Czech J. Anim. Sci., 2011, 56(12):521-528 | DOI: 10.17221/4414-CJAS

Haplotype analysis within quantitative trait locus affecting intramuscular fat content on porcine chromosome

S. Sato, C. Ohnishi, Y. Uemoto, E. Kobayashi
National Livestock Breeding Center, Nishigo, Fukushima, Japan

Previous results of fine mapping for quantitative trait loci affecting intramuscular fat content identified a 3.0-Mb chromosome interval on porcine chromosome 7, which contains at least 9 genes, based on the pig genome assembly. Therefore, we proposed these nine genes (LOC100154481, LOC100155711, LOC100155276, SPATA7, PTPN21, ZCH14, EML5, TTC8, and FOXN3) as positional candidate genes. The coding exons of the nine genes were characterized, and 45 polymorphisms were detected in F2 Duroc × Meishan population. Within the nine genes, 10 non-synonymous substitutions and 1 insertion were genotyped among three European breeds (Landrace, Large White, and Duroc) and 1 Chinese breed (Meishan). Genotyping data was used to perform the haplotype analysis. Polymorphisms were found in all the studied genes, except ZCH14. We surveyed the frequency of 33 haplotypes that formed non-synonymous substitutions in four breeds. One of them was distributed widely in the Landrace, Large White, and Meishan breeds, but not in Duroc. Each breed had different major haplotypes.

Keywords: pig; chromosome 7; intramuscular fat; positional candidate genes; polymorphism

Published: December 31, 2011  Show citation

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Sato S, Ohnishi C, Uemoto Y, Kobayashi E. Haplotype analysis within quantitative trait locus affecting intramuscular fat content on porcine chromosome. Czech J. Anim. Sci. 2011;56(12):521-528. doi: 10.17221/4414-CJAS.
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    References

    1. Amaral A.J., Megens H.J., Crooijmans R.P.M.A., Heuven H.C.M., Groenen M.A.M. (2008): Linkage disequilibrium decay and haplotype block structure in the pig. Genetics, 179, 569-579. Go to original source... Go to PubMed...
    2. Cardone L., Carlucci A., Affaitati A., Livigni A., de Cristofaro T., Garbi C., Varrone S., Ullrich A., Gottesman M.E., Avvedimento E.V., Feliciello A. (2004): Mitochondrial AKAP121 binds and targets protein tyrosine phosphatase D1, a novel positive regulator of src signaling. Molecular and Cellular Biology, 24, 4613-4626. Go to original source... Go to PubMed...
    3. Ciobanu D.C., Bastiaansen J.W.M., Lonergan S.M., Thomsen H., Dekkers J.C.M., Plastow G.S., Rothschild M.F. (2004): New alleles in calpastatin gene are associated with meat quality traits in pigs. Journal of Animal Science, 82, 2829-2839. Go to original source... Go to PubMed...
    4. de Koning D.J., Janss L.L.G., Rattink A.P., van Oers P.A.M., de Vries B.J., Groenen M.A.M., van der Poel J.J., de Groot P.N., (Pim) Brascamp E.W., van Arendonk A.M. (1999): Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa). Genetics, 152, 1679-1690. Go to original source... Go to PubMed...
    5. Edwards D.B., Ernst C.W., Raney N.E., Doumit M.E., Hoge M.D., Bates R.O. (2008): Quantitative trait locus mapping in an F2 Duroc × Pietrain resource population II. Carcass and meat quality traits. Journal of Animal Science, 86, 254-266. Go to original source... Go to PubMed...
    6. Fernandez X., Monin G., Talmant A., Mourot J., Lebret B. (1999): Influence of intramuscular fat content on the quality of pig meat - 2. Consumer acceptability of m. longissumus lumborum. Meat Science, 53, 67-72. Go to original source... Go to PubMed...
    7. Fortin A., Robertson W.M., Tong A.K.W. (2005): The eating quality of Canadian pork and its relationship with intramuscular fat. Meat Science, 69, 297-305. Go to original source... Go to PubMed...
    8. Grindflek E., Szyda J., Liu Z., Lien S. (2001): Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross. Mammalian Genome, 12, 299-304. Go to original source... Go to PubMed...
    9. Harlizius B., Rattink A.P., de Koning D.J., Faivre M., Joosten R.G., van Arendonk J.A.M., Groenen M.A.M. (2000): The X chromosome harbors quantitative trait loci for backfat thickness and intramuscular fat content in pigs. Mammalian Genome, 11, 800-802. Go to original source... Go to PubMed...
    10. Ihaka R., Gentleman R. (1996): R: A language for data analysis and graphics. Journal of Computational and Graphical Statistics, 5, 299-314. Go to original source...
    11. Jeon J., Carlborg Ö., Törnsten A., Giuffra E., Amarger V., Chardon P., Andersson-Eklund L., Andersson K., Hansson I., Lundström K., Andersson L. (1999): A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to IGF2 locus. Nature Genetics, 21, 157-158. Go to original source... Go to PubMed...
    12. Kim J.J., Rothschild M.F., Beever J., Rodriguez-Zas S., Dekkers J.C.M. (2005): Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. Journal of Animal Science, 83, 1229-1240. Go to original source... Go to PubMed...
    13. Livigni A., Scorziello A., Agnese S., Adornetto A., Carlucci A., Garbi C., Castaldo I., Annunziato L., Avvedimento E.V., Feliciello A. (2006): Mitochondrial AKAP121 links cAMP and src signaling to oxidative metabolism. Molecular Biology of the Cell, 17, 263-271. Go to original source... Go to PubMed...
    14. Malek M., Dekkers J.C.M., Lee H.K., Baas T.J., Prusa K., Huff-Lonergan E., Rothschild M.F. (2001): A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mammalian Genome, 12, 637-645. Go to original source... Go to PubMed...
    15. Mikawa S., Sato S., Nii M., Morozumi T., Yoshioka G., Imaeda N., Yamaguchi T., Hayashi T., Awata T. (2011): Identification of a second gene associated with variation in vertebral number in domestic pigs. BMC Genetics, 12, 5. Go to original source... Go to PubMed...
    16. Milan D., Jeon J., Looft C., Amarger V., Robic A., Thelander M., Rogel-Gaillard C., Paul S., Iannuccelli N., Rask L., Ronne H., Lundstöm K., Reinsch N., Gellin J., Kalm E., Le Roy P., Chardon P., Andersson L. (2000): A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science, 288, 1248-1251. Go to original source... Go to PubMed...
    17. Nezer C., Moreau L., Brouwers B., Coppieters W., Detilleux J., Hanset R., Karim L., Kvasz A., Leroy P., Georges M. (1999): An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nature Genetics, 21, 155-156. Go to original source... Go to PubMed...
    18. Nii M., Hayashi T., Mikawa S., Tani F., Niki A., Mori N., Uchida Y., Fujishima-Kanaya N., Komatsu M., Awata T. (2005): Quantitative trait loci mapping for meat quality and muscle fiber traits in a Japanese wild boar × Large White intercross. Journal of Animal Science, 83, 308-315. Go to original source... Go to PubMed...
    19. Ovilo C., Clop A., Noguera J.L., Oliver M.A., Barragán C., Rodríguez C., Silió L., Toro M.A., Coll A., Folch J.M., Sánchez A., Babot D., Varona L., Pérez-Enciso M. (2002): Quantitative trait locus mapping for meat quality traits in an Iberian × Landrace F2 population. Journal of Animal Science, 80, 2801-2808. Go to original source... Go to PubMed...
    20. Rohrer G.A., Thallman R.M., Shackelford S., Wheeler T., Koohmaraie M. (2005): A genome scan for loci affecting pork quality in a Duroc-Landrace F 2 population. Animal Genetics, 37, 17-27. Go to original source... Go to PubMed...
    21. Rothschild M.F. (2003): From a sow's ear to a silk purse: real progress in porcine genomics. Cytogenetic and Genome Research, 102, 95-99. Go to original source... Go to PubMed...
    22. Rothschild M.F., Hu Z.L., Jiang Z. (2007): Advances in QTL mapping in pigs. International Journal of Biological Sciences, 3, 192-197. Go to original source... Go to PubMed...
    23. Sambrook J., Russell D.W. (2001): Preparation and analysis of eukaryotic genomic DNA. In: Ford N. (ed.): Molecular Cloning: A Laboratory Manual. 3 rd Ed. Cold Spring Harbor Laboratory Press, New York.
    24. Sato S., Oyamada Y., Atsuji K., Nade T., Sato S., Kobayashi E., Mitsuhashi T., Nirasawa K., Komatsuda A., Saito Y., Terai S., Hayashi T., Sugimoto Y. (2003): Quantitative trait loci analysis for growth and carcass traits in a Meishan × Duroc F2 resource population. Journal of Animal Science, 81, 2938-2949. Go to original source... Go to PubMed...
    25. Sato S., Hasebe H., Sato S., Asahi Y., Hayashi T., Kobayashi E., Sugimoto Y. (2005): High-resolution physical mapping and construction of a porcine contig spanning the intramuscular fat content QTL. Animal Genetics, 37, 113-120. Go to original source... Go to PubMed...
    26. Stephens M., Smith N.J., Donnelly P. (2001): A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978-989. Go to original source... Go to PubMed...
    27. van Wijk H.J., Cibbits B., Baron E.E., Brings A.D., Harlizius B., Groenen M.A.M., Knol E.F., Bovenhuis H. (2006): Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross. Journal of Animal Science, 84, 789-799. Go to original source... Go to PubMed...
    28. Womack J.E. (2005): Advances in livestock genomics: Opening the barn door. Genome Research, 15, 1699- 1705. Go to original source... Go to PubMed...

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