Next Article in Journal
Chemopreventive Efficacy of Atorvastatin against Nitrosamine-Induced Rat Bladder Cancer: Antioxidant, Anti-Proliferative and Anti-Inflammatory Properties
Previous Article in Journal
Flexible and Versatile as a Chameleon—Sophisticated Functions of microRNA-199a

Int. J. Mol. Sci. 2012, 13(7), 8467-8481; doi:10.3390/ijms13078467

Article
Phylogenetic Relationships of the Mangalitsa Swine Breed Inferred from Mitochondrial DNA Variation
Sergiu Emil Georgescu , Maria Adina Manea , Andreea Dudu and Marieta Costache *
Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Splaiul Independentei 91-95, Bucharest 050095, Romania; E-Mails: georgescu_se@yahoo.com (G.S.E.); adina_manea@yahoo.com (M.M.A.); tn_andreea@yahoo.com (D.A.)
*
Author to whom correspondence should be addressed; E-Mail: marietacostache@yahoo.com; Tel.: +4-021-3181575 (ext. 112); Fax: +4-021-3181575 (ext. 102).
Received: 15 May 2012; in revised form: 25 June 2012 / Accepted: 26 June 2012 /
Published: 9 July 2012

Abstract

: The Mangalitsa pig, a swine breed belonging to the protected gene fund of original and primitive animal breeds of the FAO (Food and Agriculture Organization), has been known to inhabit Romanian territories since the 19th century. The aim of this study was to compare the Mangalitsa breed with several European and Asiatic swine breeds in order to emphasize its uniqueness and to elucidate its origin. For this purpose, we analyzed a 613 bp mitochondrial DNA D-loop fragment and 1140 bp of the cytochrome b gene in a population of Mangalitsa pigs and the polymorphic sites were compared with sequences from GenBank originating from other swine breeds. Taking into account the total of 24 breeds and 5 different Wild Boar populations analyzed, 86 polymorphic sites representing 32 haplotypes were observed, with an average percentage of polymorphic sites of 4.9%. Three Neighbor-Joining phylogenetic trees were constructed based on Kimura 2-parameter distances, using D-loop, cytochrome b and mitochondrial reunited sequences. For the analyzed Mangalitsa population, four distinct haplotypes were identified, including one that was common to other breeds. Our study suggests that the Mangalitsa swine originate from primitive breeds which might be directly derived from the Wild Boar.
Keywords:
mangalitsa pig; primitive breed; mitochondrial DNA; phylogeny

1. Introduction

In the last years, the conservation of animal and plant biodiversity has become a major international goal in environmental sciences. As a result, maintaining the biodiversity of local breeds of domestic animals, especially the ones of economic interest, has become a priority.

At the international level, there is an increasing concern regarding the study and genetic characterization of local populations, the so-called rare animal breeds. Most of the research performed to date refers to the breeds’ genetic characterization and the assessment of the phylogenetic relations among them. During recent years, a series of studies were performed regarding local horse breeds [13], bovines [4,5], swine [610] and sheep [11,12]. The genealogic analysis of these breeds provided valuable information regarding the current status of unimproved specimens. The characterization of the genetic variability of local breeds is, currently, one of the priorities of scientific research in animal genetics, as it is dictated by the re-assessment of practices in livestock breeding as well as by the conservation of genetic resources.

The Mangalitsa breed is considered to be a direct descendant of the Wild Boar and is part of the European primitive breeds that have not been ameliorated by crossbreeding with other swine breeds. By contrast to the swine breeds specialized in meat production, the Mangalitsa breed is specialized in lard production. Nevertheless, apart from excess fat, swine from this breed also produce interstratified meat of superior quality.

According to FAO (Food and Agriculture Organization) the Mangalitsa breed originates from the current territory of Hungary and was officially acknowledged in 1927. To be more specific, the Mangalitsa breed originates from the Balkan region and is a result of the cross-breeding of individuals from the Sumadija breed from Serbia with the Bakonyi and Szalontai breeds from the territory of the Austro-Hungarian Empire which took place in in the 19th century [13]. Following the steep decline in the number of specimens after the Second World War, the Mangalitsa breed is now classified as an endangered breed, on the brink of extinction, with only three varieties surviving to date (i.e., Blonde, Swallow-Bellied and Red), which can be distinguished by fur colour [13].

