An association analysis between a polymorphism in the SEC24A gene and lipid traits recorded in Duroc pigs

References

• Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B. 57(1):289–300.
   Google Scholar
• Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30(15):2114–2120.
   PubMed Web of Science ®Google Scholar
• Bonifacino JS, Glick BS. 2004. The mechanisms of vesicle budding and fusion. Cell. 116(2):153–166.
   PubMed Web of Science ®Google Scholar
• Cayuela JM, Garrido MD, Bañón SJ, Ros JM. 2003. Simultaneous HPLC analysis of alpha-tocopherol and cholesterol in fresh pig meat. J Agric Food Chem. 51(5):1120–1124.
   PubMed Web of Science ®Google Scholar
• Chen XW, Wang H, Bajaj K, Zhang P, Meng ZX, Ma D, Bai Y, Liu HH, Adams E, Baines A, et al. 2013. SEC24A deficiency lowers plasma cholesterol through reduced PCSK9 secretion. Elife. 2013(2):444.
   Google Scholar
• Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16(22):10881–10890.
   PubMed Web of Science ®Google Scholar
• Fossati P, Prencipe L. 1982. Serum triglycerides determined colorimetrically with an enzyme that produces hydrogen peroxide. Clin Chem. 28(10):2077–2080.
   PubMed Web of Science ®Google Scholar
• Friedewald WT, Levy RI, Fredrickson DS. 1972. Estimation of the concentration of low-density lipoprotein cholesterol in plasma, without use of the preparative ultracentrifuge. Clin Chem. 18(6):499–502.
   PubMed Web of Science ®Google Scholar
• Gallardo D, Quintanilla R, Varona L, Díaz I, Ramírez O, Pena RN, 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(4):410–417.
   PubMed Web of Science ®Google Scholar
• Gallardo D, Pena RN, Amills M, Varona L, Ramírez O, Reixach J, Díaz I, Tibau J, Soler J, Prat-Cuffi JM, et al. 2008. Mapping of quantitative trait loci for cholesterol, LDL, HDL, and triglyceride serum concentrations in pigs. Physiol Genomics. 35(3):199–209.
   PubMed Web of Science ®Google Scholar
• González-Prendes R, Quintanilla R, Cánovas A, Manunza A, Figueiredo Cardoso T, Jordana J, Noguera JL, Pena RN, Amills M. 2017. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits. Sci Rep. 7:39830.
   PubMed Web of Science ®Google Scholar
• Groenen MAM, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens H-J, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature. 491(7424):393–398.
   PubMed Web of Science ®Google Scholar
• Lagace TA. 2014. PCSK9 and LDLR degradation: regulatory mechanisms in circulation and in cells. Curr Opin Lipidol. 25(5):387–393.
   PubMed Web of Science ®Google Scholar
• Lee MCS, Miller EA, Goldberg J, Orci L, Schekman R. 2004. Bi-directional protein transport between the ER and Golgi. Annu Rev Cell Dev Biol. 20:87–123.
   PubMed Web of Science ®Google Scholar
• Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 3:13033997. http://arxiv.org/abs/1303.3997.
   Google Scholar
• Mach N, Devant M, Díaz I, Font-Furnols M, Oliver MA, García JA, Bach A, 2006. Increasing the amount of n-3 fatty acid in meat from young Holstein bulls through nutrition. J Anim Sci. 84(11):3039–3048.
   PubMed Web of Science ®Google Scholar
• Madeira F, Park YM, Lee J, Buso N, Gur T, Madhusoodanan N, Basutkar P, Tivey ARN, Potter SC, Finn RD, et al. 2019. The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47(W1):W636–W641.
   PubMed Web of Science ®Google Scholar
• Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. 2021. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genet Sel Evol. 53(1):43.
   PubMed Web of Science ®Google Scholar
• Mármol-Sánchez E, Luigi-Sierra MG, Quintanilla R, Amills M. 2020. Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene. Anim Genet. 51(1):106–110.
   PubMed Web of Science ®Google Scholar
• McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20(9):1297–1303.
   PubMed Web of Science ®Google Scholar
• Quintanilla R, Pena RN, Gallardo D, Cánovas A, Ramírez O, Díaz I, Noguera JL, Amills M. 2011. Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects. J Anim Sci. 89(10):2963–2971.
   PubMed Web of Science ®Google Scholar
• Rafai N, Warnick GR. 1994. Lipoproteins and apolipoproteins. Laboratory measurement of lipids. Washington (DC): AACC.
   Google Scholar
• Richmond W. 1992. Analytical reviews in clinical biochemistry: the quantitative analysis of cholesterol. Ann Clin Biochem. 29(6):577–597.
   PubMedGoogle Scholar
• Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, et al. 2020. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience. 9(6):1–14.
   Web of Science ®Google Scholar
• Zanetti G, Pahuja KB, Studer S, Shim S, Schekman R. 2011. COPII and the regulation of protein sorting in mammals. Nat Cell Biol. 14(1):20–28.
   PubMed Web of Science ®Google Scholar
• Zhou X, Stephens M. 2012. Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 44(7):821–824.
   PubMed Web of Science ®Google Scholar