Vol.2, No.6, 527-534 (2010) Natural Science
http://dx.doi.org/10.4236/ns.2010.26066
Differentiation of wild boar and domestic pig
populations based on the frequency of
chromosomes carrying endogenous
retroviruses
Sergey V. Nikitin1, Nikolay S. Yudin1, Sergey P. Knyazev2*, Ruslan B. Aitnazarov1,
Vitaliy A. Bekenev3, Valentina S. Deeva3, Galina M. Goncharenko3, Victor F. Kobzev1,
Margarita A. Savina1, Viktor I. Ermolaev1
1Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
2Novosibirsk State Agrarian University, Novosibirsk, Russia; *Corresponding Author:
3Siberian Research Institute of Animal Husbandry Siberian Branch, Russian Academy of Agricultural Sciences, Krasnoobsk, Russia
Received 25 March 2010; revised 30 April 2010; accepted 13 May 2010.
ABSTRACT
Analysis of the frequencies of chromosomes
carrying various classes of porcine endogenous
retroviruses (PERVs) and combinations of these
classes was performed in the swine species Sus
scrofa L. by using maps constructed in two
principal component coordinates. Four popula-
tion clusters can be recognized in the maps.
Cluster 1 is formed by wild boars,cluster 2 by
domestic meat breeds, cluster 3 by meat-and-
lard (universal) breeds, and cluster 4 by minia-
ture pigs. The maps indicate that modern do-
mesticated swine meat breeds are the closest to
the wild type. Meat-and-lard domestic swine br-
eeds are more distant from wild boars, and
miniature pigs are diverged the most. The maps
showed that microevolution processes associ-
ated with PERV carriership frequency had two
basic dimensions, or vectors: the vector of fat
deposition variation and the “minus” selection
vector (determination of commercial traits).
Thus, PERVs may cause variation in pig physi-
ology.
Keywords: Sus scrofa; Endogenous Retroviruses;
Pig Genetics; Microevolution; Genetic Distance
Determination
1. INTRODUCTION
Porcine endogenous retroviruses (PERVs) became an
integral part of swine genomes, including Sus scrofa L.
1758 (Suidae , Mammalia), before the formation of the
Sus genus. This is confirmed by their presence in bush-
pigs (Potamochoerus larvatus and P. porcus) and wart-
hogs (Phacochoerus africanus) [1]. Three PERV classes
are known: A, B, and C. Different classes are highly
similar in the nucleotide sequences of the gag (group-
specific antigens) and pol (polymerase) genes but differ
in the nucleotide sequence of the receptor-binding do-
main of the env (envelope) gene, which encodes the en-
velope protein of the virus [2-4]. This difference is re-
sponsible for the host range in various virus classes.
Porcine endogenous retrovirus copies carried by dif-
ferent pig varieties are distinct in nucleotide composition,
expression, and ability to produce infectious virions. It is
believed that the pig genome can carry 6-10 replication-
competent proviruses, 30-50 full-size PERV copies, and
100-200 loci carrying truncated virus sequences [1].
Comprehensive studies of pigs belonging to the Large
White breed were undertaken to evaluate the number of
genomic sequences coding for full-length replication-
competent proviruses [5-7]. As a result, significant va-
riations in the distribution and number of proviruses
were found in this breed. Viral genomes were also ana-
lyzed in the following breeds: Westran [8,9], Duroc,
Landrace, Yorkshire, Berkshire, and their hybrids
[10,11]; Chinese breeds Banna miniature pig, Wu-Zhi-
Shan, Nei Jiang [12], and Meishan [11]; and west Euro-
pean wild boars [9]. In these breeds, as in Large White
pigs, PERV sequences are dispersed throughout the ge-
nome. The breeds differ in the PERV copy number,
chromosomal distribution, and presence of full-length
sequences. These traits also varied within the breeds.
Previously, differences in the prevalence of individu-
als with chromosomes carrying PERVs of various clas-
ses and their combinations between domestic pig breeds,

