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 †Institute of Biotechnology (IBT),
National Center for Natural Science & Technology, 18-Hoang Quoc Viet Rd, Cau Giay, Hanoi, Vietnam
ABSTRACT: This study characterized autochtho-
nous 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 York-
shire), 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 microsatel-
lite loci. The Vietnamese autochthonous breeds showed
higher degrees of polymorphism, allelic diversity, and
Key words: genetic distance, genetic diversity, microsatellite, pig breed
©2006 American Society of Animal Science. All rights reserved.
INTRODUCTION
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 Organiza-
tion 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 world-
wide. 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 indige-
nous breeds are being extinguished more rapidly.
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@t-online.de
Received November 4, 2005.
Accepted May 22, 2006.
2601
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heterozygosity than the other pig breeds. Also, large
genetic diversity was observed across the area of distri-
bution, with village-specific subpopulations, which led
to significant inbreeding coefficients. As expected, ge-
netic distances showed large differences among Euro-
pean-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 consider-
able amount of genetic diversity and, therefore, will be
of significance for livestock bioconservation.
J. Anim. Sci. 2006. 84:2601–2608
doi:10.2527/jas.2005-641
A number of studies have already analyzed the ge-
netic 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 con-
cerning characteristics and performance of Vietnamese
local breeds are available (e.g., Molenat and Tran,
1991). Hongo et al. (2002) described mitochondrial se-
quence variation of Vietnamese pigs and their relation-
ships to Asian domestic animals and the Japanese Wild
Boar. However, microsatellite markers provide a pow-
erful tool to analyze genetic diversity within and be-
tween breeds and have been used widely to investigate
domestic animals.
This study is the first to apply a panel of 20 microsa-
tellite loci for the genetic characterization of several
autochthonous Vietnamese pig breeds in comparison
with European breeds, a Chinese breed, and the Euro-
pean Wild Boar (Sus scrofa scrofa). The aim was to
provide data for bioconservation activities concerning
pig breeds.
MATERIALS AND METHODS
The procedure involving animals was the blood collec-
tion from vena jugularis; it was approved according to
 2602 Thuy et al.
Table 1. Breeds and samples
Country Breed/Subspecies1 Abbreviation
Vietnam Muong Khuong MK
Co CO
Meo ME
Tap Na TN
Mong Cai MC
Landrace LV
Yorkshire YV
Germany Landrace LG
Piétrain PI
Large White LW
European Wild Boar WB
Meishan MS
1
Pig breeds, except for Tap Na, are described in Internet databases (e.g., www.ansi.okstate.edu/breeds/
swine/ and http://dad.fao.org/en/).
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 cli-
mate 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 con-
cave back; shoulder, abdomen, and legs are white.
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 Chi-
nese breed Meishan were from a colony kept at an ex-
perimental station of the University of Hohenheim,
Germany. Large White, German Landrace, and Pié-
train were from herd book populations in Germany (Ba-
den Württemberg). The DNA from blood, muscle tissue,
and sperm was isolated according to standard pro-
tocols.
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No. of
animals Sample
32 Blood
31 Blood
32 Blood
25 Blood
32 Blood
22 Blood
17 Blood
32 Blood, sperm
32 Blood, sperm
30 Blood, sperm
32 Muscle tissue, blood
26 Blood
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-␮L 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, frag-
ment length analysis was performed on an Automated
Laser Fluorescent Sequencer (ALF, Pharmacia, Frei-
burg, Germany) using 5% Hydrolink gels, prepared by
using Hydrolink Long Ranger Gel Solution (Serva, Hei-
delberg, 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 equi-
librium, F-statistics (Wright, 1965, 1978) according to
Weir and Cockerham (1984), and Nei’s 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. Confi-
dence intervals for FIS values were determined with
 Comparing Vietnamese and European pig breeds
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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2603
bootstrapping by using the GENETIX software (Belkhir
et al., 2002). The effective number of alleles and poly-
morphism information content were determined ac-
cording 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).
RESULTS AND DISCUSSION
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 infor-
mation available at www.marc.usda.gov/genome, we re-
vealed 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 Meis-
han, 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 classifica-
tion. 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 geno-
type observations per locus and breed was equal to or
slightly lower than the number of animals included
(compare Table 1). In Vietnamese Landrace and Euro-
pean Wild Boar there was 1 locus per breed with 3
missing genotype observations, so we successfully de-
termined 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 Euro-
pean 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 ar-
 2604 Thuy et al.