The Mangalitsa is currently found only on the territory of the former Austro-Hungarian Empire. These pigs have woolly coat, lop ears and are adapted to adverse conditions of feeding and management. Due to the low meat production and reduced prolificacy, the Mangalitsa breed has been slowly but gradually replaced. Presently, it is the only European swine breed whose body is entirely covered with thick fur, consisting of long and curly hairs. Conversely, only two centuries ago, such primitive breeds could have been encountered in the Mediterranean basin and in the entire Balkan region [14]. However, these breeds have been lost largely due to their replacement by modern, improved breeds, with a much higher production of meat.

The mitochondrial genome of vertebrates presents some useful features such as maternal transmission, higher rate of mutation in comparison to the nuclear DNA, rapid evolution and lack of recombination; consequently, these characteristics recommend it as a useful tool for phylogenetics studies. Past studies have already determined the complete sequence of the pig mitochondrial genome and the organization of mitochondrial genes [15]. The mitochondrial genome has a size of 16,613 bp and, with the exception of the D-loop region, consists only of structural genes without any non-encoding bases. In order to investigate specific mitochondrial DNA (mtDNA) phylogenetic markers, sequence specific primers were designed flanking these markers. Amplified fragments were sequenced, and the results were analysed using molecular phylogeny specific software. These fragments can be analyzed in terms of conservation by comparison to other populations and will serve for the construction of phylogenetic trees.

The aim of this study was to compare the Mangalitsa breed with various swine breeds with distinct geographical distribution in order to assign their origins. The comparative analysis was performed at a molecular level by investigating a fragment from the D-loop mitochondrial region and the cytochrome b gene. Different haplotypes obtained for the Romanian Mangalitsa individuals were compared with haplotypes from different European and Asian breeds.

2. Results and Discussion

In this study, partial sequences of 613 bp from the D-loop control region and 1140 bp from the cytochrome b gene were determined for all the sampled individuals (45 individuals from the Mangalitsa breed and 15 Wild Boars from Romania). Four distinct haplotypes were identified among the 45 sequences from Romanian Mangalitsa, while only one haplotype was identified for the 15 sequences from Romanian Wild Boar.

For an overview of the phylogenetic information content, our sequences representing different haplotypes were aligned and compared with sequences from other European and Asian swine breeds available from GenBank. This analysis showed 86 variable sites (75 transitions, 10 transversions and one deletion), representing 4.9% from the total number of nucleotides.

For the animal specimens we have analyzed in our study, at the level of the cytochrome b gene we identified 43 single-nucleotide polymorphisms from which 38 are transitions and 5 are transversions: A→T (14,339, 14,651); T→G (14,746); C→G (14,765) and C→A (14,961). Regarding the D-loop region, 43 single-nucleotide polymorphisms were identified, including 37 transitions, 5 transversions (A→T, 15,558; C→A, 15,782, 15,894 and 15,896; C→G, 15,939) and one deletion at position 15571. A total number of 32 different haplotypes was identified in all pig populations. From the 32 haplotypes, five represent haplotypes discovered by us in Romanian Mangalitsa breed (ROMg1, ROMg2, ROMg3 and ROMg4) and Romanian Wild Boar (ROWB). The polymorphic sites observed per each breed are shown in Table 1 and the results obtained in terms of nucleotide variation and haplotypes are presented in Figure 1.

Among the 32 distinct haplotypes, two were common for various breeds: the H7 haplotype is common in the Mangalitsa breed in Romania, Hungary, Landrace, Duroc and Basque, while the H9 haplotype is common in the Large White and Spotted Black Jagubo from Spain. Four haplotypes were identified in 45 individuals of Romanian Mangalitsa with haplotype diversity (Hd) 0.755, nucleotide diversity (Pi) 0.00158, Theta (per sequence) Eta 1.37214 and Theta (per site) Eta 0.00078. One of these haplotypes (ROMg2) is common in other breeds, as well as in the Mangalitsa breed from Hungary. Moreover, for the Romanian Wild Boar there is only one distinct haplotype (H27).

By using the “Kimura 2-parameter” algorithm [16], the genetic distances as well as their standard deviations were calculated. Based on these results, the phylogenetic relationships among swine breeds were inferred by the Neighbor-Joining algorithm. We constructed three phylogenetic trees: two of them were based on the cytochrome b gene and on the partial sequence of the D-loop region, respectively, while the third tree was built using both mitochondrial markers.

