J. Anim Sci. 2006. 84:2601-2608. doi:10.2527/jas.2005-641
© 2006 American Society of Animal Science
Comparison of Vietnamese and European pig breeds using microsatellites1
N. T. D. Thuy*,
,
E. Melchinger-Wild*,
A. W. Kuss*,2,
N. V. Cuong
,
H. Bartenschlager* and
H. Geldermann*,3
* University of Hohenheim, Department of Animal Breeding and Biotechnology, Garbenstr. 17, D-70599 Stuttgart, Germany; and
and
Institute of Biotechnology (IBT), National Center for Natural Science & Technology, 18-Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
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Abstract
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This study characterized autochthonous pig breeds of Vietnam and compared them with breeds from other regions. A total of 343 animals were considered from 5 indigenous pig breeds of Vietnam (Muong Khuong, Co, Meo, Tap Na, and Mong Cai), 2 exotic breeds kept in Vietnam (Landrace and Yorkshire), 3 European commercial breeds (German Land-race, Piétrain, and Large White), the Chinese breed Meishan, and the European Wild Boar. Each individual was genotyped for 20 selected polymorphic microsatellite loci. The Vietnamese autochthonous breeds showed higher degrees of polymorphism, allelic diversity, and heterozygosity than the other pig breeds. Also, large genetic diversity was observed across the area of distribution, with village-specific subpopulations, which led to significant inbreeding coefficients. As expected, genetic distances showed large differences among European-based, Chinese, and Vietnamese indigenous breeds and reflected the geographical distribution of breeds. In comparison with the European breeds, the Vietnamese indigenous pig breeds harbored a considerable amount of genetic diversity and, therefore, will be of significance for livestock bioconservation.
Key Words: genetic distance genetic diversity microsatellite pig breed
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INTRODUCTION
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Breeding on economic traits leads to genetic drift and often even to extinction of breeds. Such a loss of genetic diversity in farm animals can reduce the genetic gain for production traits, viability, and fertility. According to the inventory of the Food and Agriculture Organization of the United Nations (FAO, 2000
) the Asian (37%) and European pig populations (46%) together share more than 80% of the total number of pig breeds worldwide. However, whereas in Asia about 11 (6%) of the 184 existing breeds are endangered, this ratio has reached almost 28% (63 of 228) in Europe (FAO, 2000
). Progress in animal production is now leading to a small number of economically promising breeds, whereas the indigenous breeds are being extinguished more rapidly.
A number of studies have already analyzed the genetic diversity of European (Laval et al., 2000
; Fabuel et al., 2004
) or Chinese pig breeds (Li et al., 2000
; Zhang et al., 2003
; Fang et al., 2005
) or both (Paszek et al., 1998
; Giuffra et al., 2000
), but only a few reports concerning characteristics and performance of Vietnamese local breeds are available (e.g., Molenat and Tran, 1991
). Hongo et al. (2002)
described mitochondrial sequence variation of Vietnamese pigs and their relationships to Asian domestic animals and the Japanese Wild Boar. However, microsatellite markers provide a powerful tool to analyze genetic diversity within and between breeds and have been used widely to investigate domestic animals.
This study is the first to apply a panel of 20 microsatellite loci for the genetic characterization of several autochthonous Vietnamese pig breeds in comparison with European breeds, a Chinese breed, and the European Wild Boar (Sus scrofa scrofa). The aim was to provide data for bioconservation activities concerning pig breeds.
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MATERIALS AND METHODS
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The procedure involving animals was the blood collection from vena jugularis; it was approved according to the local animal care standards and accepted by the local animal care officials.
Samples and DNA Isolation
As shown in Table 1
, samples were from several pig breeds in Vietnam and Germany. Muong Khuong, Co, Meo, Tap Na, and Mong Cai are autochthonous North Vietnam breeds kept in small traditional farms and are shown in Figure 1
. All Vietnamese breeds show high prolificacy, adaptation to poor-quality feed, tropical climate and disease resistance, with a high proportion of fat in the carcass. Muong Khuong boars are about 150 kg and sows about 130 kg of BW. The animals are black with mostly white spots at head, tail, and feet. The small-sized Co (boars are 30 to 40 kg, sows 30 to 35 kg of BW) has a black color. The breed Meo is black with white spots; boars are about 60 kg and sows about 50 kg of BW. Tap Na is a small-sized breed (boars are about 65 kg, sows about 50 kg of BW); the color varies between entirely black and black with white spots at the head, tail, feet, and belly. Mong Cai is the major local breed in North Vietnam, is medium-sized (boars are 100 to 110 kg and sows 90 to 100 kg of BW) and shows high fertility, with an average litter size at birth of approximately 12. The head of Mong Cai is black together with a black saddle over the middle of a concave back; shoulder, abdomen, and legs are white.

