박사

Delineating the genetic landscape of mammals on the bases of genome-wide association study and positive selection scan using single nucleotide polymorphism : 단일염기 다형성 기반 포유류 유전지형 탐색을 위한 연관분석 및 양성선택 연구

김재민 2015년
논문상세정보
' Delineating the genetic landscape of mammals on the bases of genome-wide association study and positive selection scan using single nucleotide polymorphism : 단일염기 다형성 기반 포유류 유전지형 탐색을 위한 연관분석 및 양성선택 연구' 의 주제별 논문영향력
논문영향력 선정 방법
논문영향력 요약
주제
  • complex traits
  • genome-wide association study
  • genotype-by-environment interaction
  • heritability
  • positive selection
동일주제 총논문수 논문피인용 총횟수 주제별 논문영향력의 평균
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' Delineating the genetic landscape of mammals on the bases of genome-wide association study and positive selection scan using single nucleotide polymorphism : 단일염기 다형성 기반 포유류 유전지형 탐색을 위한 연관분석 및 양성선택 연구' 의 참고문헌

  • Zhu, M. and S. Zhao (2007). "Candidate gene identification approach:progress and challenges." International Journal of Biological Sciences 3(7):420.
  • Zheng, J.-S., D. K. Arnett, Y.-C. Lee, J. Shen, L. D. Parnell, et al. (2013)."Genome-Wide Contribution of Genotype by Environment Interaction toVariation of Diabetes-Related Traits." PLoS One 8(10): e77442.
  • Zhao, J., J. P. Bradfield, M. Li, K. Wang, H. Zhang, et al. (2012). "The Role ofObesity?associated Loci Identified in Genome?wide Association Studies in theDetermination of Pediatric BMI." Obesity 17(12): 2254-2257.
  • Zhang, C. and G. Plastow (2011). "Genomic Diversity in Pig (Sus scrofa) andits Comparison with Human and other Livestock." Current Genomics 12(2):138.
  • Zenger, K., M. Khatkar, J. Cavanagh, R. Hawken and H. Raadsma (2007)."Genome?wide genetic diversity of Holstein Friesian cattle reveals newinsights into Australian and global population variability, including impact ofselection." Animal Genetics 38(1): 7-14.
  • Yi, X., Y. Liang, E. Huerta-Sanchez, X. Jin, Z. X. P. Cuo, et al. (2010)."Sequencing of 50 human exomes reveals adaptation to high altitude."Science 329(5987): 75-78.
  • Yerle, M., Y. Lahbib-Mansais, P. Pinton, A. Robic, A. Goureau, et al. (1997)."The cytogenetic map of the domestic pig (Sus scrofa domestica)."Mammalian Genome 8(8): 592-607.
  • Yang, Z. (2005). "The power of phylogenetic comparison in revealing proteinfunction." Proceedings of the National Academy of Sciences of the UnitedStates of America 102(9): 3179-3180.
  • Yang, S., X. Li, K. Li, B. Fan and Z. Tang (2014). "A genome-wide scan forsignatures of selection in Chinese indigenous and commercial pig breeds."BMC Genetics 15(1): 7.
  • Yang, J., T. Lee, J. Kim, M.-C. Cho, B.-G. Han, et al. (2013). "UbiquitousPolygenicity of Human Complex Traits: Genome-Wide Analysis of 49 Traitsin Koreans." PLoS Genetics 9(3): e1003355.
  • Yang, J., S. H. Lee, M. E. Goddard and P. M. Visscher (2011). "GCTA: a toolfor genome-wide complex trait analysis." The American Journal of HumanGenetics 88(1): 76-82.
  • Yang, J., S. H. Lee, M. E. Goddard and P. M. Visscher (2011). "GCTA: a toolfor genome-wide complex trait analysis." American journal of human genetics88(1): 76.
  • Yang, J., B. Benyamin, B. P. McEvoy, S. Gordon, A. K. Henders, et al. (2010)."Common SNPs explain a large proportion of the heritability for humanheight." Nature Genetics 42(7): 565-569.
  • Wu, L., B. Xi, M. Zhang, Y. Shen, X. Zhao, et al. (2010). "Associations of sixsingle nucleotide polymorphisms in obesity-related genes with BMI and riskof obesity in Chinese children." Diabetes 59(12): 3085-3089.
  • Woods, S. and R. Seeley (2002). "Understanding the physiology of obesity:review of recent developments in obesity research." International Journal ofObesity and Related Metabolic Disorders: Journal of the InternationalAssociation for the Study of Obesity 26: S8.
  • Wood, J., R. Richardson, G. Nute, A. Fisher, M. Campo, et al. (2004). "Effectsof fatty acids on meat quality: a review." Meat Science 66(1): 21-32.