The phylogenetic tree obtained based on the cytochrome b sequence highlighted two major clades: the European, containing the majority of the swine breeds from Europe, including the Mangalitsa breed and the Romanian Wild Boar, and the Asian comprising all the breeds from Asia, as well as some breeds from Europe, such as the Large White, Pietran, Berkshire or Spotted Black Jagubo. The Romanian and Italian Wild Boars form distinct clusters within the European clade, although this distribution is supported by a low bootstrap value (Figure 2). At the same time, all the haplotypes of the Mangalitsa breed, from both Romania and Hungary, were grouped together with other European breeds, in a distinct cluster.

The tree obtained based on the D-loop fragment shows a slightly different topology compared to the tree obtained based on the cytochrome b gene (Figure 3). In this case, the two clades are not as clearly separated, since the North-East China Wild Boar is categorized as an isolated cluster at the level of the European clade. Within the European clade, the breeds are disposed in separate clusters and as a result the uniformity present in the tree constructed based on the cytochrome b gene disappears in this case. A haplotype of the Mangalitsa breed from Romania (ROMg1) appears in the same cluster with the Romanian Wild Boar, while two other haplotypes (ROMg3 and ROMg4) form separate branches together with the haplotypes of the Spanish Wild Boar. The Large White, Pietran, Berkshire and Spotted Black Jagubo breeds are also included in the Asian clade. Unfortunately, these phyologenetic relationships were supported by low bootstrap values.

Within the tree constructed based on the joint analysis of the two mitochondrial sequences (Figure 4) we can clearly notice only two clades, a European one and an Asian one. The North-East China Wild Boar is currently included, with a 91% bootstrap value, in the Asian clade. As expected, the European Large White, Pietran, Berkshire and Spotted Black Jagubo breeds still appear in the Asian clade. Their inclusion in this clade is not surprising and it was emphasized by other authors as well [17,18]. The presence in the Asian clade reflects the introduction of the Asian swine in Europe [19] and denotes the fact that European domestic breeds could have a more diverse genetic base than initially supposed. Consequently, it was suggested that swine breeds from East Asia, imported to England from the 17th to the 19th century, have contributed to the formation of the Large White and Berkshire breeds [20]. The inclusion of the Pietran breed in the Asian clade was emphasized by Alves et al., 2003 [18]. This affiliation can be correlated with the fact that the Large White and Berkshire specimens took part in the formation of the breed [19].

The four haplotypes of the Mangalitsa breed in Romania can be found in similar positions with those from the tree constructed based only on the fragment from the D-loop mitochondrial region. The exception is the ROMg2 haplotype that appears together with the Mangalitsa swine from Hungary in a separate cluster in the clade of the European breeds. The other three haplotypes appear to be clustered with those originating from the Wild Boars from Romania or Spain.

Thus, despite the low bootstrap support, the molecular data suggest that the Mangalitsa swine originates from primitive breeds that are probably derived directly from the Wild Boars in Central and Eastern Europe.

As far as the European Wild Boar is concerned, our results confirm previous studies undertaken on mtDNA sequences in domestic swine and boars [17,21] that have also shown that the Italian Wild Boar represents a distinct monophyletic group in the European clade. Kijas and Andersson, 2001 [22] have suggested that a distinct subspecies might have evolved in this region due to the isolation during the last glacial period. The results of our study are in agreement with this suggestion, as the Italian Wild Boar is clearly separate from the other European breeds.

Ultimately we calculated the net-average genetic distances between the European and the Asian clades (K) taking into account both the synonymous substitutions, as well as the non-synonymous ones, at the level of the cytochrome b gene. In the case of the D-loop region, the genetic distances were calculated separately for the two domains: ETAS and Central. The time period (T) that has elapsed since the separation of the two clades can be determined from the T = K/2r equation [23], where r represents the rate of nucleotide substitutions, a rate that was accurately determined by Pesole et al., 1999 [24], for the various regions at the level of the mammal mtDNA. The net-average genetic distances between the clades (expressed as divergence percentages) as well as the time period that has passed since the two clades were separated, is shown in Table 2.

Our study results suggest that the divergence between the European and the Asian clades occurred approximately 700,000 years ago. This assessment is in close agreement with the one obtained by Alves et al., 2003 [18], who stated that this divergence had occurred 780,000 years ago. Sbisa et al., 1997 [25] consider that the central domain of the D-loop region has great statistical fluctuations and thus will not always fit in the estimation of the divergence between the clades. Consequently, if we eliminate the very high value obtained for the central domain we will get an estimation of approximately 580,000 years, a value that is close to the value of 660,000 years achieved by Alves et al., 2003 [18].