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Figure 1. Typical individuals of the autochthonous Vietnamese pig breeds: (a) Muong Khuong, (b) Co, (c) Meo, (d) Tap Na, and (e) Mong Cai.
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Samples from Mong Cai as well as the introduced Vietnamese Landrace and Yorkshire were collected at a breeding station in Hanoi, Vietnam. Blood from the other Vietnamese breeds was collected in the different farms. For comparison, samples from individuals of the European Wild Boar (Sus scrofa scrofa) were included from different regions across Germany. Pigs of the Chinese breed Meishan were from a colony kept at an experimental station of the University of Hohenheim, Germany. Large White, German Landrace, and Piétrain were from herd book populations in Germany (Baden Württemberg). The DNA from blood, muscle tissue, and sperm was isolated according to standard protocols.
Microsatellites, PCR Conditions, and Fragment Length Analysis
As listed in Table 2
, the 20 microsatellite loci used in this study are all located on different autosomes. A 25-µL PCR reaction mix contained 0.4 mM of each nucleotide, 100 ng of template DNA, and 20 pmol of each primer, one of them being fluorescein labeled. Magnesium chloride concentrations ranged from 1.9 to 3.0 mM, and annealing temperatures were between 54 and 60°C. Denaturation at 92°C for 2 min and 15 s was followed by 32 cycles with annealing times between 20 and 40 s and extension (72°C) times between 35 and 45 s. The final cycle was concluded by an extension interval of 5 min. Following standard protocols, fragment length analysis was performed on an Automated Laser Fluorescent Sequencer (ALF, Pharmacia, Freiburg, Germany) using 5% Hydrolink gels, prepared by using Hydrolink Long Ranger Gel Solution (Serva, Heidelberg, Germany). Fragment length determination was based on internal length markers, using the ALF win/Instrument Control and the Allele Links software (Pharmacia, Freiburg, Germany).
Statistical Analyses
The breeds were considered separately as well as arranged in groups (Table 3
). Mong Cai was always kept separate because it was the only autochthonous breed that was commercially used and kept in a station.
The BIOSYS-2 software package [based on BIOSYS-1 by Swofford and Selander (1989)
, modified by Black (1997)
] was used for analysis of Hardy-Weinberg equilibrium, F-statistics (Wright, 1965
, 1978
) according to Weir and Cockerham (1984)
, and Neis standard genetic distances (Nei, 1972
). Genetic distances were used for the construction of the unweighted pair-group method using arithmetic averages dendrograms (Sneath and Sokal, 1973
). As suggested by the FAO guidelines (FAO, 2004
), SE of genetic distances were calculated. Confidence intervals for FIS values were determined with bootstrapping by using the GENETIX software (Belkhir et al., 2002
). The effective number of alleles and polymorphism information content were determined according to Kimura and Crow (1964)
and Botstein et al. (1980)
, respectively. Genetic distances were submitted to 1,000 bootstrap resamplings, applying the BOOT-DIST routine of BIOSYS-2 and the NEIGHBOR and CONSENSE routines of the PHYLIP software (version 3.57; Felsenstein, 1995
).
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RESULTS AND DISCUSSION
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Allelic Diversity
As shown in Table 2
, the number of alleles varied widely between loci, with as few as 5 at locus SW1041 and as many as 19 at loci SW1067, SW1083, S0385, and SW2519. Comparing these data with marker information available at www.marc.usda.gov/genome, we revealed 78 new alleles for the 20 loci in this study. At the locus SW1041, the whole range of alleles occurred in the Vietnamese breeds Co, Meo, and Tap Na. Locus SW787 showed the complete allele range only in the breed Muong Khuong, whereas at locus S0215 only 1 allele (151 bp) was found in the Vietnamese Landrace and Yorkshire. Breed-specific alleles occurred at all loci except for SW489, SW2410, SW1041, SW957, and SW787, yet in most cases with low frequencies (<0.06). For 8 loci, specific alleles were found in the group of autochthonous breeds, especially in the breed Muong Khuong. In 2 cases, namely allele 142 bp at locus SW2427 in Wild Boar and 143 bp at SW1067 in Meishan, the specific alleles were those with the highest frequency for the respective locus and group. Moreover, the Vietnamese breed Muong Khuong had a specific allele (144 bp) with the second highest frequency (0.22) at locus SW780. The alleles 142 bp at locus SW2427, 143 bp at SW1067, and 144 bp at SW780 might therefore be markers for the considered breeds, whereas the other breed specific alleles were too rare for such a classification. Further genotyping of animals will help to verify which marker alleles do not occur in other breeds, and those that occur only at low frequencies.
