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Identification of mitochondrial markers for genetic traceability of European wild boars and Iberian and Duroc pigs

Published online by Cambridge University Press:  28 May 2009

E. Alves ,
A. I. Fernández ,
A. Fernández-Rodríguez ,
D. Pérez-Montarelo ,
R. Benitez ,
C. Óvilo ,
C. Rodríguez  and
L. Silió
E. Alves
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
A. I. Fernández*
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
A. Fernández-Rodríguez
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
D. Pérez-Montarelo
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
R. Benitez
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
C. Óvilo
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
C. Rodríguez
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
L. Silió
Affiliation:
Departmento de Mejora Genética Animal, INIA, Carretera de la Coruña km 7.5, 28040 Madrid, Spain
*
†E-mail: avila@inia.es
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Abstract

Iberian pigs and wild boars are the source of highly priced meat and dry-cured products. Iberian maternal origin is mandatory for labeled Iberian products, making necessary the authentication of their maternal breed origin. Discrimination between wild and domestic pig maternal origin may be useful to distinguish labeled wild boar meat obtained from hunting or farming. In order to detect useful polymorphisms to trace Iberian, Duroc and wild boar maternal lineages, we herein investigated the complete porcine mitochondrial DNA (mtDNA) using three complementary approaches. Near-complete mtDNA sequences (16989 bp), excluding the minisatellite present in the displacement loop region (D-loop), were successfully determined in six Iberian pigs, two Duroc and six European wild boars. To complete the mtDNA analysis, the D-loop minisatellite region was also analyzed in the same set of samples by amplification and capillary electrophoresis detection. Finally, the frequencies of Asian and European Cytochrome B (Cyt B) haplotypes were estimated in Iberian (n = 96) and Duroc (n = 125) breeds. Comparison of near-complete mtDNA sequences revealed a total of 57 substitutions and two Indels. Out of them, 32 polymorphisms were potential Iberian markers, 10 potential Duroc markers and 16 potential wild boar markers. Fourteen potential markers (five Iberian and nine Duroc), were selected to be genotyped in 96 Iberian and 91 Duroc samples. Five wild boar potential markers were selected and tested in samples of wild boars (73) and domestic pigs including: 96 Iberian, 16 Duroc, 16 Large White and 16 Landrace. Genotyping results showed three linked markers (m.7998C>T, m.9111T>C, m.14719A>G) absent in Duroc and present in Iberian pigs with a frequency 0.72. Six markers (m.8158C>T, m.8297T>C, m.9230G>A, m.11859A>G, m.13955T>C, m.16933T>C), three of them linked, were absent in Iberian pigs and present in Duroc with a joint frequency of almost 0.50. Finally three linked markers (m.7188G>A, m.9224T>C, m.15823A>G) were solely detected in wild boars with a frequency 0.22. The D-loop minisatellite results showed overlapping ranges of fragment sizes and suggested heteroplasmy, a result that nullify the use of this region for the development of breed diagnostic markers. The Cyt B haplotype results showed the presence of European haplotypes in Iberian while one of the Asian haplotypes was detected in Duroc with a frequency 0.22, linked to the Duroc marker m.9230G>A. Our results are valuable to resolve the problems of Iberian and wild boar maternal origin determination but additional markers are required to achieve totally useful genetic tests.

Keywords

mtDNA markerstraceabilityIberianDurocwild boar
Type
Full Paper
Information
animal , Volume 3 , Issue 9 , September 2009 , pp. 1216 - 1223
Copyright
Copyright © The Animal Consortium 2009