3. Experimental Section

3.1. Sampling and DNA Extraction

Fresh blood samples from 45 Mangalitsa swine (“Suinprod” Farm, Roman, Romania) and 15 Wild Boars were harvested. The Mangalitsa specimens were chosen at random and closely related animals were avoided in the selection process. The isolation of genomic DNA from fresh blood was performed with Wizard Genomic DNA Extraction Kit (Promega) according to the manufacturer’s instructions.

3.2. DNA Amplification and Sequencing

The cytochrome b gene was amplified and sequenced using two pairs of primers: first pair (cytb1) amplified a fragment of 831 bp, and the second (cytb2) a fragment of 576 bp. The two amplified fragments were partially overlapped in the median area. The reactions were carried out in a 25 μL final volume containing PCR Buffer, 1.5 mM MgCl2, 200μM dNTP, 0.5 μM of each primer (cytbF1: 5′-ACCACGACCAATGACATGAA-3′; cytbR1: 5′-TGCTGGGGTGTAGTTGTCTG-3′; cytbF2: 5′-ACAACCCTACCGGAATCTCA-3′; cytbR2: 5′-GGCCCTCCTTTTCTGGTTTA-3′), 0.5 units of AmpliTaq Gold DNA Polymerase, DNA and nuclease-free water. PCR were performed using a 45 cycles thermocycler program with denaturation at 95 °C (30 s), annealing at 58 °C (30 s/cytb1), 61 °C (30 s/cytb2), respectively, and extension at 72 °C (60 s).

For the D-loop region, we have designed a pair of primers that amplified a fragment of 678 bp. The reactions were carried out in a 25 μL final volume containing PCR Buffer, 1.5 mM MgCl2, 200 μM dNTP, 0.5 μM of each primer (DLoopF: 5′-TTCGTATGCAAACCAAAACG-3′; DLoopR: 5′-TGTCCCGTAACCATTGACTG-3′), 0.5 units of AmpliTaq Gold DNA Polymerase, DNA and nuclease-free water. PCR was performed using a 45 cycles thermocycler program with denaturation at 95 °C (30 s), annealing at 58 °C (30 s) and extension at 72 °C (60 s).

PCR products were purified with the Wizard PCR Preps DNA Purification System Kit (Promega) and sequenced using the ABI Prism®BigDye Terminator Cycle Sequencing Reaction Kit (AppliedBiosystems) in an ABI Prism 3130 Genetic Analyzer. The sequencing reactions were performed both for forward and reverse strands. The sequences were processed using DNA Sequencing Analysis 5.1 Software (AppliedBiosystems), aligned with the BioEdit program [26] and refined manually.

3.3. Sequence Alignment and Molecular Phylogenetic Analysis

The final sequence for the cytochrome b gene was 1140 bp in length. The D-loop sequences were truncated to nps 15,455–16,068 to accommodate the short sequences already published (Table 3). The cytochrome b and D-loop sequences were aligned using the ClustalX 2.0.9 software [27], with a 10-gap opening penalty and a 0.10-gap extension penalty parameter, while the rest of the settings were kept as default. The genetic diversity in terms of number of haplotypes, haplotype and nucleotide diversity was estimated using DNAsp v5 [28]. In addition to our sequences representing different haplotypes in Mangalitsa and Wild Boar from Romania, mtDNA sequences available in GenBank were included in our study to ensure the best possible phylogenetic evaluation. The warthog (Phacochoerus africanus) was used as an outgroup species. The accession numbers and references for the published sequences are presented in Table 3.

The best-fit model of nucleotide substitution was selected with ModelTest [29]. A Neighbor-Joining phylogenetic tree was constructed on the basis of the Kimura 2-parameter distances [16] implemented in MEGA 4.0 [30]. Bootstrap analyses (1000 replications) were used to assess the confidence of each node. The GenBank sequence with the accession number AJ002189 [15] was used as reference and a basis for the sequence numbering.

4. Conclusions

This is the first study focusing on the phylogenetic relationships of the Mangalitsa breed and other swine breeds from Europe and Asia.

The results obtained establish the influence of the Asian breeds on the following European breeds: Large White, Berkshire, Spotted Black Jagubo and Pietran. The Mangalitsa breed was included in the European breed cluster, while three out of the four haplotypes discovered were associated with separate clusters that include the Spanish or Romanian Wild Boars. The results of our study show a remarkable closeness of the Mangalitsa breed to the European Wild Boars, a closeness that was also confirmed by phenotypic similarities including the presence of fur on the entire body. The primitive character of this breed is also emphasized by its distribution in monophyletic groups with European Wild Boars and other primitive breeds.