As presented in Table 3
, the mean number of genotype observations per locus and breed was equal to or slightly lower than the number of animals included (compare Table 1
). In Vietnamese Landrace and European Wild Boar there was 1 locus per breed with 3 missing genotype observations, so we successfully determined 6,833 (99.6%) out of 6,860 genotypes. The numbers of polymorphic loci were between 18 and 20 per breed. The mean number of alleles per breed varied between 3.9 (Meishan) and 9.3 (Meo). Except for Mong Cai, values for indigenous Vietnamese breeds were higher (8.1 to 9.3) than those for the breeds with European background (4.3 to 4.8). High mean numbers of alleles were found for the Vietnamese breeds, which were sampled in small holder husbandries in their areas of origin. Distinctly lower values (3.9 to 5.4) occurred in breeds (Mong Cai, Landrace Vietnam, York-shire Vietnam, Landrace Germany, Piétrain, Large White, Meishan; Table 3
), which are kept in stations or included in commercial breeding programs. In a study of Iberian pig breeds, also using microsatellites, Martinez et al. (2000)
found average numbers of alleles also between 3.4 and 5.8. Likewise, corresponding values have been observed in 11 European pig breeds, with averages between 3.7 and 5.7 (Laval et al., 2000
). Similar numbers of alleles (3.7 to 5.8) were found by Fan et al. (2002)
for 3 Chinese indigenous breeds. Lemus-Flores et al. (2001)
reported for Mexican hairless pigs and commercial breeds mean allele numbers of 6.8 and 6.7, respectively, thus ranging between the Vietnamese and European breeds.
Interestingly, the tested European Wild Boar individuals had a low mean number of alleles (5.3). This indicates that although samples were taken by numerous hunters from 6 areas that are between about 100 and 800 km apart, the animals of the wild species were from a relatively homogeneous population. As can be seen in Table 3
as well, the group of Vietnamese breeds showed an approximately 2-fold higher mean number of alleles (12.4) compared with the breeds of European origin (5.6 and 6.3). These findings correspond with the results of Li et al. (2000)
who observed distinctly higher values in 4 indigenous Chinese pig breeds as compared with 1 Australian breed.
The low allelic diversity observed for Mong Cai and Meishan can be explained by founder effects during the onset of each colony. Moreover, these animals are kept under controlled mating in an experimental station and no gene flow between different stations is allowed. On the other hand, breeds showing the largest range of alleles per locus were all of Vietnamese origin and maintained in their original environments (Table 3
). Like in wild populations, the high allelic diversity of the Vietnamese indigenous breeds is probably due to less controlled mating. When gathering the Vietnamese indigenous breeds into a group we observed the whole range of allele lengths for 9 of the 20 loci. In comparison, the breeds of European descent, combined in groups, did not show the complete set of alleles for any of the 20 loci.
Thus, the polymorphic loci allow an evaluation of the genetic variability and differences between breeds. For these purposes population specific alleles are not required, but profiles of allele frequencies. As well documented, the allele frequencies of a sufficient number of loci provide criteria for an environmental independent identification of a breed and its comparison with other breeds.
Genotypic Diversity
The observed heterozygosity (Table 3
) varied between 0.48 (Wild Boar) and 0.74 (Meo), which is within the range reported by Zhang et al. (2003)
from a study of 56 Chinese indigenous breeds and 3 introduced pig breeds (Duroc, Landrace, and Large White). However, for the Vietnamese autochthonous breeds, except for Mong Cai, values were between 0.69 and 0.74, whereas breeds with European background showed heterozygosity from 0.50 to 0.60. Similar values have been reported for Belgian pigs, where the observed heterozygosity ranged from 0.54 to 0.63 (Van Zeveren et al., 1995
) as well as for 11 European pig breeds, where it was found to be between 0.35 and 0.60 (Laval et al., 2000
). In a study on Mexican hairless pigs, heterozygosity ranged from 0.28 to 0.66 (Lemus-Flores et al., 2001
). Expected heterozygosity was higher in the Vietnamese indigenous breeds than in the other breeds and the European Wild Boar.
The number of loci with deviations (P < 0.05) from Hardy-Weinberg equilibrium ranged from 0 to 3 in the individual breeds and from 2 to 4 in grouped breeds (Table 3
). This is in the randomly expected range because altogether 234 locus x breed combinations were tested, but only 11 were different (P < 0.05) from Hardy-Weinberg equilibrium.