Table 2. Microsatellite loci

Locus1 SSC Repeat motif2 NA3 Allele range,3 bp Specific allele,4 bp

SW780 1 (GT)11(GA)9 9 115 – 170 144 (MK 0.22)

SWR345 2 (CA)12 11 134 – 160 154 (WB 0.02)
SW72 3 (GT)15 12 97 – 119 105 (TN 0.02); 119 (TN 0.02)
SW489 4 (GT)16 14 148 – 181 —
IFNG 5 (GA)11 9 221 – 245 237 (MK 0.11); 245 (MK 0.02)
SW1067 6 (CT)20(CA)22 19 137 – 175 137 (MK 0.02); 139 (MK 0.03); 143 (MS 0.39); 153 (WB 0.02)
SW1083 7 (GT)15 19 108 – 152 114 (MK 0.02);126 (MK 0.02); 136 (ME 0.03); 140 (MK 0.11);
148 (MS 0.02); 150 (TN 0.02); 152 (MS 0.15)
TNFB 7 (CTG)20 18 142 – 203 188 (WB 0.02); 203 (WB 0.03)
SW2019 7 (GT)14AT(GT)4 10 127 – 147 133 (MK 0.02)
SW2410 8 (GT)15 17 103 – 137 —
SW911 9 (CA)22 15 147 – 177 177 (MK 0.03); 151 (MC 0.05)
SW1041 10 (CA)9 5 93 – 101 —
S0385 11 (CA)21 19 145 – 192 192 (MK 0.06); 180 (ME 0.09); 155 (WB 0.02)
S0090 12 (CA)24 11 227 – 251 227 (ME 0.02); 233 (TN 0.04); 251 (TN 0.04)
SW957 12 (GT)28 17 112 – 157 —
S0215 13 (CT)18(CA)12 17 125 – 194 161 (MK 0.05); 171 (MK 0.06); 194 (MS 0.10)
SW2519 14 (CA)20 19 187 – 232 218 (MK 0.06)
SW2083 15 (GT)10 11 143 – 167 145 (MK 0.02)
SW2427 17 (GT)13 15 116 – 146 124 (TN 0.02); 142 (WB 0.22)
SW787 18 (CA)19 10 144 – 164 —
1
Map positions, DNA sequences, references, etc. for the loci are given at http://www.thearkdb.org
2
Based on GenBank sequence data available at: http://www.ncbi.nlm.nih.gov
3
The total number of detected alleles (NA) and the range of allelic fragment lengths detected in this study.
4
Fragment lengths of the breed/subspecies-specific alleles are indicated with their allele frequencies in brackets together with the breed/
subspecies. Abbreviations of breeds: CO = Co; LG = Landrace Germany; LV = Landrace Vietnam; LW = Large White; MC = Mong Cai; ME =
Meo; MK = Muong Khuong; MS = Meishan; PI = Piétrain; TN = Tap Na; WB = European Wild Boar; and YV = Yorkshire Vietnam. A dash
(—) indicates that no breed-specific allele was found.

Table 3. Allelic diversity, heterozygosity, and F-statistics for the various pig breeds
Group1 MNO2 NPL3 MNA4 ENA5 ± SD PIC6 HE7 ± SE HO8 ± SE NDL9 FIS10

