Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle

[EN] An mRNA expression study has been performed in 20-to 25-min postmortem-obtained samples from Longissimus dorsi muscle of 59 Duroc x Landrace/Large White (LD/LW) pigs to search for gene sequences related to meat quality (pH(24), pH(45), "Lab" color coordinates, curing yield, and exudation at 3 different times) or meat composition [intramuscular fat, content of several fatty acids (C16:0, C18:0, C18:1, and C18:2), ratio of saturated, monounsaturated, and polyunsaturated fatty acids, and protein and humidity contents] traits to find targets for selection. Gene ontology analysis, biological pathway, and gene network studies all show that many more differentially expressed genes (506 vs. 279) are related to meat quality (Group P or perimortem characters) than to meat composition traits (Group L or whole life traits). The difference between the number of gene ontology terms annotated, biological pathways, and gene networks in groups P and L is notable due to the differences in the complexity of the "generation process" of P-traits and involvement of other tissues or organs in the generation of variability of L-traits. Also, interactions between differentially expressed genes were found in extracellular matrix (ECM)-receptor interaction, tumor growth factor (TGF)-beta signaling pathway, fatty acid elongation in mitochondria, and adipocytokine signaling pathway, indicating that a substantial fraction of the gene networks could be associated with interactions between differentially expressed genes related to traits under study. A large number of the most overexpressed genes are related to muscle development and functionality and repair mechanisms; they could be good candidates for breeding programs in which the main goal is to enhance meat quality.This work was supported by projects Diputacion General de Aragon PI043/09 to Luis Varona Aguado and AGL2008-01487 ALI to Pascual Lopez Buesa. Almudena Galve thanks the Diputacion General de Aragon for a predoctoral fellowship.Cánovas, A.; Varona, L.; Burgos, C.; Galve, A.; Carrodeguas, JA.; Ibáñez-Escriche, N.; Martin-Burriel, I.... (2012). Early postmortem gene expression and its relationship to composition and quality traits in pig Longissimus dorsi muscle. Journal of Animal Science. 90(10):3325-3336. https://doi.org/10.2527/jas.2011-4799332533369010Alexeyenko, A., & Sonnhammer, E. L. L. (2009). Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Research, 19(6), 1107-1116. doi:10.1101/gr.087528.108Bian, Z.-Y., Huang, H., Jiang, H., Shen, D.-F., Yan, L., Zhu, L.-H., … Li, H. (2010). LIM and Cysteine-Rich Domains 1 Regulates Cardiac Hypertrophy by Targeting Calcineurin/Nuclear Factor of Activated T Cells Signaling. Hypertension, 55(2), 257-263. doi:10.1161/hypertensionaha.109.135665BIERIE, B., & MOSES, H. (2006). TGF-β and cancer. Cytokine & Growth Factor Reviews, 17(1-2), 29-40. doi:10.1016/j.cytogfr.2005.09.006Bligh, E. G., & Dyer, W. J. (1959). A RAPID METHOD OF TOTAL LIPID EXTRACTION AND PURIFICATION. Canadian Journal of Biochemistry and Physiology, 37(1), 911-917. doi:10.1139/y59-099Burgos, C., Moreno, C., Carrodeguas, J. A., Barcelona, J. A., Tarrafeta, L., & López-Buesa, P. (2010). The influence of diet, sex, IGF2 and RYR1 genotypes and anatomical location on pork loin composition. Journal of Food Composition and Analysis, 23(4), 307-313. doi:10.1016/j.jfca.2009.12.005Cánovas, A., Estany, J., Tor, M., Pena, R. N., & Doran, O. (2009). Acetyl-CoA carboxylase and stearoyl-CoA desaturase protein expression in subcutaneous adipose tissue is reduced in pigs selected for decreased backfat thickness at constant intramuscular fat content1. Journal of Animal Science, 87(12), 3905-3914. doi:10.2527/jas.2009-2091C�novas, A., Quintanilla, R., Amills, M., & Pena, R. N. (2010). Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits. BMC Genomics, 11(1), 372. doi:10.1186/1471-2164-11-372Cánovas, A., Quintanilla, R., Gallardo, D., Díaz, I., Noguera, J. L., Ramírez, O., & Pena, R. N. (2009). Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme. animal, 4(02), 224-233. doi:10.1017/s1751731109991145Casas-Terradellas, E., Tato, I., Bartrons, R., Ventura, F., & Rosa, J. L. (2008). ERK and p38 pathways regulate amino acid signalling. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1783(12), 2241-2254. doi:10.1016/j.bbamcr.2008.08.011Casellas, J., Piedrafita, J., & Varona, L. (2007). Bayes factor for testing between different structures of random genetic groups: A case study using weaning weight in Bruna dels Pirineus beef cattle. Genetics Selection Evolution, 39(1), 39. doi:10.1186/1297-9686-39-1-39Dhillon, A. S., Hagan, S., Rath, O., & Kolch, W. (2007). MAP kinase signalling pathways in cancer. Oncogene, 26(22), 3279-3290. doi:10.1038/sj.onc.1210421Finley, D. (2009). Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome. Annual Review of Biochemistry, 78(1), 477-513. doi:10.1146/annurev.biochem.78.081507.101607Fujii, J., Otsu, K., Zorzato, F., de Leon, S., Khanna, V., Weiler, J., … MacLennan, D. (1991). Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Science, 253(5018), 448-451. doi:10.1126/science.1862346Geier, C., Gehmlich, K., Ehler, E., Hassfeld, S., Perrot, A., Hayess, K., … Özcelik, C. (2008). Beyond the sarcomere: CSRP3 mutations cause hypertrophic cardiomyopathy. Human Molecular Genetics, 17(18), 2753-2765. doi:10.1093/hmg/ddn160Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., … Zhang, J. (2004). Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80Glover, J. R., & Lindquist, S. (1998). Hsp104, Hsp70, and Hsp40. Cell, 94(1), 73-82. doi:10.1016/s0092-8674(00)81223-4Guàrdia, M. D., Estany, J., Balasch, S., Oliver, M. A., Gispert, M., & Diestre, A. (2005). Risk assessment of DFD meat due to pre-slaughter conditions in pigs. Meat Science, 70(4), 709-716. doi:10.1016/j.meatsci.2005.03.007He, Z.-H., Hu, Y., Li, Y.-C., Bao, D.-P., Ruiz, J. R., & Lucia, A. (2010). Polymorphisms in the calcineurin genes are associated with the training responsiveness of cardiac phenotypes in Chinese young adults. European Journal of Applied Physiology, 110(4), 761-767. doi:10.1007/s00421-010-1558-8Hirosawa, M., Nakahara, M., Otosaka, R., Imoto, A., Okazaki, T., & Takahashi, S. (2009). The p38 pathway inhibitor SB202190 activates MEK/MAPK to stimulate the growth of leukemia cells. Leukemia Research, 33(5), 693-699. doi:10.1016/j.leukres.2008.09.028Honikel, K. O. (1998). Reference methods for the assessment of physical characteristics of meat. Meat Science, 49(4), 447-457. doi:10.1016/s0309-1740(98)00034-5Iacobazzi, V., Invernizzi, F., Baratta, S., Pons, R., Chung, W., Garavaglia, B., … Taroni, F. (2004). Molecular and functional analysis ofSLC25A20 mutations causing carnitine-acylcarnitine translocase deficiency. Human Mutation, 24(4), 312-320. doi:10.1002/humu.20085McFate, T., Mohyeldin, A., Lu, H., Thakar, J., Henriques, J., Halim, N. D., … Verma, A. (2008). Pyruvate Dehydrogenase Complex Activity Controls Metabolic and Malignant Phenotype in Cancer Cells. Journal of Biological Chemistry, 283(33), 22700-22708. doi:10.1074/jbc.m801765200Medina, I., Carbonell, J., Pulido, L., Madeira, S. C., Goetz, S., Conesa, A., … Dopazo, J. (2010). Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research, 38(suppl_2), W210-W213. doi:10.1093/nar/gkq388Milan, D. (2000). A Mutation in PRKAG3 Associated with Excess Glycogen Content in Pig Skeletal Muscle. Science, 288(5469), 1248-1251. doi:10.1126/science.288.5469.1248Park, B. Y., Kim, J. H., Cho, S. H., Hah, K. H., Lee, S. H., Choi, C. H., … Hwang, I. H. (2006). Evidence of Significant Effects of Stunning and Chilling Methods on PSE Incidences. Asian-Australasian Journal of Animal Sciences, 20(2), 257-262. doi:10.5713/ajas.2007.257Sabatini, D. M. (2006). mTOR and cancer: insights into a complex relationship. Nature Reviews Cancer, 6(9), 729-734. doi:10.1038/nrc1974Sosnicki, A. A., & Newman, S. (2010). The support of meat value chains by genetic technologies. Meat Science, 86(1), 129-137. doi:10.1016/j.meatsci.2010.04.034Weiskirchen, R., & Günther, K. (2003). The CRP/MLP/TLP family of LIM domain proteins: Acting by connecting. BioEssays, 25(2), 152-162. doi:10.1002/bies.10226Wu, P., Blair, P. V., Sato, J., Jaskiewicz, J., Popov, K. M., & Harris, R. A. (2000). Starvation Increases the Amount of Pyruvate Dehydrogenase Kinase in Several Mammalian Tissues. Archives of Biochemistry and Biophysics, 381(1), 1-7. doi:10.1006/abbi.2000.1946Wu, Z., Irizarry, R. A., Gentleman, R., Martinez-Murillo, F., & Spencer, F. (2004). A Model-Based Background Adjustment for Oligonucleotide Expression Arrays. Journal of the American Statistical Association, 99(468), 909-917. doi:10.1198/016214504000000683Xu, X., Zhao, Y., & Simon, R. (2007). Gene Set Expression Comparison kit for BRB-ArrayTools. Bioinformatics, 24(1), 137-139. doi:10.1093/bioinformatics/btm54