As far as the divergence between the European and the Asian clades is concerned, the results we obtained, based on the data resulting from the cytochrome b gene sequences and the ETAS domain at the level of the D-loop region, suggest that it occurred approximately 580,000 years ago. This divergence supports the hypothesis of a multiple and independent domestication process that occurred a long time after the divergence of the two clades. This hypothesis is also supported by other studies [34,39].

References

  1. Luís, C.; Bastos-Silveira, C.; Cothran, E.G.; Om, M. Variation in the mitochondrial control region sequence between the two maternal lines of the Sorraia horse breed. Genet. Mol. Biol 2002, 25, 309–311. [Google Scholar]
  2. Aberle, K.; Hamann, H.; Drögemüller, C.; Distl, O. Genetic diversity in german draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers. Anim. Genet 2004, 35, 270–277. [Google Scholar]
  3. Georgescu, S.E.; Manea, M.A.; Dudu, A.; Costache, M. Phylogenetic relationships of the Hucul horse from Romania inferred from mitochondrial D-loop variation. Genet. Mol. Res 2011, 10, 4104–4113. [Google Scholar]
  4. Kim, K.; Yeo, J.; Choi, C. Genetic diversity of north-east Asian cattle based on microsatellite data. Anim. Genet 2002, 33, 201–204. [Google Scholar]
  5. Lai, S.; Liu, Y.; Li, X.; Yao, Y. Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Mol. Phylogenet. Evol 2006, 38, 146–154. [Google Scholar]
  6. Li, K.; Chen, Y.; Moran, C.; Fan, B.; Zhao, S.; Peng, Z. Analysis of diversity and genetic relationships between four Chinese indigenous pig breeds and one Australian commercial pig breed. Anim. Genet 2000, 31, 322–325. [Google Scholar]
  7. Kim, K.I.; Lee, J.H.; Li, K.; Zhang, Y.P.; Lee, S.S.; Gongora, J.; Moran, C. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim. Genet 2002, 33, 19–25. [Google Scholar]
  8. Fabuel, E.; Barragan, C.; Silio, L.; Rodriguez, M.C.; Toro, M.A. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 2004, 93, 104–113. [Google Scholar]
  9. Fang, M.; Hu, X.; Jiang, T.; Braunschweig, M.; Hu, L.; Du, Z.; Feng, J.; Zhang, Q.; Wu, C.; Li, N. The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers. Anim. Genet 2005, 36, 7–13. [Google Scholar]
  10. Fang, M.; Andersson, L. Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication. Proc. Biol. Sci 2006, 273, 1803–1810. [Google Scholar]
  11. Pedrosa, S.; Uzun, M.; Arranz, J.; Gutierrez-Gil, B.; Primitivo, F.; Bayon, Y. Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events. Proc. R. Soc. Lond 2005, B272, 2211–2217. [Google Scholar]
  12. Peter, C.; Brufford, M.; Perez, T.; Dalamitra, S.; Hewitt, G.; Erhardt, G. Econogene consortium, genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Anim. Genet 2007, 38, 37–44. [Google Scholar]
  13. Radnóczi, L. The hungarian mangalica; Agroservice AgriBusiness Club, 2003. Web site. Available online: http://www.agroservice.hu/mangainfo1.htm accessed on 30 May 2012.
  14. Ciobanu, D.C.; Day, A.E.; Nagy, A.; Wales, R.; Rothschild, M.F.; Plastow, G.S. Genetic variation in two conserved local Romanian pig breeds using type 1 DNA markers. Genet. Sel. Evol 2001, 33, 417–432. [Google Scholar]
  15. Ursing, B.M.; Arnason, U. The complete mitochondrial DNA sequence of the pig (Sus scrofa). J. Mol. Evol 1998, 47, 302–306. [Google Scholar]
  16. Kimura, M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol 1980, 16, 111–120. [Google Scholar]
  17. Giuffra, E.; Kijas, J.M.; Amarger, V.; Carlborg, O.; Jeon, J.T.; Andersson, L. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 2000, 154, 1785–1791. [Google Scholar]
  18. Alves, E.; Ovilo, C.; Rodriguez, M.C.; Silio, L. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Anim. Genet 2003, 34, 319–324. [Google Scholar]
  19. Jones, G.F. Genetic Aspects of Domestication, Common Breeds and Their Origins. In The Genetics of the Pig; Rothschild, M.F., Ruvinsky, A., Eds.; CAB International: Wallingford, Oxon, UK, 1998; pp. 17–50. [Google Scholar]
  20. Epstein, J.; Bichard, M. Pig. In Evolution of Domesticated Animals; Mason, I.L., Ed.; John Wiley & Sons: New York, NY, USA, 1986; pp. 145–162. [Google Scholar]