MK 32.0 20 9.1 5.14 ± 1.84 0.75 0.79 ± 0.02 0.71 ± 0.02 2 +0.108* (0.044 ↔ 0.137)
CO 31.0 20 8.4 4.70 ± 1.71 0.73 0.77 ± 0.02 0.71 ± 0.03 1 +0.086* (0.025 ↔ 0.112)
ME 32.0 20 9.3 4.98 ± 1.59 0.75 0.79 ± 0.02 0.74 ± 0.03 0 +0.062* (0.0003 ↔ 0.090)
TN 25.0 20 8.1 4.86 ± 1.78 0.73 0.77 ± 0.03 0.69 ± 0.03 1 +0.109* (0.014 ↔ 0.165)
MC 31.9 20 5.4 3.03 ± 1.18 0.58 0.63 ± 0.03 0.63 ± 0.04 1 −0.007 (−0.076 ↔ 0.031)
LV 21.8 19 4.8 2.83 ± 1.08 0.54 0.60 ± 0.04 0.60 ± 0.04 1 +0.009 (−0.080 ↔ 0.049)
YV 16.9 19 4.7 2.88 ± 1.33 0.53 0.59 ± 0.05 0.54 ± 0.05 0 +0.073 (−0.059 ↔ 0.139)
LG 31.9 18 4.4 2.27 ± 1.03 0.43 0.48 ± 0.05 0.50 ± 0.05 1 −0.029 (−0.099 ↔ 0.010)
PI 32.0 19 4.8 2.74 ± 1.64 0.49 0.54 ± 0.05 0.52 ± 0.05 1 +0.038 (−0.026 ↔ 0.067)
LW 30.0 20 4.3 2.71 ± 1.02 0.51 0.58 ± 0.04 0.60 ± 0.04 0 −0.040 (−0.121 ↔ 0.004)
WB 31.4 19 5.3 2.53 ± 1.30 0.46 0.51 ± 0.06 0.48 ± 0.06 3 +0.049 (−0.031 ↔ 0.094)
MS 25.9 20 3.9 2.09 ± 0.65 0.42 0.48 ± 0.04 0.53 ± 0.05 0 −0.116 (−0.208 ↔ −0.075)
VB11 119.9 20 12.4 6.04 ± 2.20 0.79 0.81 ± 0.04 0.71 ± 0.04 3 +0.090* (0.044 ↔ 0.137)
XB11 38.7 19 5.6 2.97 ± 1.31 0.55 0.60 ± 0.06 0.57 ± 0.06 2 +0.037 (0.025 ↔ 0.112)
EB11 93.8 20 6.3 3.08 ± 1.78 0.55 0.48 ± 0.04 0.53 ± 0.05 4 −0.009 (0.0003 ↔ 0.090)
1
Abbreviations of breeds: CO = Co; LG = Landrace Germany; LV = Landrace Vietnam; LW = Large White; MC = Mong Cai; ME = Meo;
MK = Muong Khuong; MS = Meishan; PI = Piétrain; TN = Tap Na; WB = European Wild Boar; and YV = Yorkshire Vietnam.
2
MNO = Mean number of genotype observations per locus.
3
NPL = Number of polymorphic loci. A locus was considered to be polymorphic if the frequency of the most frequent allele was <0.95.
4
MNA = Mean number of alleles per locus across all loci.
5
ENA = Effective number of alleles.
6
PIC = Polymorphism information content.
7
HE = Mean expected heterozygosity (unbiased estimate).
8
HO = Mean observed heterozygosity (direct count).
9
NDL = Number of loci deviating from Hardy Weinberg equilibrium (P < 0.05). In cases of more than 2 alleles per locus, the pooled test
was used.
10
FIS = Inbreeding coefficient of individuals in subpopulations. Confidence intervals (95%) by 10,000 bootstrap resamplings of individuals
are presented in brackets. *Values with P < 0.05 deviation from 0.
11
VB = Vietnamese breeds from villages (MK, CO, ME, and TN). Mong Cai (MC) was station kept and therefore regarded separately. XB =
Exotic breeds LV and YV. EB = European breeds LG, PI, and LW.