Inbreeding coefficients (FIS) were higher in the Vietnamese breeds Muong Khuong, Co, and Tap Na than in the other breeds (Table 3
). Station kept and pedigree breeds had the lowest FIS values. The largest negative FIS values were observed for Meishan, Large White, and German Landrace. Inbreeding was detected (P < 0.05) for Vietnamese breeds in their original habitats. This indicated that the local breeds form village-specific subpopulations with inbreeding, and according to Wahlund (1928)
, positive FIS values were obtained because individuals from different subpopulations were pooled for analysis. In Vietnam we included only a few animals per village and from a number of villages.
The Wrights coancestry coefficient FST of the Vietnamese breeds showed an intermediate FST (0.050), whereas it was highest (0.138) in the European commercial breeds and lowest (0.019) in the Vietnamese exotic breeds. These values are all below 0.15 and therefore describe moderate differentiation between populations (Wright, 1978
; Hartl and Clark, 1997
). The group of European commercial breeds had the highest FST, which could to some degree be the result of selection (Neigel, 2002
). The Vietnamese exotic breeds on the other hand are most similar, which is in agreement with studies of Yorkshire and Landrace from other regions (Li and Enfield, 1989
; Paszek et al., 1998
) and can be explained by adaptation.
Genetic Distances and Phylogenetic Tree
The genetic distances were closest between the 2 Vietnamese exotic breeds (0.07), between Meo and Co (0.11), as well as between German and Vietnamese Landrace (0.13). The largest distance was found between European Wild Boar and Meishan (2.41). Regarding the grouped breeds (Table 4
), the 2 groups of European origin (exotic breeds and European breeds) were most related (0.07) and the large distances occurred between Meishan and exotic breeds or European breeds (1.93 and 1.92, respectively). Distances between the Vietnamese breeds and European-based breeds were in most cases smaller than the distances between the Vietnamese breeds and the European Wild Boar. This illustrates the introgression of Asian domestic pigs into European breeds in the late 18th and early 19th centuries (Jones, 1998
). Giuffra et al. (2000)
found genetic evidence for introgression during that period, when investigating mitochondrial DNA variants in Asian and European pigs.
The dendrogram (Figure 2
, panel a) shows that the 12 breeds formed 2 branches, one composed of all the European breeds as well as European Wild Boar and the other including the Asian breeds. This is in agreement with the results of a study using mitochondrial DNA polymorphisms from a variety of Asian and European breeds as well as the Wild Boar (Kim et al., 2002
). Interestingly, in our study the inclusion of Meishan into the branch of the Vietnamese breeds had only 50% bootstrap support. This reflects that in half of the repeats, Meishan was forming a separate branch from Vietnamese and European pigs. This result was even more pronounced in our analysis of genetic groups (Figure 2
, panel b). However, as mentioned above, the Meishan samples included in this study were not collected in China but from a colony kept in Europe, so further investigation needs the inclusion of Meishan pigs directly from China.
With a bootstrapping affirmation of 59%, Mong Cai was clustered together with Co and Meo. All other clusters were strongly confirmed with bootstrap values of more than 65%. The results thus establish a clear genetic topology not only among European-based breeds but also among the Vietnamese indigenous breeds for which genetic distances are in agreement with their geographical distribution. For example, the closely related Co and Meo originate from regions only about 150 km apart in the Nghe An province, whereas Muong Khuong and Tap Na, which also form a cluster, are both from the northern part of Vietnam.
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IMPLICATIONS
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This study is the first to apply a panel of microsatellite markers for the genetic characterization of autochthonous Vietnamese pig breeds. The markers used were selected according to their genome wide spanning, polymorphism information content values, and precise genotyping. It was possible to describe genetic differentiation and establish a clear cut genetic structuring among the studied populations, including European commercial breeds, the European Wild Boar and Meishan. The results also yielded evidence that the tested Tap Na breed, which is so far not listed as such by the Food and Agriculture Organization of the United Nations, can be considered to be an independent breed. Furthermore, we observed loci with specific alleles for European Wild Boar, Meishan, and Muong Khuong. Thus our findings demonstrate that Vietnamese indigenous breeds harbor an abundant reservoir of genetic diversity and can support livestock bioconservation activities.
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Footnotes
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1 This study was supported by the Deutsche Forschungsge-meinschaft (DFG) and the German Federal Ministry of Education and Research (BMBF). 
2 Current address: Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany. 
3 Corresponding author: hermann.geldermann{at}t-online.de
Received for publication November 4, 2005.
Accepted for publication May 22, 2006.
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