Rothschild MF. Porcine genomics delivers new tools and results: This little piggy did more than just go to market. Genetic Res. 2004;83:1–6.
Article
CAS
Google Scholar
Jiang Z, Rothschild MF. Swine genome science comes of age. Int J Biol Sci. 2007;3(3):129–31.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schook L, Beattie C, Beever J, Donovan S, Jamison R, Zuckermann F, et al. Swine in biomedical research: creating the building blocks of animal models. Anim Biotechnol. 2005;16:183–90.
Article
PubMed
Google Scholar
Lunney JK. Advances in swine biomedical model genomics. Int J Biol Sci. 2007;3(3):179–84.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tang Z, Li Y, Wan P, Li X, Zhao S, Liu B, et al. Long SAGE analysis of skeletal muscle at three prenatal stages in Tongcheng and Landrace pigs. Genome Biol. 2007;8:R115. doi:10.1186/gb-2007-8-6-r115.
Article
PubMed Central
PubMed
Google Scholar
Zak R, Martin AF, Prior G, Rabinowitz M. Comparison of turnover of several myofibrillar proteins and critical evaluation of double isotope method. J Biol Chem. 1977;252:3430–5.
CAS
PubMed
Google Scholar
Low RB, Vournakis JN, Rich A. Identification of separate polysomes active in the synthesis of the light and heavy chains of myosin. Biochem. 1971;10:1813–8.
Article
CAS
Google Scholar
Xu H, Xu G, Wang D, Ma J, Wan L. Molecular cloning, sequence identification and expression analysis of novel caprine MYLPF gene. Mole Biol Rep. 2013;40:2565–72. doi:10.1007/s11033-012-2342-0.
Article
CAS
Google Scholar
Ryu YC, Lee MH, Lee SK, Kim BC. Effects of muscle mass and fiber type composition of Longissimus dorsi muscle on postmortem metabolic rate and meat quality in pigs. J Muscle Foods. 2006;17:343–53.
Article
CAS
Google Scholar
Karlsson AH, Klont RE, Fernandez X. Skeletal muscle fibers as factors for pork quality. Livest Prod Sci. 1999;60:255–69.
Article
Google Scholar
Depreux FF, Grant AL, Anderson DB, Gerrard DE. Paylean alters myosin heavy chain isoform content in pig muscle. J Anim Sci. 2002;80:1888–94.
CAS
PubMed
Google Scholar
Baldwin KM, Haddad F. Effects of different activity and inactivity paradigms on myosin heavy chain gene expression in striated muscle. J Appl Physiol. 2001;90(1):345–57.
Article
CAS
PubMed
Google Scholar
Lijun W, Xiaolin L, Fubiao N, Hongliang W, Hua H, Yulan G. Single nucleotide polymorphisms, haplotypes and combined genotypes in MYH3 gene and their associations with growth and carcass traits in Qinchuan cattle. Mole Biol Rep. 2013;40:417–26.
Article
Google Scholar
Gorni C, Iacuaniello S, Castiglioni B, Pagnacco G, Pig MP, KALRN. MYH1, MLC2V, SNX13, AK1, and PPIA loci RH mapping and chromosome position refining. Genet Mole Res. 2008;7(4):982–5.
Article
CAS
Google Scholar
Lefaucheur L, Hoffman RK, Gerrard DE, Okamura CS, Rubinstein N, Kelly A. Evidence for three adult fast myosin heavy chain isoforms in type II skeletal muscle fibers in pigs. J Anim Sci. 1998;76:1584–93.
CAS
PubMed
Google Scholar
Zhang X, Dube TJ, Esser KA. Working around the clock: circadian rhythms and skeletal muscle. J Appl Physiol. 2009;107:1647–54. doi:10.1152/japplphysiol.00725.2009.
Article
PubMed Central
PubMed
Google Scholar
Luo W, Cheng D, Chen S, Wang L, Li Y, Ma X, et al. Genome-wide association analysis of meat quality trails in a Procine Large White X Minzhu intercross population. Int J Biol Sci. 2012;8(4):580–95. doi:10.7150/ijbs.3614.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cho IC, Park HB, Yoo CK, Lee GJ, Lim HT, Lee JB, et al. QTL analysis of white blood cell, platelet and red blood cell, related traits in an F2 intercross between Landrace and Korean Native Pigs. Anim Genet. 2011;42:621–6.
Article
CAS
PubMed
Google Scholar
Ghosh M, Sodhi SS, Song KD, Kim JH, Mongre RK, Sharma N, et al. Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire. Anim Genet. 2015;46(3):255–64.
Article
CAS
PubMed
Google Scholar
Kim KI, Lee JH, Li K, Zhang YP, Lee SS, Gongora J, et al. Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism. Anim Genet. 2002;33:19–25.
Article
CAS
PubMed
Google Scholar
Murani E, Muraniova M, Ponsuksili S, Schellander K, Wimmers K. Identification of genes differentially expressed during prenatal development of skeletal muscle in two pig breeds differing in muscularity. BMC Dev Biol. 2007;7:107.
Article
Google Scholar
Xu L, Zhao F, Ren H, Li L, Lu J, Liu J, et al. Co-expression analysis of fetal weight-related genes in ovine skeletal muscle during mid and late fetal development stages. Int J Biol Sci. 2014;10(9):1039–50. doi:10.7150/ijbs.9737.
Article
PubMed Central
PubMed
Google Scholar
Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next generation sequencing data. Nat Rev Genet. 2011;12(6):443–51.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mitra K, Carvunis AR, Ramesh SK, Ideker T. Integrative approaches for finding modular structure in biological networks. Nat Rev Genet. 2013;14:719–32. doi:10.1038/nrg3552.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang L, Zhao X, Tang X. Predicting disease-related proteins based on clique backbone in Protein-Protein interaction network. Int J Biol Sci. 2014;10(7):677–88. doi:10.7150/ijbs.84.
Article
PubMed Central
CAS
PubMed
Google Scholar
Barabasi AL, Oltvai ZN. Network biology: understanding the cell’s functional organization. Nat Rev Genet. 2004;5:101–13. doi:10.1038/nrg1272.
Article
CAS
PubMed
Google Scholar
Erb HN. A statistical approach for calculating the minimum number of animals needed in research. ILAR J. 1990;32(1):11–6. doi:10.1093/ilar.32.1.11.
Article
Google Scholar
Charan J, Kantharia ND. How to calculate sample size in animal studies? J Pharmacol Pharmacother. 2013;4(4):303–6.
Article
PubMed Central
PubMed
Google Scholar
Xiong X, Liu X, Zhou L, Yang J, Yang B, Ma H, et al. Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs. Mamm Genome. 2015;26(3–4):181–90. doi:10.1007/s00335-015-9558-y.
Article
PubMed
Google Scholar
Yoo CK, Park HB, Lee JB, Jung EJ, Kim BM, Kim HI, et al. QTL analysis of body weight and carcass body length traits in an F2 intercross between Landrace and Korean native pigs. Anim Genet. 2014;45:589–92.
Article
CAS
PubMed
Google Scholar
Kerstens HHD, Kollers S, Kommadath A, Rosario del M, Dibbits B, Kinders MS, et al. Mining for single nucleotide polymorphisms in pig genome sequence data. BMC Genomic. 2009;10:4. doi:10.1186/1471-2164-10-4.
Article
Google Scholar
Wang J, Wang H, Jiang J, Kang H, Feng X, Zhang Q, et al. Identification of genome-wide copy number variations among diverse pig breeds using SNP genotyping arrays. PLos One. 2013;8(7):e68683. doi:10.1371/journal.pone.0068683.
Article
PubMed Central
CAS
PubMed
Google Scholar
Singh AK, Abhimanyu, Yadav AB, Sharma S, Garg R, Bose M, et al. HLA-DRB1*1501 and VDR polymorphisms and survival of Mycobacterium tuberculosis in human macrophages exposed to inhalable microparticles. Pharmacogeno. 2013;14(5): 531–40
King DP, Zhao Y, Sangoram AM, Wilsbacher LD, Tanaka M, Antoch M, et al. Positional cloning of the mouse circadian clock gene. Cell. 1997;89:641–53.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sodhi SS, Ghosh M, Song DK, Sharma N, Kim JH, Kim NE, et al. An approach to Identify SNPs in the gene encoding Acetyl-CoA Acetyltransferase-2 (ACAT-2) and their proposed role in metabolic processes in pig. PLoS One. 2014;9:e102432. doi:10.1371/journal.pone.0102432.
Article
PubMed Central
PubMed
Google Scholar
McGuigan J, You Y, Liu C. RNA-Seq analysis with NextGENe Software. J Biomol Tech. 2011;22:S35. PMC3186635.
PubMed Central
Google Scholar
Keller A, Harz C, Matzas M, Meder B, Katus HA, Ludwig N, et al. Identification of novel SNPs in glioblastoma using targeted resequencing. PLoS One. 2011;6:e18158. doi:10.1371/journal.pone.0018158.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cisneros F, Ellis M, Baker DH, Easter RA, McKeith FK. The influence of short-term feeding of amino acid-deficient diets and high dietary leucine levels on the intramuscular fat content of pig muscle. Anim Sci. 1996;63:517–22.
Article
CAS
Google Scholar
Li P, Yin YL, Kim SW, Wu G. Amino acids and immune function. Br J Nutr. 2007;98:237–52.
Article
CAS
PubMed
Google Scholar
Kim J, Cho S, Anolles CK, Kim H, Ryu YC. Genome wide detection and characterization of positive selection in Korean Native Pig from Jeju Island. BMC Genet. 2015;16:3. doi:10.1186/s12863-014-0160-1.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zhang J, Yin J, Zhou X, Li F, Ni J, Bing D. Effects of lower dietary Lysine and energy content on carcass characteristics and meat quality in growing finishing pigs. Asian Aust J Anim Sci. 2008;21:1758–93.
Google Scholar
Gobert M, Sayd T, Gatellier P, Lhoutellier S. Application to proteomics to understand and modify meat quality. Meat Sci. 2014;98:539–43.
Article
CAS
PubMed
Google Scholar
Dilger RN, Toue S, Kimura T, Sakai R, Baker DH. Excess Dietary L-Cysteine, but not L-Cystine, is lethal for chicks but not for rats or pigs. J Nutr. 2007;137(2):331–8.
CAS
PubMed
Google Scholar
Wu G, Bazzer WF, Davis TA, Jaeer LA, Johnson GA, Kim SW, et al. Important roles for the arginine family of amino acids in swine nutrition and production. Livest Sci. 2007;112:8–22.
Article
Google Scholar
Breuer Jr LH, Warner RG, Bnton DA, Loosli JK. Dietary requirement for Asparagine and its metabolism in rats. J Nutr. 1966;88:143–50.
CAS
PubMed
Google Scholar
Chang TW, Goldberg AL. The metabolic fates of amino acids and the formation of Glutamine in skeletal muscle. J Bio Chem. 1978;253(10):3685–95.
CAS
Google Scholar
Wang W, Wu Z, Lin G, Hu S, Wang B, Dai Z, et al. Glycine stimulates protein synthesis and inhibits oxidative stress in pig small intestinal epithelial calls. J Nutr. 2014;144(10):1540–8.
Article
CAS
PubMed
Google Scholar
Zou XT, Zheng GH, Fang XJ, Jiang JF. Effects of glutamine on growth performance of weanling piglets. Czech J Anim Sci. 2006;51(10):444–8.
CAS
Google Scholar
Wang X, Qiao S, Yin Y, Yue L, Wang Z, Wu G. A deficiency or excess of dietary Threonine reduces protein synthesis in jejunum and skeletal muscle of young pigs. J Nutr. 2007;137:1442–6.
CAS
PubMed
Google Scholar
Li X, Yang X, Shan B, Shi J, Xia D, Wegner J, et al. Meat quality is associated with muscle metabolic status but not contractile myofiber type composition in premature pigs. Meat Sci. 2009;81(1):218–23. doi:10.1016/j.meatsci.2008.07.022.
Article
CAS
PubMed
Google Scholar
Li Y, Xu Z, Li H, Xiong Y, Zuo B. Differential transcriptional analysis between red and white skeletal muscle of Chinese Meishan pigs. Inter J Biol Sci. 2010;6(4):350–60.
Article
CAS
Google Scholar
Agarwal SM, Raghav D, Singh H, Raghava GP. CCDB: a curated database of genes involved in cervix cancer. Nucleic Acids Res. 2010;39:D975–9. doi:10.1093/nar/gkq1024.
Article
PubMed Central
PubMed
Google Scholar
Wang LL, Li Y, Zhou SF. A bioinformatics approach for the phenotype prediction of nonsynonymous single nucleotide polymorphisms in human cytochromes P450. Drug Metab Dispos. 2009;37(5):977–91.
Article
PubMed
Google Scholar
Arkin MR, Wells JA. Small-molecule inhibitors of protein–protein interactions: progressing towards the dream. Nat Rev Drug Discov. 2004;3(4):301–17. doi:10.1038/nrd1343.
Article
CAS
PubMed
Google Scholar
Wang Z, Moult J. SNPs, protein structure, and disease. Hum Mutat. 2001;17(4):263–70.
Article
PubMed
Google Scholar
Priya DCG, Nagasundaram N. Molecular docking and molecular dynamics study on the effect of ERCC1 deleterious polymorphisms in ERCC1-XPF heterodimer. Appl Biochem Biotechnol. 2014;172(3):11266–81. doi:10.1007/s12010-013-0592-5.
Google Scholar
Garber JC. Guide for the Care and Use of Laboratory Animals. 8th ed. Washington, DC: The National Academies Press; 2011.
Google Scholar
Lionikas A, Meharg C, Derry JMJ, Ratkevicius A, Carroll AM, Vandenbergh DJ, et al. Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses. BMC Genomics. 2012;13:592.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bustin SA, Benes V, Garson JA, Helleman J, Huggett J, Kubista M, et al. The MIQE guidelines: Minimum information for publication of quantitative Real-Time PCR experiments. Clin Chem. 2009;55:611–22.
Article
CAS
PubMed
Google Scholar
Sodhi SS, Song KD, Ghosh M, Sharma N, Lee SJ, Kim JH, et al. Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig. Gene. 2014;233–242.
George PDC, Rajith B. Computational refinement of functional single nucleotide polymorphisms associated with ATM gene. PLoS One. 2012;7(4):e34573. doi:10.1371/journal.pone.0034573.
Article
Google Scholar
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics. 2009;25(21):2744–50.
Article
PubMed Central
CAS
PubMed
Google Scholar
Venselaar H, Beek te AHT, Kuiper RKP, Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable disease. An e-science approach with life scientist friendly interfaces. BMC Bioinformatics. 2010;11:548.
Article
PubMed Central
PubMed
Google Scholar
Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, et al. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41:D808–15. doi:10.1093/nar/gks1094.
Article
PubMed Central
CAS
PubMed
Google Scholar
Erkens T, VanPoucke M, Vandesompele J, Goossens K, VanZevere A, Peelman LJ. Development of a new set of reference genes for normalization of realtime RT-PCR data of porcine back fat and longissimus dorsi muscle, and evaluation with PPARGC1A. BMC Biotechnol. 2006;6:41. doi:10.1186/1472-6750-6-41.
Article
PubMed Central
PubMed
Google Scholar
Van Poucke M, Yerle M, Tuggle C, Piumi F, Genet C, VanZeveren A, et al. Integration of porcine chromosome 13 maps. Cytogenet Cell Genet. 2001;93(3–4):297–303.
Article
PubMed
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14(4):R36.
Article
PubMed Central
PubMed
Google Scholar
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29(1):308–11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hubbard T, Barker D, Birney E, Carmeron G, Chen Y, Clark L, et al. The ensemble genome database project. Nucleic Acids Res. 2002;30(1):38–41.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mi H, Muruganujan A, Casagrande JT, Thomas PD. Large-scale gene function analysis with the PANTHER classification system. Nat Protocol. 2013;8:1551–66.
Article
Google Scholar
Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 2000;28(1):27–30.
Article
PubMed Central
CAS
PubMed
Google Scholar
Liekens AML, Knijf JD, Daelemans W, Goethals B, Rijk PD, Del-Favero J. BioGraph: unsupervised biomedical knowledge discovery via automated hypothesis generation. Genome Biol. 2011;12(6):R57.
Article
PubMed Central
PubMed
Google Scholar
Chen J, Bardes EE, Aronow BJ, Jegga AG. ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009;37:W305–11. doi:10.1093/nar/gkp427.
Article
PubMed Central
CAS
PubMed
Google Scholar
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;1–12.
Hu ZL, Park CA, Reecy JM. Developmental progress and current status of the Animal QTLdb. Nucleic Acids Res. 2015;1. doi: 10.1093/nar/gkv1233
Ng PC, Henikoff S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31(13):3812–4.
Article
PubMed Central
CAS
PubMed
Google Scholar
Adzhubei IA, Schmidt S. peshkin Leonid, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Capriotti E, Fariselli P, Rossi I, Casadio R. A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics. 2008;9:S6.
Article
PubMed Central
PubMed
Google Scholar
Li B, Krishna VG, Mort ME, Xin F, Kamati KK, Cooper DN, et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics. 2009;25(21):2744–50.
Article
PubMed Central
CAS
PubMed
Google Scholar
Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Prot Sci. 2000;9:1753–73.
Article
CAS
Google Scholar
Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21(2):263–5.
Article
CAS
PubMed
Google Scholar