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 Comparing Vietnamese and European pig breeds
eas of origin. Distinctly lower values (3.9 to 5.4) oc-
curred 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 val-
ues 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 hair-
less 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 individ-
uals had a low mean number of alleles (5.3). This indi-
cates 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 re-
quired, but profiles of allele frequencies. As well docu-
mented, 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
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2605
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 heterozygos-
ity 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 indige-
nous 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 be-
cause altogether 234 locus × breed combinations were
tested, but only 11 were different (P < 0.05) from Hardy-
Weinberg equilibrium.
Inbreeding coefficients (FIS) were higher in the Viet-
namese 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 Wah-
lund (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 Wright’s coancestry coefficient FST of the Viet-
namese breeds showed an intermediate FST (0.050),
whereas it was highest (0.138) in the European com-
mercial breeds and lowest (0.019) in the Vietnamese
exotic breeds. These values are all below 0.15 and there-
fore describe moderate differentiation between popula-
tions (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 re-
gions (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 Viet-
namese 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 Euro-
pean 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
 2606 Thuy et al.

Table 4. Matrix of genetic distances for the various pig breeds according to Nei (1972)
Group1 VB MC XB EB WB

Genetic distance ± SE
MC 0.30 ± 0.05
XB 0.82 ± 0.09 1.00 ± 0.25
EB 0.81 ± 0.11 0.91 ± 0.29 0.07 ± 0.02
WB 1.40 ± 0.14 1.68 ± 0.29 0.31 ± 0.09 0.28 ± 0.10
MS 0.92 ± 0.17 1.26 ± 0.32 1.92 ± 0.30 1.93 ± 0.33 2.41 ± 0.36
1
MC = Mong Cai; VB = Vietnamese breeds Muong Khuong, Co, Meo, and Tap Na; XB = Exotic breeds
Landrace and Yorkshire in Vietnam; EB = European breeds Landrace, Piétrain, and Large White in Germany;
WB = European Wild Boar; and MS = Meishan.

related (0.07) and the large distances occurred between most cases smaller than the distances between the Viet-
Meishan and exotic breeds or European breeds (1.93 namese breeds and the European Wild Boar. This illus-
and 1.92, respectively). Distances between the Viet- trates the introgression of Asian domestic pigs into Eu-
namese breeds and European-based breeds were in ropean breeds in the late 18th and early 19th centuries

Figure 2. The unweighted pair-group method using arithmetic averages dendrograms based on Nei’s (1972) genetic
distances: a) Individual breeds; and b) Grouped breeds. Numbers represent the results of 1,000 bootstrap resamplings
(%). Abbreviations of breeds: CO = Co; LG = Landrace Germany; LV = Landrace Vietnam; LW = Large White; MC =
Mong Cai; ME = Meo; MK = Muong Khuong; MS = Meishan; PI = Piétrain; TN = Tap Na; WB = European Wild Boar;
YV = Yorkshire Vietnam; VB = Vietnamese breeds Muong Khuong, Co, Meo, and Tap Na; XB = Exotic breeds Landrace
and Yorkshire in Vietnam; EB = European breeds Landrace, Piétrain, and Large White in Germany. The scale indicates
Nei’s standard distance values (a measure of genetic dissimilarity between animal populations) calculated using the
BIOSYS-2 software (Swofford and Selander, 1989, modified by Black, 1997).

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 Comparing Vietnamese and European pig breeds
(Jones, 1998). Giuffra et al. (2000) found genetic evi-
dence for introgression during that period, when in-
vestigating 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 mitochon-
drial 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 Meis-
han 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 (Fig-
ure 2, panel b). However, as mentioned above, the Meis-
han 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 di-
rectly from China.
With a bootstrapping affirmation of 59%, Mong Cai
was clustered together with Co and Meo. All other clus-
ters were strongly confirmed with bootstrap values of
more than 65%. The results thus establish a clear ge-
netic 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 re-
lated 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.
IMPLICATIONS
This study is the first to apply a panel of microsatel-
lite markers for the genetic characterization of autoch-
thonous Vietnamese pig breeds. The markers used were
selected according to their genome wide spanning, poly-
morphism information content values, and precise gen-
otyping. It was possible to describe genetic differentia-
tion and establish a clear cut genetic structuring among
the studied populations, including European commer-
cial 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. Further-
more, 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 diver-
sity and can support livestock bioconservation ac-
tivities.
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