S. V. Nikitin et al. / Natural Science 2 (2010) 527-534
528
between wild and domestic pigs, and between wild pigs
of East Europe and Central Asia were demonstrated
[13,14].
In this work, we analyze the differentiation between
populations of wild and domestic pigs. For this purpose,
we performed statistical assessment of the population
frequencies of chromosomes carrying certain PERV
classes and combinations is using maps constructed in
two principal component coordinates.
2. MATERIALS AND METHODS
Experiments were performed with blood samples from
three subspecies of wild boars, five commercial breeds
of domestic pigs, and one breed of laboratory miniature
pigs (Table 1). Wild boar animals of the European Sus
scrofa scrofa variety (SSS) were obtained from the Vo-
ronezh Biosphere Reservation. Wild boars of the Roma-
nian subspecies S. s. attila were taken from two southern
Ukrainian populations (SAS and SAN). The Central
Asian Wild Boar subspecies S. s. nigripes (SSN) was
represented by animals hunted down in the Chu Valley,
Kyrgyzstan. Domestic pigs Sus scrofa domestica of the
Large White breed included animals of the Achinsk
(LWA) and Novosibirsk (LWN) types bred at the Inya
stud Farm. Landrace pigs were obtained from the
Kudryashovskoe farm (LNK) and the Experimental
Farm of the Siberian Branch of the Russian Academy of
Sciences, hereafter referred to as the Experimental Farm
(LNE). Duroc pigs were obtained from the Kudrya-
shovskoe farm (DRK). Animals of the SM1 precocious
meat breed were obtained from the Tulinskoe work-
study unit. The Kemerovo breed included animals from
the Yurginskii breeding farm (KMR). Miniature pigs
(MS) were obtained from the Experimental Farm. A
total of 636 blood samples were studied: 35 from mature
wild boar males and females and 601 from domestic pigs
(mature breeding males and females and youngsters be-
low two months). Blood was taken from the anterior
vena cava of living domestic pigs or from the heart of
killed wild boars.
DNA was isolated from blood samples and analyzed
for the presence of PERV classes by polymerase chain
reaction (PCR) [11]. The sequences of primers comple-
mentary to the env gene sequences of various PERV
classes were adopted from the literature. Primers for
envA: forward 5′-TGG AAA GAT TGG CAA CAG
CG-3′ and reverse 5′-AGT GAT GTT AGG CTC AGT
GG-3′ [3]. Primers for envB: forward 5′-TTC TCC TTT
GTC AAT TCC GG-3′ and reverse 5′-TAC TTT ATC
GGG TCC CAC TG-3′ (ibid.) Primers for envC: forward
5′-CTG ACC TGG ATT AGA ACT GG-3′ and reverse
5′-ATG TTA GAG GAT GGT CCT GG-3′ [4].
The population frequencies of chromosomes carrying
various PERV classes and their combinations were deter-
mined by Bernstein method modified for a gene with mul-
tiple copies located on different chromosomes [14].
Phylogenetic relationships among the populations un-
der study were studied in maps constructed in two princi-
pal component coordinates. Determination of genetic dis-
tances was followed by sample ordination [15]. After scal-
ing, each population was defined as a point in a 500 500
arbitrary unit area. Three types of genetic distances
were used: 1) Euclidean distances 2
1
1
()
n
ii
i
Dpq


,
Table 1. Populations of wild boars and domestic pigs.
Subspecies or breed, locality Designation Sample size
Wild boar S. s. scrofa, Voronezh Biosphere Reservation SSS 12
Wild boar S. s. attila, Carpathians (Ukraine) SAC 12
Wild boar S. s. attila, Ukraine, Nikolaev Region SAN 7
Wild boar S. s. nigripes, Kyrgyzstan SSN 4
Large White breed, Novosibirsk type, Inya farm LWN 101
Large White breed, Achinsk type, Inya farm LWA 99
Kemerovo breed, Yurginskii breeding farm KMR 165
Landrace, Kudryashovskoe farm LNK 15
Landrace, Experimental Farm LNE 30
SM1 precocious meat breed, Tulinskoe work-study unit SM1 21
Duroc, Kudryashovskoe farm DRK 10
Miniature pigs, Experimental Farm MS 160

S. V. Nikitin et al. / Natural Science 2 (2010) 527-534
529
529
where n is the number of phenotypes, and pi and qi
are frequencies of phenotypes in populations to be com-
pared [16]; 2)Harpending–Jenkins distances 2
1
Dn

1
(-)(-)
(1 -)
n
ii
i
ppqp
pp



, where p
 is the weighted mean
frequency of a certain phenotype in populations to be
compared, and n is the number of genes according to
which the populations are compared [17]; 3) Nei’s dis-
tances 3ln1 2(lnln)
p
qpq
DJ JJ , where 2
1
n
p
i
i=
J
p