  21. Watanobe, T.; Ishiguro, N.; Nakano, M.; Matsui, A.; Hongo, H.; Yamazaki, K.; Takahashi, O. Prehistoric Sado Island populations of Sus scrofa distinguished from contemporany Japanese Wild boar by ancient mitochondrial DNA. Zoolog. Sci 2004, 21, 219–228. [Google Scholar]
  22. Kijas, J.M.; Andersson, L. A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome. J. Mol. Evol 2001, 52, 302–308. [Google Scholar]
  23. Li, W.H. Molecular Evolution; Sinauer Associates: Sunderland, MA, USA, 1997; p. 432. [Google Scholar]
  24. Pesole, G.; Gissi, C.; de Chirico, A.; Saccone, C. Nucleotide substitution rate of mammalian mitochondrial genomes. J. Mol. Evol 1999, 48, 427–434. [Google Scholar]
  25. Sbisà, E.; Tanzariello, F.; Reyes, A.; Pesole, G.; Saccone, C. Mammalian mitochondrial D-loop region structural analisis: Identification of new conserved sequences and their functional and evolutionary implications. Genetics 1997, 205, 125–140. [Google Scholar]
  26. Hall, T.A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids Symp. Ser 1999, 41, 95–98. [Google Scholar]
  27. Larkin, M.A.; Blackshields, G.; Brown, N.P.; Chenna, R.; McGettigan, P.A.; McWilliam, H.; Valentin, F.; Wallace, I.M.; Wilm, A.; Lopez, R.; et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23, 2947–2948. [Google Scholar]
  28. Librado, P.; Rozas, J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 2009, 25, 1451–1452. [Google Scholar]
  29. Posada, D.; Crandall, K.A. Modeltest: Testing the model of DNA substitution. Bioinformatics 1998, 14, 817–818. [Google Scholar]
  30. Tamura, K.; Dudley, J.; Nei, M.; Kumar, S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol 2007, 24, 1596–1599. [Google Scholar]
  31. Wang, J.F.; Li, S.; Ran, X.Q. Department of Animal Science, Guizhou University, Xueshi Road, Huaxi, Guiyang, Guizhou Province 550025, ChinaSus scrofa breed Nuogu mitochondrion, complete genome. In Unpublished work; 2006. [Google Scholar]
  32. Su, X.X.; Cheng, W.M.; Zeng, Y.Z. Complete mitochondrial genome of Banan mini-pig inbred line. In Unpublished work; Key Laboratory of Banna Mini-Pig Inbred Line of Yunnan Province, Yunnan Agricultural University: Longquan Load, Kunming, Yunnan 650201, China, 2009. [Google Scholar]
  33. Su, X.X.; Cheng, W.M.; Zeng, Y.Z. Complete sequence and gene organization of the Dahe pig mitochondrial genome. In Unpublished work; Key Laboratory of Banna Mini-Pig Inbred Line of Yunnan Province, Yunnan Agricultural University: Longquan Load, Kunming, Yunnan 650201, China, 2009. [Google Scholar]
  34. Wu, G.S.; Yao, Y.G.; Qu, K.X.; Ding, Z.L.; Li, H.; Palanichamy, M.G.; Duan, Z.Y.; Li, N.; Chen, Y.S.; Zhang, Y.P. Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biol 2007, 8, R245. [Google Scholar]
  35. Cho, I.C.; Han, S.H.; Lee, S.S.; Ko, M.S.; Lee, J.G.; Jeon, J.T. The complete mitochondrial DNA sequence of Korean wild boar. In Unpublished work; Division of Livestock, National Institute of Subtropical Agriculture: R.D.A., 175-6, O-deung dong, Jeju, 690-150, South Korea, 2007. [Google Scholar]
  36. Yu, H.; Li, L.; Liu, D. Phylogeography of Boar based on mtDNA evolution. In Unpublished work; Animal Science and Technology College, Northeast Agricultural University: 59 Mucai Street, Harbin, HeiLongjiang 150030, China, 2007. [Google Scholar]
  37. Cho, I.C.; Park, J.J.; Jeon, J.T. The complete sequence of mitochondrial DNA of Berkshire (Sus scrofa). In Unpublished work; National Institute of Subtropical Agriculture: R.D.A., 1696, Odeung dong, Jeju 690-150, South Korea, 2004. [Google Scholar]
  38. Cho, I.C.; Park, J.J.; Jeon, J.T. The complete sequence of mitochondrial DNA of Hampshire (Sus scrofa). In Unpublished work; National Institute of Subtropical Agriculture: R.D.A., 1696, Odeung dong, Jeju 690-150, South Korea, 2004. [Google Scholar]
  39. Larson, G.; Dobney, K.; Albarella, U.; Fang, M.; Matisoo-Smith, E.; Robins, J.; Lowden, S.; Finlayson, H.; Brand, T.; Willerslev, E.; et al. Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 2005, 307, 1618–1621. [Google Scholar]
Ijms 13 08467f1 1024
Figure 1. Haplotypes and variable sites in the D-loop region (between nucleotides 15,455 and 16,068) and cytochrome b gene in 24 swine breeds, 5 Wild Boar populations and the reference sequence (GenBank AJ002189). The numbers represent the position occupied in the sequence. Identical sites are indicated by the symbol “·” and the deletions with “−”.

