and reproductive performance compared well with other commercial sheep breeds. By combining the conservation effort with a commercial application, the future existence of the breed could be ensured. As part of the conservation effort, surplus animals of the CES and KES flocks are made available to farmers interested in conserving this breed. The establishment of more flocks, comprising rams and ewes from both the CES and KES flocks, could contribute to increased genetic diversity in the breed, without endangering the existing purebred flocks.



Arora, R. & Bhatia, S., 2004. Genetic structure of Muzzafarnagri sheep based on microsatellite analysis. Small Rumin. Res. 54, 227-230.

Arora, R., Bhatia, S. & Jain A., 2010. Morphological and genetic characterisation of Ganjam sheep. Anim. Gen. Res. 46, 1-9.

Buduram, P., 2004. Genetic characterisation of Southern African sheep breeds using molecular markers. MSc-Thesis, Department of Animal, Wildlife and Grassland Sciences, University of the Free State.

Cloete, S.W.P., Snyman, M.A. & Herselman, M.J., 2000. Productive performance of Dorper sheep. Small Rumin. Res. 36, 119-135.

Dalvit, C., Sacca, E., Cassandro, M., Gervaso, M., Pastore, E. & Piasentier, E., 2008. Genetic diversity and variability in Alpine sheep breeds. Small Rumin. Res. 80, 45-51.

Dixit, S.P., Verma, N.K., Aggarwal, R.A.K., Vyas, M.K., Rana, J., Sharma, A., Tyagi, P., Arya, P. & Ulmek, B.R., 2010. Genetic diversity and relationship among southern Indian goat breeds based on microsatellite markers. Small Rumin. Res. 91, 153-159.

Hartl, D., 1980. Principles of population Genetics. Sinauer Associates Inc, Sunderland Massachussets, USA.

Kunene, N., Bezuidenhout, C.C. & Nsahli, I.V., 2009. Genetic and phenotypic diversity in Zulu sheep populations; implication for exploitation and conservation. Small Rumin. Res. 84, 100-107.

Littell, R.C., Freud, R.J. & Spector, P.C., 1991. SAS-system for linear models, 3rd  Edition., Cary NC : SAS Institute Inc. pp. 137-198.

Martinez, A.M., Carrera, M.P., Acosta, J.M., Rodriguez-Gallardo, P.P., Cabello, A., Camacho, E. & Delgado, J.V., 2004. Genetic characterisation of the Blanca goat based on microsatellite markers. S. Afr. J. Anim. Sci. 34(1), 17-19.

Muigai, A.W.T., Okey, A.M., Kwallah, A.K., Mburu, D. & Hanotte, O., 2009. Characterisation of Sheep populations of Kenya using microsatellite markers: Implications for conservation and management of indigenous sheep populations. S. Afr. J. Anim. Sci. 39(1), 93-96.

Nahas, S.M.E., Hassan, A.A., Mossallam, A.A., Mahfouz, E.R., Bibars, M.A., Oraby, H.S. & de Hondt, H.A., 2008. Analysis of genetic variation in different sheep breeds using microsatellite markers. Afr. J. Biotech. 7(8), 1060-1068.

Olivier, W.J., Herselman, M.J. & van Heerden, M., 2010 Production norms of the Grootfontein Dohne Merino flock. Grootfontein Agric 10(1), 55-66.

Olivier, W.J., Olivier, J.J., Snyman, M.A., Pretorius, A.P. & van Heerden, M., 2002. Production and reproduction norms of fine woolled Merino sheep on natural pastures in the Karoo. Grootfontein Agric 5(1), 29-31.

Park, S., 2001. Microsatellite Toolkit.

Pritchard, J.K., Stephens, M. & Donnely, P., 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.

Reed, D.H., 2007. Natural selection and genetic diversity. J. Heredity 99, 1-2. 

SAS Institute Inc., 2009. SAS OnlineDoc® 9.2. Cary, NC, SAS Institute Inc.

Scherf, B., Rischkowsky, B., Pilling, D. & Hoffmann, I., 2006. The state of the world’s animal genetic resources. 8th World Congress of Genetics Applied to Livestock Production, 13-18 Aug 2006, Belo Horizonte, MG, Brazil.

Selvam, R., Rahumathulla, P.S., Sivaselvam, S.N., Karthickeyan, S.M.K. & Rajendran, R., 2009. Molecular Genetic Characterisation of Madras Red sheep in Tamil Nadu, India using microsatellite markers. Livest. Res. Rural Dev. 21(4), 1-5.

Shrestha, J.N.B., 2005. Review article. Conserving domestic animal diversity among composite  populations. Small Rumin. Res. 56, 3-20.

Snyman, M.A., 2011. Establishment of the South African biological reserve for small stock research and conservation at Grootfontein. Grootfontein Agric 11(1), 1-9.

Snyman, M.A., Erasmus, G.J., Van Wyk, J.B. & Olivier, J.J., 1995. Non-genetic factors influencing growth and fleece traits in Afrino sheep. S. Afr. J. Anim. Sci. 25(3), 70-74.

Snyman, M.A. & Herselman, M.J., 2005. Comparison of productive and reproductive efficiency of Afrino, Dorper and Merino sheep in the False Upper Karoo. S. Afr. J. Anim. Sci. 35(2), 98-108.

Snyman, M.A. & Olivier, W.J., 2002. Productive performance of hair and wool type Dorper sheep under extensive conditions. Small Rumin. Res. 45(1), 17-23.

Snyman, M.A., Olivier, J.J. & Cloete J.A.N., 1993. Productive and reproductive performance of Namaqua Afrikaner sheep. Karoo Agric 5(2), 21-24.

Snyman, M.A., Olivier, J.J., Erasmus, G.J. & Van Wyk, J.B., 1997. Genetic parameter estimates for total weight of lamb weaned in Afrino and Merino sheep.  Livest. Prod. Sci. 48(2), 111-116.

Van Wyk, J.B., Erasmus, G.J. & Konstantinov, K.V., 1993. Non-genetic factors influencing early growth traits in the Elsenburg Dormer sheep stud. S. Afr. J. Anim. Sci. 23(3/4), 67-71.

Visser, C., Hefer, C.A., van Marle-Köster, E. & Kotze, A., 2004. Genetic variation of three commercial and three indigenous goat populations in South Africa. S. Afr. J. Anim. Sci. 34(5), 24-27.

Visser, C. & van Marle-Köster, E., 2009. Genetic variation of the reference population for quantitative trait loci research in South African Angora goats. Anim. Gen. Res. 45, 113-119.

Zhong, T., Han, J.L., Guo, J., Zhao, Q.J., Fu, B.L. He, X.H. , Jeon, J.T., Guan, W.J. & Ma, Y.H., 2010. Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers. Small Rumin. Res. 90, 88-94.




Grootfontein Agric 13 (1)