,
2
1
n
qi
i
=
J
=q
, 22
1
n
pqi i
i=
J
=pq
, Jp is the theoretical homo-
zygosity in the first population, Jq is the theoretical ho-
mozygosity in the second population, and Jpq is the mu-
tual identity of the populations under comparison [16].
Two models were considered for construction of maps
in two principal component coordinates. In model M-1,
the frequencies of chromosomes carrying PERV classes
were presented as frequencies of three independent factors
with two variables: envA+ and envA–, envB+ and
envB–, envC+ and envC–. In model M-2, the frequencies of
chromosomes carrying PERV class combinations were
presented as frequencies of seven independent factors
with two variables: envA+ and envA–, envB+ and envB–,
envC+ and envC–, envAB+ and envAB–, envAC+ and env
AC–, envBC+ and envBC–, envABC+ and envABC–. For
each model, three versions of maps of the phylogenetic
relationship among the varieties were constructed.
3. RESULTS
As shown in our previous study [14], frequencies of
chromosomes carrying various PERV classes and their
combinations vary significantly among the subspecies of
wild boars and breeds of domesticated pigs (Sus scrofa L.
1758) (SUIDAE, MAMMALIA), as well as among
herds within a breed. One to three distinct PERV classes
were detected in chromosomes of the populations under
study. In addition to single provirus copies, such chro-
mosomes contained combinations AB, AC, BC, and
ABC (Table 2).
Maps in two principal component coordinates con-
structed on the base of models M-1 and M-2 demon-
strate features of the phylogenetic relationship between
populations determined by microevolutionary processes
(Figure 1). It should be emphasized that model M-1,
which considers the frequencies of chromosomes carry-
ing certain PERV classes, and model M-2 that deals with
the frequencies of chromosomes carrying combinations
of these classes, yield different results (Figure 1).
Four population clusters can be recognized in maps
constructed on the base of frequencies of chromosomes
carrying PERV classes. Cluster 1 is formed by wild
boars; cluster 2 by domestic meat breeds; cluster 3 by
meat-and-lard (universal) breeds, and cluster 4 by
miniature pigs (Figure 1). These clusters form a certain
logical order. Three clusters form one straight line: wild
boars, meat breeds, and universal breeds. The fourth
cluster, miniature pigs, is distant from this line. Thus,
according to the M-1 model, the frequencies of PERV
classes show the following trend associated with mor-
photypes: wild boar commercial meat morphotype 
commercial meat-and-lard morphotype. The maps also
indicate that variation among populations within the
Table 2. Frequencies of chromosomes carrying certain PERV classes and combinations of these classes in wild boar and domestic pig
populations. The classes are identified by env gene sequences.
Frequencies of PERV class carriers Frequencies of PERV class combination carriers
Population*
envA envB envC A B C AB AC BC ABC
SSS 0.011 0.023 0.008 0.000 0.012 0.000 0.003 0.000 0.000 0.008
SAC 0.000 0.039 0.027 0.000 0.012 0.000 0.000 0.000 0.027 0.000
SAN 0.000 0.029 0.013 0.000 0.016 0.000 0.000 0.000 0.013 0.000
SSN 0.008 0.004 0.020 0.008 0.004 0.020 0.000 0.000 0.000 0.000
LWN 0.068 0.047 0.005 0.064 0.041 0.000 0.001 0.000 0.005 0.000
LWA 0.065 0.114 0.013 0.000 0.045 0.000 0.060 0.005 0.008 0.000
KMR 0.087 0.079 0.037 0.000 0.006 0.000 0.055 0.019 0.005 0.013
LNK 0.042 0.034 0.008 0.041 0.034 0.008 0.000 0.000 0.000 0.000
LNE 0.052 0.052 0.036 0.000 0.000 0.000 0.024 0.007 0.007 0.022
SM1 0.028 0.051 0.051 0.000 0.000 0.000 0.000 0.000 0.023 0.028
DRK 0.042 0.018 0.009 0.042 0.018 0.009 0.000 0.000 0.000 0.000
MS 0.109 0.099 0.109 0.000 0.000 0.000 0.000 0.010 0.000 0.099
*Designations follow Table 1.

S. V. Nikitin et al. / Natural Science 2 (2010) 527-534
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Figure 1. Maps constructed in two principal component coordinates on the base of frequencies of chromosomes car-
rying PERV classes (M-1) and class combinations (M-2). Designations: D1, D2, D3 are genetic distances: Euclidean,
Harpending–Jenkins’, and Nei’s ones, respectively. Population designations follow Table 1.

