Transcriptome analysis reveals key information on improving duck yolk lipid contents induced by dietary fish oil or flaxseed oil

References

• Antruejo A, Azcona JO, Garcia PT, Gallinger C, Rosmini M, Ayerza R, Coates W, Perez CD. 2011. Omega-3 enriched egg production: the effect of alpha -linolenic omega -3 fatty acid sources on laying hen performance and yolk lipid content and fatty acid composition. Br Poult Sci. 52(6):750–760.
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 25(1):25–29.
   PubMed Web of Science ®Google Scholar
• Audic S, Claverie JM. 1997. The significance of digital gene expression profiles. Genome Res. 7(10):986–995.
   PubMed Web of Science ®Google Scholar
• Basmacioglu H, Cabuk M, Unal K, Ozkan K, Akkan S, Yalcin H. 2004. Effects of dietary fish oil and flax seed on cholesterol and fatty acid composition of egg yolk and blood parameters of laying hens. S Afr J Anim Sci. 33(4):266–273.
   Web of Science ®Google Scholar
• Chen X, Du X, Shen J, Lu L, Wang W. 2017. Original research: effect of various dietary fats on fatty acid profile in duck liver: efficient conversion of short-chain to long-chain omega-3 fatty acids. Exp Biol Med (Maywood). 242(1):80–87.
   PubMed Web of Science ®Google Scholar
• Cherian G, Wolfe FW, Sim JS. 1996. Dietary oils with added tocopherols: effects on egg or tissue tocopherols, fatty acids, and oxidative stability. Poult Sci. 75(3):423–431.
   PubMed Web of Science ®Google Scholar
• Chuang SS, Helvig C, Taimi M, Ramshaw HA, Collop AH, Amad M, White JA, Petkovich M, Jones G, Korczak B. 2004. CYP2U1, a novel human thymus- and brain-specific cytochrome P450, catalyzes omega- and (omega-1)-hydroxylation of fatty acids. J Biol Chem. 279(8):6305–6314.
   PubMed Web of Science ®Google Scholar
• Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 21(18):3674–3676.
   PubMed Web of Science ®Google Scholar
• Couch JR, Saloma AE. 1973. Effect of diet on triglyceride structure and composition of egg yolk lipids. Lipids. 8(7):385–392.
   PubMed Web of Science ®Google Scholar
• Cruickshank EM. 1934. Studies in fat metabolism in the fowl: the composition of the egg fat and depot fat of the fowl as affected by the ingestion of large amounts of different fats. Biochem J. 28(3):965–977.
   PubMedGoogle Scholar
• David SJ. 2016. Dietary cholesterol and egg yolk should be avoided by patients at risk of vascular disease. J Transl Int Med. 4(1):20–24.
   PubMed Web of Science ®Google Scholar
• Deng W, Dong XF, Tong JM, Xie TH, Zhang Q. 2012. Effects of an aqueous alfalfa extract on production performance, egg quality and lipid metabolism of laying hens. J Anim Physiol An N. 96(1):85–94.
   PubMed Web of Science ®Google Scholar
• Du X, Liu Y, Lu L, Wang W, Zeng T, Tian Y, Xu X, Shen J, Niu D, Lu Y. 2017. Effects of dietary fats on egg quality and lipid parameters in serum and yolks of Shan Partridge duck. Poult Sci. 96(5):1184–1190.
   PubMed Web of Science ®Google Scholar
• Geiker N, Larsen ML, Dyerberg J, Stender S, Astrup A. 2018. Egg consumption, cardiovascular diseases and type 2 diabetes. Eur J Clin Nutr. 72(1):44–56.
   PubMed Web of Science ®Google Scholar
• Giusto NM, Pasquare SJ, Salvador GA, Castagnet PI, Roque ME, Ilincheta DBM. 2000. Lipid metabolism in vertebrate retinal rod outer segments. Prog Lipid Res. 39(4):315–391.
   PubMed Web of Science ®Google Scholar
• Graves JP, Gruzdev A, Bradbury JA, DeGraff LM, Li H, House JS, Hoopes SL, Edin ML, Zeldin DC. 2015. Quantitative polymerase chain reaction analysis of the mouse Cyp2j subfamily: tissue distribution and regulation. Drug Metab Dispos. 43(8):1169–1180.
   PubMed Web of Science ®Google Scholar
• Gregory MK, James MJ. 2014. Functional characterization of the duck and Turkey fatty acyl elongase enzymes ELOVL5 and ELOVL2. J Nutr. 144(8):1234–1239.
   PubMed Web of Science ®Google Scholar
• Guo H, Liu G, Zhong R, Wang Y, Wang D, Xia M. 2012. Cyanidin-3-O-beta-glucoside regulates fatty acid metabolism via an AMP-activated protein kinase-dependent signaling pathway in human HepG2 cells. Lipids Health Dis. 11:10.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1):27–30.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. 2012. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 40(Database issue):D109–D114.
   PubMed Web of Science ®Google Scholar
• Li-Hawkins J, Gafvels M, Olin M, Lund EG, Andersson U, Schuster G, Bjorkhem I, Russell DW, Eggertsen G. 2002. Cholic acid mediates negative feedback regulation of bile acid synthesis in mice. J Clin Invest. 110(8):1191–1200.
   PubMed Web of Science ®Google Scholar
• Liu WM, Lai SJ, Lu LZ, Shi FX, Zhang J, Liu Y, Yu B, Tao ZR, Shen JD, Li GQ, et al. 2011. Effect of dietary fatty acids on serum parameters, fatty acid compositions, and liver histology in Shaoxing laying ducks. J Zhejiang Univ Sci B. 12(9):736–743.
   PubMed Web of Science ®Google Scholar
• Lundblad MS, Stark K, Eliasson E, Oliw E, Rane A. 2005. Biosynthesis of epoxyeicosatrienoic acids varies between polymorphic CYP2C enzymes. Biochem Biophys Res Commun. 327(4):1052–1057.
   PubMed Web of Science ®Google Scholar
• Maere S, Heymans K, Kuiper M. 2005. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics. 21(16):3448–3449.
   PubMed Web of Science ®Google Scholar
• Munoz G, Ovilo C, Noguera JL, Sanchez A, Rodriguez C, Silio L. 2003. Assignment of the fatty acid synthase (FASN) gene to pig chromosome 12 by physical and linkage mapping. Anim Genet. 34(3):234–235.
   PubMed Web of Science ®Google Scholar
• Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, et al. 2003. TIGR gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics. 19(5):651–652.
   PubMed Web of Science ®Google Scholar
• Soupene E, Kuypers FA. 2008. Mammalian long-chain acyl-CoA synthetases. Exp Biol Med (Maywood. 233(5):507–521.
   PubMed Web of Science ®Google Scholar
• Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al. 2003. The COG database: an updated version includes eukaryotes. Bmc Bioinformatics. 4:41.
   PubMed Web of Science ®Google Scholar
• Trapnell C, Pachter L, Salzberg SL. 2009. Tophat: discovering splice junctions with RNA-Seq. Bioinformatics. 25(9):1105–1111.
   PubMed Web of Science ®Google Scholar
• Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S, Kong L, Gao G, Li CY, Wei L. 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39(Web Server issue):W316–W322.
   PubMedGoogle Scholar
• Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J. 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res. 34(Web Server issue):W293–W297.
   PubMed Web of Science ®Google Scholar