Click here to enlarge figure

Figure 1. Haplotypes and variable sites in the D-loop region (between nucleotides 15,455 and 16,068) and cytochrome b gene in 24 swine breeds, 5 Wild Boar populations and the reference sequence (GenBank AJ002189). The numbers represent the position occupied in the sequence. Identical sites are indicated by the symbol “·” and the deletions with “−”.
Ijms 13 08467f1 1024
Ijms 13 08467f2 1024
Figure 2. Neighbor-Joining tree based on cytochrome b sequence of 32 different haplotypes, including 24 swine breeds and 5 Wild Boar populations. Figures on the internodes are bootstrap probabilities based on 1000 replications. Outgroup: Phacochoerus africanus (NC_008830).

Click here to enlarge figure

Figure 2. Neighbor-Joining tree based on cytochrome b sequence of 32 different haplotypes, including 24 swine breeds and 5 Wild Boar populations. Figures on the internodes are bootstrap probabilities based on 1000 replications. Outgroup: Phacochoerus africanus (NC_008830).
Ijms 13 08467f2 1024
Ijms 13 08467f3 1024
Figure 3. Neighbor-Joining tree based on D-loop sequence of 32 different haplotypes, including 24 swine breeds and 5 Wild Boar populations. Figures on the internodes are bootstrap probabilities based on 1000 replications. Outgroup: Phacochoerus africanus (NC_008830).

Click here to enlarge figure

Figure 3. Neighbor-Joining tree based on D-loop sequence of 32 different haplotypes, including 24 swine breeds and 5 Wild Boar populations. Figures on the internodes are bootstrap probabilities based on 1000 replications. Outgroup: Phacochoerus africanus (NC_008830).
Ijms 13 08467f3 1024
Ijms 13 08467f4 1024
Figure 4. Neighbor-Joining tree based on D-loop and cytochrome b sequences. Figures on the internodes are bootstrap probabilities based on 1000 replications. Outgroup: Phacochoerus africanus (NC_008830).

Click here to enlarge figure

Figure 4. Neighbor-Joining tree based on D-loop and cytochrome b sequences. Figures on the internodes are bootstrap probabilities based on 1000 replications. Outgroup: Phacochoerus africanus (NC_008830).
Ijms 13 08467f4 1024
Table Table 1. Total number of haplotypes and polymorphic sites with their dispersion within 24 different swine breeds and 5 Wild Boar populations.

Click here to display table

Table 1. Total number of haplotypes and polymorphic sites with their dispersion within 24 different swine breeds and 5 Wild Boar populations.
Breed namePolymorphic sitesHaplotypesTransitionsTransversionsDeletions
European breeds

Mangalitsa (Romania)9481-
Mangalitsa (Hungary)3121-
Black Hairless313--
Red4131-
Duroc3121-
Large White33232-1
Landrace424--
Pietran32231-1
Hampshire6142-
Spotted Black Jabugo29128-1
Basque3121-
Berkshire3313021

Asiatic breeds

Nuogu31130-1
Banna Mini32131-1
Dahe26125-1
Saba30129-1
Zang31130-1
Wei27126-1
Qing Ping27126-1
Bamei29128-1
Huzu29128-1
Yimenghei32131-1
Bihu28127-1
Xiang28127-1
Meishan3613231

Asiatic and European Wild Boars

Wild Boar (N-E China)26125-1
Wild Boar (Koreea)3213011
Wild Boar (Italy)241222-
Wild Boar (Romania)212--
Wild Boar (Spain)113101-
Table Table 2. Net-average genetic distances between clades (K) and the time period that had passed since the separation of the two clades (T).