S. V. Nikitin et al. / Natural Science 2 (2010) 527-534
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531
clusters is nonrandom. The vector of this variation is
directed to point 0, 500 (bottom-right corner of the map).
Thus, it is reasonable to suggest that cluster 4 (miniature
pigs) is the farthest deviation from this vector and that
these pigs originated from a population initially belong-
ing to cluster 3 (meat-and-lard morphotype).
A markedly different pattern is seen in the maps con-
structed on the base of frequencies of chromosomes car-
rying PERV class combinations (Figure 1). It is similar
to that obtained by using the M-1 model (Figure 1) in
that the miniature pig population is distant from other
populations, whereas wild boar populations still form a
compact cluster. However, the clusters of meat and uni-
versal meat-and-lard breeds are extended in parallel to
the 0, 0; 500, 500 line, so that the populations belonging
to these clusters are located on the opposite sides of the
wild boar cluster (Figure 1). The populations can be
combined into clusters according to their locations in the
maps (Figure 1). Cluster 1 includes Landrace and Duroc
domestic pigs from the Kudryashovskoe farm and the
Novosibirsk subbreed of Large White pigs. Noteworthy,
these pigs have a history of the most intensive selection
for meat yield. Cluster 2 includes Large White pigs of
the Achinsk subbreed and the Kemerovo breed. These
populations belong to the universal meat-and-lard mor-
photype. Cluster 3 is formed by miniature pigs. Cluster 4,
located in the centres of the maps, is of special interest.
It includes wild boars, SM-1 pigs, and Landrace pigs
from the Experimental Farm. This combination is rea-
sonable. The intensity of selection for meat yield in these
two populations was less than in populations of the first
cluster, and this is the cause of the reversion to the wild
morphotype observed in these populations. It is known
that meat breeds had been raised from meat-and-lard and
lard morphotypes [18]; therefore, they deviated even
more from wild boars. In Landrace pigs of the Experi-
mental Farm, this shift is directed to the cluster of
meat-and-lard populations, and in the SM-1 breed to
miniature pigs, which can be considered closer to their
ancestral Asian lard breeds [19,20]. The Kemerovo breed
is located between the Achinsk Large White subbreed
and miniature pigs in both maps. The most likely cause
of this location is that the Kemerovo breed was at first
raised as a lard breed [21], and later selection was di-
rected to the universal meat-and-lard type [22]. Thus,
maps constructed on the frequencies of chromosomes
carrying PERV class combinations reveal finer features
of population differentiation than maps of simple PERV
class carriership. These features are associated with the
differentiation among populations within large groups,
such as wild boars and commercial domestic pig mor-
photypes, rather than with the differentiation among the
groups.
There were two questions to be raised in our work:
what wild boar population is closer to the present-day
domestic pig according to PERV prevalence and what
domestic pig breeds are closer to wild boars? To answer
these questions, we employed maps constructed in two
principal component coordinates according to two mod-
els: a model named M-1 that considers frequencies of
PERV classes, and a model M-2 that deals with various
PERV class combinations. The distances between popu-
lations seen in the maps (Figure 1) are presented as bar
graphs (Figure 2). The graphs obtained on the base of
the M-1 model show that the European wild boar Sus
scrofa scrofa subspecies from the Voronezh Biosphere
Reserve is the closest to the domestic pig, and the Cen-
tral Asian wild boar subspecies Sus scrofa nigripes is the
farthest. The distances determined on the base of the
M-2 model show the same result, although less clearly.
Both models indicate that modern domesticated swine
meat breeds are the closest to the wild type. Meat-and-
lard domestic swine breeds are farther from wild boars,
and miniature pigs are the farthest.
4. DISCUSSION
Different aspects of PERV-associated features of differ-
entiation of swine (Sus scrofa) populations were re-
vealed by using the models presented in this study. Pre-
vious results [13,14] were summarized, and hypotheses
concerning the role of PERVs in microevolutionary
changes occurring in Sus scrofa populations were sub-
stantiated. The variation in the frequencies of chromo-
somes carrying certain PERV classes and class combina-
tions follows two microevolutionary vectors. The first
vector is more specific: wild boars meat pig breeds
meat-and-lard pig breeds. It can be defined as an in-
crease in fat deposition rate in pig subspecies and breeds.
The second vector is of a more general nature: wild
boars and commercial domestic pig breeds miniature
pigs. It is a “minus” selection vector. It can be suggested
that in the first case PERVs tag loci affecting fat deposi-
tion rate and in the second case are associated with loci
controlling some commercial and adaptive traits. How-
ever, the following hypothesis appears to be more plau-
sible: retroviral copies are inserted into certain function-
ally important genome regions, thereby disrupting the
normal function of genes located in the insertion sites or
nearby. These aberrations may give rise to undesirable or,
to the contrary, desirable traits. Thus, the vector of in-
creasing fat deposition appears to be a special manifesta-
tion of the “minus” selection vector. The latter should be
more accurately termed the genomic aberration vector.
This hypothesis is in agreement with the formerly re-
ported data that the frequencies of individuals and

S. V. Nikitin et al. / Natural Science 2 (2010) 527-534
532
chromosomes carrying PERVs in populations naturally
selected for fitness (wild boars) or intensively selected
for pork production (pigs of the Kudryashovskoe herd) are
much lower than in populations undergoing a less inten-
sive selection [14]. Also, it was shown that a class B
PERV copy was inserted into the BAT1 gene (coding for
RNA helicase) of Large White pigs [9]. It should be men-
tioned that the frequency of PERV carriers was higher
among miniature pigs, the product of “minus” selection.
They can be considered a pathological form because of
their slow growth, small size, low fertility, high postnatal
mortality, and a tendency to obesity. Note that in minia-
ture pigs not only the highest PERV carriership frequency
was recorded but also the highest frequency of chromo-
somes carrying all the three PERV classes in comparison
to all other populations investigated (Table 2).
The proximity of wild boars from the Voronezh Bio-
sphere Reserve located in the centre of European Russia
to present-day domestic pigs (Figure 2) appears to be
due to convergence rather than divergence. The Vo-
ronezh wild boar population was formed by a recent
natural crossing between the subspecies Sus scrofa
scrofa and Sus scrofa attila during migrations of wild
boars from the West (from Europe) and South (from
Ukraine and Caucasus) [23,24]. Therefore, its early as-
signment to S. s. scrofa is entirely formal. Both these
subspecies were among the ancestors of modern Euro-
pean breeds of Sus scrofa domestica [23,25,26]. Thus,
the similarity between these two forms, the wild boar
and domestic pig that originate from common ancestral
subspecies is natural and of a convergent nature.
It is reasonable to suggest that the graph series ob-
tained by the ranking similarity of domestic pig popula-
tions to wild boar are related to the vector of genomic
changes induced by PERVs. Breeds of the meat type are
in the closest proximity to wild boars. They were raised
Figure 2. Distances between wild boar populations and domestic pig breeds according to maps con-
structed in two principal component coordinates. For each breed, the first bar presents Euclidean dis-
tances; the second, Harpending–Jenkins’ ones; and the third, Nei’s ones, respectively. Population desig-
nations follow Table 1.

S. V. Nikitin et al. / Natural Science 2 (2010) 527-534
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533
by selection for a less intense fat deposition. The ele-
vated fat deposition in domestic pigs in comparison with
wild or early domesticated forms is an obvious abnor-
mality, which may have been caused by the breakdown
of some genes owing to PERV insertion. Therefore, the
natural selection against these breaks favoured alleles
characteristic of the original wild boar or similar. This
may have resulted in convergent similarity between meat
pig breeds and wild boars. Domestic breeds of the uni-
versal meat-and-lard morphotype should possess a cer-
tain number of loci in the genome that would determine
the fat deposition degree corresponding to this morpho-
type. Mutations in some of these loci caused by PERV
insertion give rise to the desirable trait; therefore, this
morphotype diverges more from wild boars than breeds
of the meat type in the frequencies of chromosomes car-
rying certain PERV classes and type combinations.
Miniature pigs were raised by intensive selection for a
smaller adult body size with minimum selection for
other traits. The development of irrelevant traits should
be sufficient for no more than maintenance of the popu-
lation. For this reason, it is likely that the miniature pig
genome was enriched in loci whose function was dis-
rupted by PERV insertions. In some cases, this favoured
the desired trait (small size), and in other cases this was
of no significance, because no selection for commercial
traits was conducted.
In summary, we analyzed in this study patterns of dif-
ferentiation of domestic and wild pigs in the frequencies
of chromosomes carrying certain PERV classes and type
combinations. With regard to this differentiation, we
demonstrated that the convergence processes were at
least no less significant than the divergence ones. It ap-
pears that PERVs were not neutral elements in the evo-
lution of the pig genome.
5. ACKNOWLEDGEMENTS
This study was supported by the Gene pool dynamics project of the
Russ. Acad. Sci Presidium program Biodiversity and gene pool dy-
namics.
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