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References

Alves, E, Óvilo, C, Rodríguez, MC, Silió, L 2003. Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and pig populations. Animal Genetics 34, 319–324.CrossRefGoogle ScholarPubMed
Carrodeguas, JA, Burgos, C, Moreno, C, Sánchez, AC, Ventanas, S, Tarrafeta, L, Barcelona, JA, López, MO, Oria, R, López-Buesa, P 2005. Incidence in diverse pig population of an IGF2 mutation with potential influence on meat quality and quantity: an assay based on real time PCR (RT-PCR). Meat Science 71, 577–582.CrossRefGoogle ScholarPubMed
Ciampolini, R, Cetica, V, Ciani, E, Mazzanti, E, Fosilla, X, Marrón, F, biagetti, M, Sebastián, C, Papa, P, Filippini, G, Cianci, D, Presciuttini, S 2006. Statistical analysis of individual assignment test among four cattle breeds using fifteen STR loci. Journal of Animal Science 84, 11–19.CrossRefGoogle Scholar
Clop, A, Amills, M, Noguera, JL, Fernández, A, Capote, J, Ramón, MM, Nelly, L, Kijas, JMH, Andersson, L, Sánchez, A 2004. Estimating the frequency of Asian cytochrome B haplotypes in standard European and local Spanish pig breeds. Genetics Selection Evolution 36, 97–104.CrossRefGoogle ScholarPubMed
Dalvit, C, De Marchi, M, Cassandro, M 2007. Genetic traceability of livestock products: a review. Meat Science 77, 437–449.CrossRefGoogle ScholarPubMed
Fabuel, E, Barragán, C, Silió, L, Rodríguez, MC, Toro, MA 2004. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 93, 104–113.CrossRefGoogle ScholarPubMed
Fajardo, V, González, I, Martín, I, Rojas, M, Hernández, PE, García, T, Martín, R 2008. Differentiation of European wild boar (Sus scrofa scrofa) and domestic swine (Sus scrofa domestica) meats by PCR analysis targeting the mitochondrial D-loop and the nuclear melanocortin receptor 1 (MC1R) genes. Meat Science 78, 314–322.CrossRefGoogle ScholarPubMed
Fernández, A 2003. Study of the genetic basis of the coat colour and practical applications in pig breeding. PhD, Complutense University, Madrid.Google Scholar
Fernández, A, Alves, E, Fernández, A, De Pedro, E, López-García, MA, Óvilo, C, Rodriguez, MC, Silió, L 2008. Mitochondrial genome polymorphisms associated with longissimus muscle composition in Iberian pigs. Journal of Animal Science 86, 1283–1290.CrossRefGoogle ScholarPubMed
Fernández, A, Fabuel, E, Alves, E, Rodriguez, C, Silió, L, Óvilo, C 2004. DNA tests based on coat colour genes for authentication of the raw material of meat products from Iberian pigs. Journal of the Science of Food and Agriculture 84, 1855–1860.CrossRefGoogle Scholar
Gandini, GC, Oldenbroek, JK 2007. Strategies for moving from conservation to utilisation. In Utilisation and conservation of farm animal genetic resources (ed. Kor Oldenbroek), pp. 29–54. Wageningen Academic Publishers, The Netherlands.CrossRefGoogle Scholar
Ghivizzani, SC, Mackay, SLD, Madsen, CS, Laipis, PJ, Hauswirth, WW 1993. Transcribed heteroplasmic repeated sequences in the porcine mitochondrial DNA D-loop region. Journal of Molecular Evolution 37, 36–47.CrossRefGoogle ScholarPubMed
Giuffra, E, Kijas, JMH, Amarger, V, Carlbörg, Ö, Jeon, JT, Andersson, L 2000. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785–1791.CrossRefGoogle ScholarPubMed
Jones, GF 1998. Genetic aspects of domestication, common breeds and their origin. In The genetics of the pig (ed. MF Rothschild and A Ruvinsky), pp. 17–50. CABI Publishing, Wallingford, UK.Google Scholar
Kim, KI, Lee, JH, Li, K, Zhang, YP, Lee, SS, Gongora, J, Moran, C 2002. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Animal Genetics 33, 19–25.CrossRefGoogle ScholarPubMed
López-Bote, C 1998. Sustained utilization of the Iberian pig breed. Meat Science 49 (suppl. 1), S17–S128.CrossRefGoogle Scholar
Montiel-Sosa, JF, Ruiz-Pesini, E, Montoya, J, Roncalés, P, López-Pérez, MJ, Pérez-Martos, A 2000. Direct and highly species-specific detection of pork meat and fat in meat products by PCR amplification of mitochondrial DNA. Journal of Agricultural and Food Chemistry 48, 2829–2832.CrossRefGoogle ScholarPubMed
Naya, Y, Horiuchi, M, Ishiguro, N, Shinagawa, M 2003. Bacteriological and genetic assessment of game meat from Japanese wild boars. Journal of Agricultural and Food Chemistry 51, 345–349.CrossRefGoogle ScholarPubMed
Pfeiffer, I, Burger, J, Brenig, B 2004. Diagnostic polymorphisms in the mitochondrial cytochrome b gene allow discrimination between cattle, sheep, goat, roe buck and deer by PCR-RFLP. BMC Genetics 5, 30–34.CrossRefGoogle ScholarPubMed
Tamura, K, Dudley, J, Nei, M, Kumar, S 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24, 1596–1599.CrossRefGoogle ScholarPubMed
Watanabe, T, Hirano, T, Takano, A, Mizoguchi, Y, Sugimoto, Y, Tasakuga, A 2008. Linkage disequilibrium structures in cattle and their application to breed identification testing. Animal Genetics 39, 374–382.CrossRefGoogle ScholarPubMed
Wolf, C, Rentsch, J, Hübner, P 1999. PCR-RFLP analysis of mitochondrial DNA: a reliable method for species identification. Journal of Agricultural and Food Chemistry 47, 1350–1355.CrossRefGoogle ScholarPubMed
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