  • Windsor, P. and J. S. Agerholm (2009). "Inherited diseases of AustralianHolstein?Friesian cattle." Australian Veterinary Journal 87(5): 193-199.
  • Williams, F. (1979). Reasoning with statistics, Holt, Rinehart and WinstonNew York.
  • Willer, C. J., E. K. Speliotes, R. J. F. Loos, S. Li, C. M. Lindgren, et al. (2008)."Six new loci associated with body mass index highlight a neuronal influenceon body weight regulation." Nature Genetics 41(1): 25-34.
  • Weinshilboum, R. (2001). "Thiopurine pharmacogenetics: clinical andmolecular studies of thiopurine methyltransferase." Drug Metabolism andDisposition 29(4): 601-605.
  • Wang, Y., J. R. O'Connell, P. F. McArdle, J. B. Wade, S. E. Dorff, et al. (2009)."Whole-genome association study identifies STK39 as a hypertensionsusceptibility gene." Proceedings of the National Academy of Sciences 106(1):226-231.
  • Wang, E. T., G. Kodama, P. Baldi and R. K. Moyzis (2006). "Globallandscape of recent inferred Darwinian selection for Homo sapiens."Proceedings of the National Academy of Sciences of the United States ofAmerica 103(1): 135-140.
  • Walsh, E. C., P. Sabeti, H. B. Hutcheson, B. Fry, S. F. Schaffner, et al. (2006)."Searching for signals of evolutionary selection in 168 genes related toimmune function." Human Genetics 119(1-2): 92-102.
  • Walley, A. J., J. E. Asher and P. Froguel (2009). "The genetic contribution tonon-syndromic human obesity." Nature Reviews Genetics 10(7): 431-442.
  • Visscher, P. M., W. G. Hill and N. R. Wray (2008). "Heritability in thegenomics era?concepts and misconceptions." Nature Reviews Genetics 9(4):255-266.
  • Via, S. and R. Lande (1985). "Genotype-environment interaction and theevolution of phenotypic plasticity." Evolution: 505-522.
  • Van Eenennaam, A. and J. F. Medrano (1991). "Milk protein polymorphismsin California dairy cattle." Journal of Dairy Science 74(5): 1730-1742.
  • VODI?KA, P., K. SMETANA JR, B. DVO?ANKOVA, T. Emerick, Y. Z. Xu,et al. (2005). "The miniature pig as an animal model in biomedical research."Annals of the New York Academy of Sciences 1049(1): 161-171.
  • Thorleifsson, G., G. B. Walters, D. F. Gudbjartsson, V. Steinthorsdottir, P.Sulem, et al. (2008). "Genome-wide association yields new sequence variantsat seven loci that associate with measures of obesity." Nature Genetics 41(1):18-24.
  • Teshima, K. M., G. Coop and M. Przeworski (2006). "How reliable areempirical genomic scans for selective sweeps?" Genome Research 16(6): 702-712.
  • Taylor, A., M. Sandeep, C. Janipalli, C. Giambartolomei, D. Evans, et al.(2011). "Associations of FTO and MC4R variants with obesity traits inIndians and the role of rural/urban environment as a possible effect modifier."Journal of Obesity 2011.
  • Tanner, J. M. and R. H. Whitehouse (1975). "Revised standards for triceps andsubscapular skinfolds in British children." Archives of Disease in Childhood50(2): 142-145.
  • Tang, K., K. R. Thornton and M. Stoneking (2007). "A new approach forusing genome scans to detect recent positive selection in the human genome."PLoS Biology 5(7): e171.
  • Tajima, F. (1989). "Statistical method for testing the neutral mutationhypothesis by DNA polymorphism." Genetics 123(3): 585-595.
  • Tabor, H. K., N. J. Risch and R. M. Myers (2002). "Candidate-geneapproaches for studying complex genetic traits: practical considerations."Nature Reviews Genetics 3(5): 391-396.
  • Strasburg, G. and W. Chiang (2009). "Pale, soft, exudative turkey?The roleof ryanodine receptor variation in meat quality." Poultry Science 88(7): 1497-1505.
  • Stoltenberg, S. F. (1997). "Coming to terms with heritability." Genetica 99(2-3): 89-96.
  • Smith, J. M. and J. Haigh (1974). "The hitch-hiking effect of a favourablegene." Genetical Research 23(1): 23-35.
  • Slatkin, M. (1999). "Disequilibrium mapping of a quantitative-trait locus in anexpanding population." The American Journal of Human Genetics 64(6):1765-1773.
