Survey of SSC12 regions affecting fatty acid composition of intramuscular fat using high-density SNP data

Frontiers in Genetics

Volumn 2, Issue JAN, 2012, Pages

  Muñoz, María ^a   Alves, Estefânia ^a   Corominas, Jordi ^b   Folch, Josep María ^b   Casellas, Joaquim ^b,c   Noguera, Jose Luis ^c   Silió, Luis ^a   Fernández, Ana Isabel ^a  

^a INIA   (Spain)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^c IRTA   (Spain)

Author keywords

Fatty acid composition; High density SNP chip; SSC12

Indexed keywords

SUS;

EID: 84876020102     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00101     Document Type: Article

References (43)

1. Barrett, J. C., Fry, B., Maller, J., and Daly, M. J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265.
2. Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B Stat. Methodol. 57, 289-300.
3. Benjamini, Y., and Yekutieli, D. (2005). Quantitative trait loci analysis using the false discovery rate. Genetics 171, 783-790.
4. Cameron, N. D., and Enser, M. B. (1991). Fatty-acid composition of lipid in longissimus-dorsi muscle of Duroc and British Landrace pigs and its relationship with eating quality. Meat Sci. 29, 295-307.
5. Casellas, J., Ibanez-Escriche, N., Martinez-Giner, M., and Varona, L. (2008). GEAMM v.1.4: a versatile program for mixed model analysis of gene expression data. Anim. Genet. 39, 89-90.
6. Casellas, J., Noguera, J. L., Pena, R. N., Folch, J. M., Muñoz, M., and Ibáñez-Escriche, N. (2011). "T27 growth-related differential gene expression in the longissimusthoracis muscle of Iberian × Landrace back-crossed pigs," in American Society of Animal Science (ASAS) (New Orleans: American Society of Animal Science).
7. De Vries, A. G., and Kanis, E. (1994). "Selection for efficiency of lean tissue deposition in pigs," in Principles of Pig Science, eds D. J. A. Cole, J. Wiseman, and M. A. Varley (Nottingham: Nottingham University Press), 23-41.
8. Flowers, M. T., Keller, M. P., Choi, Y., Lan, H., Kendziorski, C., Ntambi, J. M., and Attie, A. D. (2008). Liver gene expression analysis reveals endoplasmic reticulum stress and metabolic dysfunction in SCD1-deficient mice fed a very low-fat diet. Physiol. Genomics 33, 361-372.
9. Gallardo, D., Quintanilla, R., Varona, L., Diaz, I., Ramirez, O., Pena, R. N., and Amills, M. (2009). Polymorphism of the pig acetyl-coenzyme A carboxylase alpha gene is associated with fatty acid composition in a Duroc commercial line. Anim. Genet. 40, 410-417.
10. Gelfand, A. E., and Smith, A. F. M. (1990). Sampling based approaches to calculating marginal densities. J. Am. Stat. Assoc. 85, 398-409.
11. Green, P., Falls, K., and Crooks, S. (1990). Documentation for Crimap. Available at: http://linkage.Rockefeller.Edu/soft/crimap(unpublished mimeo).
12. Jimenez-Colmenero, F., Ventanas, J., and Toldra, F. (2010). Nutritional composition of dry-cured ham and its role in a healthy diet. Meat Sci. 84, 585-593.
13. Kang, H. W., Kanno, K., Scapa, E. F., and Cohen, D. E. (2010a). Regulatory role for phosphatidylcholine transfer protein/StarD2 in the metabolic response to peroxisome proliferator activated receptor alpha (PPARalpha). Biochim. Biophys. Acta 1801, 496-502.
14. Kang, H. W., Wei, J., and Cohen, D. E. (2010b). PC-TP/StARD2: of membranes and metabolism. Trends Endocrinol. Metab. 21, 449-456.
15. Kim, J. H., Lim, H. T., Park, E. W., Ovilo, C., Lee, J. H., and Jeon, J. T. (2006). A gene-based radiation hybrid map of the pig chromosome 6q32 region associated with a QTL for fat deposition traits. Anim. Genet. 37, 522-523.
16. Lawrence, T. J. L., and Fowler, V. R. (1997). Growth of Animals. New York, NY: CAB International.
17. Lev, S. (2004). The role of the Nir/rdgB protein family in membrane trafficking and cytoskeleton remodeling. Exp. Cell Res. 297, 1-10.
18. Li, D., and Sinclair, A. J. (2002). Macronutrient innovations: the role of fats and sterols in human health. Asia Pac. J. Clin. Nutr. 11, S155-S162.
19. Lichtenstein, A. H. (2003). Dietary fat and cardiovascular disease risk: quantity or quality? J. Womens Health (Larchmt.) 12, 109-114.
20. Lonergan, S. M., Huff-Lonergan, E., Rowe, L. J., Kuhlers, D. L., and Jungst, S. B. (2001). Selection for lean growth efficiency in Duroc pigs influences pork quality. J. Anim. Sci. 79, 2075-2085.
21. Muñoz, G., Alves, E., Fernandez, A., Ovilo, C., Barragan, C., Estelle, J., Quintanilla, R., Folch, J. M., Silio, L., Rodriguez, M. C., and Fernandez, A. I. (2007). QTL detection on porcine chromosome 12 for fatty-acid composition and association analyses of the fatty acid synthase, gastric inhibitory polypeptide and acetyl-coenzyme A carboxylase alpha genes. Anim. Genet. 38, 639-646.