Click here to display table

Table 2. Net-average genetic distances between clades (K) and the time period that had passed since the separation of the two clades (T).
mtDNA regionNucleotide substitution rate (%) [24]K ± SD (%)T (× 103 years)
Cytochrome b gene

Synonymous positions27.4 ± 3.33.875 ± 0.011707
Non-synonymous positions1.8 ± 0.30.154 ± 0.001428

D-loop region

ETAS Domain19.4 ± 7.82.273 ± 0.006586
Central Domain3.8 ± 1.90.843 ± 0.0041109

Average (including Central Domain)707

Average (without Central Domain)574
Table Table 3. D-loop and cytochrome b sequences from pigs of several breeds obtained from GenBank and used in this study.

Click here to display table

Table 3. D-loop and cytochrome b sequences from pigs of several breeds obtained from GenBank and used in this study.
AbbreviationAccession numberBreed/LocationReferences
SpBkHlessAY237494/cytb
AY232852/D-loop
Black Hairless/Spain/EuropeAlves et al., 2003 [18]
SpRedAY237498/cytb
AY232856/D-loop
Red/Spain/EuropeAlves et al., 2003 [18]
SpWB1AY237510/cytb
AY232868/D-loop
Wild Boar 1/Spain/EuropeAlves et al., 2003 [18]
SpWB2AY237513/cytb
AY232871/D-loop
Wild Boar 2/Spain/EuropeAlves et al., 2003 [18]
SpWB3AY237515/cytb
AY232873/D-loop
Wild Boar 3/Spain/EuropeAlves et al., 2003 [18]
EDcAY237519/cytb
AY232877/D-loop
Duroc/EuropeAlves et al., 2003 [18]
ELW1AY237524/cytb
AY232882/D-loop
Large White 1/EuropeAlves et al., 2003 [18]
ELW2AY237525/cytb
AY232883/D-loop
Large White 2/EuropeAlves et al., 2003 [18]
ELr1AY237526/cytb
AY232884/D-loop
Landrace 1/EuropeAlves et al., 2003 [18]
ELr2AY237527/cytb
AY232885/D-loop
Landrace 2/EuropeAlves et al., 2003 [18]
EP1AY237528/citb
AY232886/D-loop
Pietran 1/EuropeAlves et al., 2003 [18]
EP2AY237529/cytb
AY232887/D-loop
Pietran 2/EuropeAlves et al., 2003 [18]
MeisAY237530/cytb
AY232888/D-loop
Meishan/ChinaAlves et al., 2003 [18]
SpSJAY237532/cytb
AY232890/D-loop
Spotted Black Jabugo/Spain/EuropeAlves et al., 2003 [18]
SpBsqAY237533/cytb
AY232891/D-loop
Basque/Spain/EuropeAlves et al., 2003 [18]
HgMgAY237534/cytb
AY232892/D-loop
Mangalitsa/Hungary/uropeAlves et al., 2003 [18]
CHNuoguDQ466081Nuogu/ChinaWang et al., 2006 [31]
CHBannaMGQ220328Banna Mini/ChinaSu et al., 2009 [32]
CHDaheGQ220329Dahe/ChinaSu et al., 2009 [33]
CHSabaEF545567Saba/ChinaWu et al., 2007 [34]
CHZangEF545576Zang/ChinaWu et al., 2007 [34]
CHWeiEF545577Wei/ChinaWu et al., 2007 [34]
CHQPEF545582Qing Ping/ChinaWu et al., 2007 [34]
CHBameiEF545583Bamei/ChinaWu et al., 2007 [34]
CHHuzuEF545588Huzu/ChinaWu et al., 2007 [34]
CHYmgEF545589Yimenghei/ChinaWu et al., 2007 [34]
CHBihuEF545591Bihu/ChinaWu et al., 2007 [34]
CHXiangEF545593Xiang/ChinaWu et al., 2007 [34]
KWBEU090703Wild Boar/KoreaCho et al., 2007 [35]
CHWB-NEEU333163Wild Boar/Nord-East ChinaYu et al., 2007 [36]
EberkAY574045Berkshire/EuropeCho et al., 2004 [37]
EHmphAY574046Hampshire/EuropeCho et al., 2004 [38]
ItWBAF304201Wild Boar/Italy/EuropeKijas and Andersson, 2001 [22]
P. africNC_008830Phacochoerus africanusWu et al., 2007 [34]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert