[1] Giuffra E, Kijas JMH, Amarger V, Carlborg Ö, Jeon JT, Andersson L. The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 2000, 154(4): 1785-1791.[2] Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. Recent and ongoing selection in the human genome. Nat Rev Genet, 2007, 8(11): 857-868.[3] Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics, 1987, 116(1): 153-159.[4] Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989, 123(3): 585-595.[5] Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics, 1993, 133(3): 693-709.[6] Fay JC, Wu CI. Hitchhiking under positive Darwinian selection. Genetics, 2000, 155(3): 1405-1413.[7] Li WH, Wu CI, Luo CC. A new method for estimating synonymous and nonsynonymous rates of nucleotide sub-stitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol, 1985, 2(2): 150-174.[8] McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature, 1991, 351(6328): 652-654.[9] Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. Detecting recent positive selection in the human genome from hap-lotype structure. Nature, 2002, 419(6909): 832-837.[10] Lewontin RC, Krakauer J. Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms. Genetics, 1973, 74(1): 175-195.[11] Wright S. Isolation by distance. Genetics, 1943, 28(2): 114-138.[12] Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NH, Zody MC, Anderson N, Biagi TM, Patterson N, Piel-berg GR, Kulbokas EJ 3rd, Comstock KE, Keller ET, Mesirov JP, von Euler H, Kämpe O, Hedhammar Å, Lander ES, Andersson G, Andersson L, Lindblad-Toh K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet, 2007, 39(11): 1321-1328.[13] Pariset L, Joost S, Marsan PA, Valentini A, Econogene Consortium (EC). Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genet, 2009, 10: 7.[14] Wahlberg P, Carlborg Ö, Foglio M, Tordoir X, Syvänen AC, Lathrop M, Gut IG, Siegel PB, Andersson L. Genetic analysis of an F2 intercross between two chicken lines divergently selected for body-weight. BMC Genomics, 2009, 10(1): 248.[15] Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, Heath S, Foulley JL, Gautier M. The genome response to artificial selection: a case study in dairy cattle. PloS One, 2009, 4(8): e6595.[16] Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, San Cristobal M, Servin B, McCulloch R, Whan V, Giet-zen K, Paiva S, Barendse W, Ciani E, Raadsma H, McE-wan J, Dalrymple B; International Sheep Genomics Con-sortium Members. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol, 2012, 10(2): e1001258.[17] Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet, 2007, 81(3): 559-575.[18] Rousset F. GENEPOP’007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour, 2008, 8(1): 103-106.[19] Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution, 1984, 38(6): 1358-1370.[20] Wright S. Evolution and the Genetics of Populations. Volume 4. Variability Within and Among Natural Popula-tions. Chicago: University of Chicago Press, 1978.[21] Herbst RS. Review of epidermal growth factor receptor biology. Int J Radiat Oncol Biol Phys, 2004, 59(2): 21-26.[22] Short TH, Rothschild MF, Southwood OI, McLaren DG, de Vries A, van der Steen H, Eckardt GR, Tuggle CK, Helm J, Vaske DA, Mileham AJ, Plastow GS. Effect of the estrogen receptor locus on reproduction and production traits in four commercial pig lines. J Anim Sci, 1997, 75(12): 3138-3142.[23] Davies G, Jiang WG, Mason MD. The interaction between beta-catenin, GSK3beta and APC after motogen induced cell-cell dissociation, and their involvement in signal transduction pathways in prostate cancer. Int J Oncol, 2001, 18(4): 843-847.[24] Livolsi A, Busuttil V, Imbert V, Abraham RT, Peyron JF. Tyrosine phosphorylation-dependent activation of NF- kappa B. Requirement for p56 LCK and ZAP-70 protein tyrosine kinases. Eur J Bio-chem, 2001, 268(5): 1508-1515.[25] Pearson G, Robinson F, Beers-Gibson T, Xu BE, Karandi-kar M, Berman K, Cobb MH. Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions. Endocr Rev, 2001, 22(2): 153-183.[26] Dong C, Davis RJ, Flavell RA. Map kinases in the immune response. Annu Rev Immunol, 2002, 20: 55-72.[27] Song G, Ouyang GL, Bao SD. The activation of Akt/PKB signaling pathway and cell survival. J Cell Mol Med, 2005, 9(1): 59-71.[28] Lee KS, Hong SH, Bae SC. Both the Smad and p38 MAPK pathways play a crucial role in RUNX2 expression following induction by trans-forming growth factor β and bone morphogenetic protein. Oncogene, 2002, 21(47): 7156-7163.[29] Sasaki T, Irie-Sasaki J, Jones RG, Oliveira-dos-Santos AJ, Stanford WL, Bolon B, Wakeham A, Itie A, Bouchard D, Kozieradzki I, Joza N, Mak TW, Ohashi PS, Suzuki A, Pernninger JM. Function of PI3Kγ in thymocyte development, T cell activation, and neutrophil migration. Science, 2000, 287(5455): 1040-1046.[30] Kraus C, Liehr T, Hülsken J, Behrens J, Birchmeier W, Grzeschik KH, Ballhausen WG. Localization of the human β-catenin gene (CTNNB1) to 3p21: a region im-plicated in tumor development. Genimics, 1994, 23(1): 272-274.[31] Nguyen A, Rauch TA, Pfeifer GP, Hu VW. Global methy-lation profiling of lymphobastoid cell lines reveals epige-netic contributions to autism spectrum disorders and a novel autism candidate gene, RORA, whose protein product is reduced in autistic brain. FASEB J, 2010, 24(8): 3036-3051.[32] Lin HM, Zhao L, Cheng SY. Cyclin D1 is a ligand-inde-pendent corepressor for thyroid hormone receptors. J Biol Chem, 2002, 277(32): 28733-28741.[33] Bhawan J, Gonzalez-Serva A, Nehal K, Labadie R, Lu-frano L, Thorne EG, Gilchrest BA. Effects of tretinoin on photodamaged skin: a histologic study. Arch Dermatol, 1991, 127(5): 666-672.[34] Huang FJ, Lin YL. Effects of retinoic acid on pre-implantation embryo development in mice. Chang Gung Med J, 2001, 24(11): 681-687.[35] Florini JR, Ewton DZ, Coolican SA. Growth hormone and the lnsulin-like growth factor system in myogenesis. Endocr Rev, 1996, 17(5): 481-517.[36] Baarsch MJ, Scamurra RW, Burger K, Foss DL, Mahes-waran SK, Murtaugh MP. Inflammatory cytokine expres-sion in swine experimentally infected with Actinoba-cillus pleuropneumoniae. Infect Immun, 1995, 63(9): 3587-3594.[37] Darwich L, Balasch M, Plnan-Durán J, Segalés J, Do-mingo M, Mateu E. Cytokine profiles of peripheral blood mononuclear cells from pigs with postweaning multisys-temic wasting syndrome in response to mitogen, superan-tigen or recall viral antigens. J Gen Virol, 2003, 84(12): 3453-3457.[38] Schlaepfer DD, Hunter T. Integrin signalling and tyrosine phosphorylation: just the FAKs? Trends Cell Biol, 1998, 8(4): 151-157.[39] Wang WL, Li Q, Xu J, Cvekl A. Lens fiber cell differen-tiation and denucleation are disrupted through expression of the N-terminal nuclear receptor box of Ncoa6 and result in p53-dependent and p53-independent apop-tosis. Mol Biol Cell, 2010, 21(14): 2453-2468.[40] Park JY, Su YQ, Ariga M, Law E, Jin SLC, Conti M. EGF-like growth factors as mediators of LH action in the ovulatory follicle. Science, 2004, 303(5658): 682-684.[41] Carraway KL, Weber JL, Unger MJ, Ledesma J, Yu N, Gassmann M, Lai C. Neuregulin-2, a new ligand of ErbB3/ErbB4-receptor tyrosine kinases. Nature, 1997, 387(6632): 512-516.[42] Li RW, Capuco AV. Canonical pathways and networks regulated by estrogen in the bovine mammary gland. Funct Integr Genomics, 2008, 8(1): 55-68.[43] Bumsted-O’Brien KM, Hendrickson A, Haverkamp S, Ashery-Padan R, Schulte D. Expression of the homeodo-main transcription factor Meis2 in the embryonic and postnatal retina. J Comp Neurol, 2007, 505(1): 58-72.[44] Tsimikas S. Oxidized low-density lipoprotein biomarkers in atherosclerosis. Curr Atheroscler Rep, 2006, 8(1): 55-61.[45] Peterson MM, Mack JL, Hall PR, Alsup AA, Alexander SM, Sully EK, Sawires YS, Cheung AL, Otto M, Gresham HD. Apolipoprotein B is an innate barrier against invasive Staphylococcus aureus infection. Cell Host Mi-crobe, 2008, 4(6): 555-566.[46] Cortesio CL, Wernimont SA, Kastner DL, Cooper KM, Huttenlocher A. Impaired podosome formation and inva-sive migration of macrophages from patients with a PSTPIP1 mutation and PAPA syndrome. Arthritis Rheum, 2010, 62(8): 2556-2558.[47] Fang MY, Larson G, Ribeiro HS, Li N, Andersson L. Con-trasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genet, 2009, 5(1): e1000341.[48] Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interro-gating a high-density SNP map for signatures of natural selection. Genome Res, 2002, 12(12): 1805-1814.[49] Innan H, Kim Y. Pattern of polymorphism after strong ar-tificial selection in a domestication event. Proc Natl Acad Sci USA, 2004, 101(29): 10667-10672. |