22. Muñoz, M., Fernandez, A. I., Rodriguez, C., Barragan, C., Folch, J. M., Noguera, J. L., Silio, L., and Alves, E. (2010). "QTL scan in SSC12 for fatty acid composition of intramuscular fat using combined information of candidate genes, microsatellites and SNP chip," in 32 Conference of International Society of Animal Genetics, Edimburgh.
23. Muñoz, M., Alves, E., Ramayo-Caldas, Y., Casellas, J., Rodriguez, C., Folch, J. M., Silió, L., and Fernández, A. I. (2011). Recombination rates across porcine autosomes inferred from high-density linkage maps. Anim. Genet. doi: 10.1111/j.1365-2052.2011.02301.x
24. Nii, M., Hayashi, T., Tani, F., Niki, A., Mori, N., Fujishima-Kanaya, N., Komatsu, M., Aikawa, K., Awata, T., and Mikawa, S. (2006). Quantitative trait loci mapping for fatty acid composition traits in perirenal and back fat using a Japanese wild boar × large white intercross. Anim. Genet. 37, 342-347.
25. Ovilo, C., Fernandez, A., Fernandez, A. I., Folch, J. M., Varona, L., Benitez, R., Nunez, Y., Rodriguez, C., and Silio, L. (2010). Hypothalamic expression of porcine leptin receptor (LEPR), neuropeptide Y (NPY), and cocaine- and amphetamine-regulated transcript (CART) genes is influenced by LEPR genotype. Mamm. Genome 21, 583-591.
26. Ovilo, C., Perez-Enciso, M., Barragan, C., Clop, A., Rodriquez, C., Oliver, M. A., Toro, M. A., and Noruera, J. L. (2000). A QTL for intramuscular fat and back fat thickness is located on porcine chromosome 6. Mamm. Genome 11, 344-346.
27. Pamplona, R., Portero-Otin, M., Riba, D., Ruiz, C., Prat, J., Bellmunt, M. J., and Barja, G. (1998). Mitochondrial membrane peroxidizability index is inversely related to maximum life span in mammals. J. Lipid Res. 39, 1989-1994.
28. Perez-Enciso, M., and Misztal, I. (2011). Qxpak.5: old mixed model solutions for new genomics problems. BMC Bioinformatics 12, 202. doi: 10.1186/1471-2105-12-202
29. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., De Bakker, P. I., Daly, M. J., and Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575.
30. Quintanilla, R., Pena, R. N., Gallardo, D., Canovas, A., Ramirez, O., Diaz, I., Noguera, J. L., and Amills, M. (2011). Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects. J. Anim. Sci. 89, 2963-2971.
31. Sanchez, M. P., Iannuccelli, N., Basso, B., Bidanel, J. P., Billon, Y., Gandemer, G., Gilbert, H., Larzul, C., Legault, C., Riquet, J., Milan, D., and Le Roy, P. (2007). Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc × Large White cross. BMC Genet. 8, 55. doi: 10.1186/1471-2156-8-55
32. Schwab, C. R., Mote, B. E., Du, Z. Q., Amoako, R., Baas, T. J., and Rothschild, M. F. (2009). An evaluation of four candidate genes for use in selection programmes aimed at increased intramuscular fat in Duroc swine. J. Anim. Breed. Genet. 126, 228-236.
33. Serra, X., Gil, F., Pérez-Enciso, M., Oliver, M. A., Vázquez, J. M., Gispert, M., Díaz, I., Moreno, F., Latorre, R., and Noguera, J. L. (1998). A comparision of carcass, meat quality and histochemical characterisitics of Iberian (Guadyerbas line) and Landrace pigs. Livest. Prod. Sci. 56, 215-223.
34. Storey, J. D., and Tibshirani, R. (2003). Statistical significance for genome wide studies. Proc. Natl. Acad. Sci. U.S.A. 100, 9440-9445.
35. Trivedi, D., and Padinjat, R. (2007). RdgB proteins: functions in lipid homeostasis and signal transduction. Biochim. Biophys. Acta 1771, 692-699.
36. Tsai, S., Cassady, J. P., Freking, B. A., Nonneman, D. J., Rohrer, G. A., and Piedrahita, J. A. (2006). Annotation of the Affymetrix porcine genome microarray. Anim. Genet. 37, 423-424.
37. Uemoto, Y., Soma, Y., Sato, S., Ishida, M., Shibata, T., Kadowaki, H., Kobayashi, E., and Suzuki, C. (2011). Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Anim. Genet. doi: 10.1111/j.1365-2052.2011.02218.x
38. Varona, L., Gomez-Raya, L., Rauw, W. M., and Noguera, J. L. (2005). A simulation study on the detection of causal mutations from F2 experiments. J. Anim. Breed. Genet. 122, 30-36.
39. Ventanas, S., Ventanas, J., Tovar, J., Garcia, C., and Estevez, M. (2007). Extensive feeding versus oleic acid and tocopherol enriched mixed diets for the production of Iberian dry-cured hams: effect on chemical composition, oxidative status and sensory traits. Meat Sci. 77, 246-256.
40. Webb, E. C., and O'Neill, H. A. (2008). The animal fat paradox and meat quality. Meat Sci. 80, 28-36.
41. Wirtz, K. W. (1991). Phospholipid transfer proteins. Annu. Rev. Biochem. 60, 73-99.
42. Wood, J. D., Enser, M., Fischer, A. V., Nute, G. R., Sheard, P. R., Richardson, R. I., Hughes, S. I., and Whittington, F. M. (2008). Fat deposition, fatty acid composition and meat quality: a review. Meat Sci. 78, 343-358.
43. Zhao, H. H., Rothschild, M. F., Fernando, R. L., and Dekkers, J. C. M. (2003). Tests of candidate genes in breed cross populations for QTL mapping in livestock. Mamm. Genome 14, 472-482.