  • Skjervold, H. and H. J. Langholz (1964). "Factors affecting the optimumstructure of AI breeding in dairy cattle." Zeitschrift fur Tierzuchtung undZuchtungsbiologie 80(1?4): 25-40.
  • Simonson, T. S., Y. Yang, C. D. Huff, H. Yun, G. Qin, et al. (2010). "Geneticevidence for high-altitude adaptation in Tibet." Science 329(5987): 72.
  • Sherman, B. T. and R. A. Lempicki (2009). "Bioinformatics enrichment tools:paths toward the comprehensive functional analysis of large gene lists."Nucleic Acids Research 37(1): 1-13.
  • Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, et al. (2003)."Cytoscape: a software environment for integrated models of biomolecularinteraction networks." Genome Research 13(11): 2498-2504.
  • Schwartz, M. W., S. C. Woods, D. Porte, R. J. Seeley and D. G. Baskin (2000)."Central nervous system control of food intake." NATURE-LONDON-: 661-671.
  • Scheinfeldt, L. B. and S. A. Tishkoff (2013). "Recent human adaptation:genomic approaches, interpretation and insights." Nature Reviews Genetics14(10): 692-702.
  • Schapira, D. V., N. B. Kumar, G. H. Lyman and C. E. Cox (1990)."Abdominal obesity and breast cancer risk." Annals of Internal Medicine112(3): 182-186.
  • Satagopan, J. M. and R. C. Elston (2012). "Evaluation of removable statisticalinteraction for binary traits." Statistics in Medicine.
  • Safran, M., I. Dalah, J. Alexander, N. Rosen, T. I. Stein, et al. (2010)."GeneCards Version 3: the human gene integrator." Database: the Journal ofBiological Databases and Curation 2010.
  • Sabeti, P. C., P. Varilly, B. Fry, J. Lohmueller, E. Hostetter, et al. (2007)."Genome-wide detection and characterization of positive selection in humanpopulations." Nature 449(7164): 913-918.
  • SASAZAKI, S., M. USUI, H. MANNEN, C. HIURA and S. TSUJI (2005)."Allele frequencies of the extension locus encoding the melanocortin?1196receptor in Japanese and Korean cattle." Animal Science Journal 76(2): 129-132.
  • Rubin, C.-J., H.-J. Megens, A. M. Barrio, K. Maqbool, S. Sayyab, et al.(2012). "Strong signatures of selection in the domestic pig genome."Proceedings of the National Academy of Sciences 109(48): 19529-19536.
  • Rotimi, C. N., A. G. Comuzzie, W. L. Lowe, A. Luke, J. Blangero, et al.(1999). "The quantitative trait locus on chromosome 2 for serum leptin levelsis confirmed in African-Americans." Diabetes 48(3): 643-644.
  • Ron, M. and J. Weller (2007). "From QTL to QTN identification in livestock?winning by points rather than knock?out: a review." Animal Genetics 38(5):429-439.
  • Rhee, M. and B. Kim (2001). "Effect of low voltage electrical stimulation andtemperature conditioning on postmortem changes in glycolysis and calpainsactivities of Korean native cattle (Hanwoo)." Meat Science 58(3): 231-237.
  • Rees, J. L. (2004). "The genetics of sun sensitivity in humans." The AmericanJournal of Human Genetics 75(5): 739-751.
  • Raven, P. and G. Johnson (2002). "Biology 6thed." NY: McGraw-HillPublishing.
  • Rasche, A., H. Al-Hasani and R. Herwig (2008). "Meta-analysis approachidentifies candidate genes and associated molecular networks for type-2diabetes mellitus." BMC Genomics 9(1): 310.
  • Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. R. Ferreira, et al.(2007). "PLINK: a tool set for whole-genome association and populationbasedlinkage analyses." The American Journal of Human Genetics 81(3):559-575.
  • Purcell, S., B. Neale, K. Todd-Brown, L. Thomas, M. A. Ferreira, et al. (2007)."PLINK: a tool set for whole-genome association and population-basedlinkage analyses." The American Journal of Human Genetics 81(3): 559-575.
  • Przeworski, M., R. R. Hudson and A. Di Rienzo (2000). "Adjusting the focuson human variation." Trends in Genetics 16(7): 296-302.
  • Pruitt, K. D., T. Tatusova and D. R. Maglott (2005). "NCBI ReferenceSequence (RefSeq): a curated non-redundant sequence database of genomes,transcripts and proteins." Nucleic Acids Research 33(suppl 1): D501-D504.
  • Pritchard, J. K. (2001). "Are rare variants responsible for susceptibility tocomplex diseases?" The American Journal of Human Genetics 69(1): 124-137.
  • Price, A. L., N. J. Patterson, R. M. Plenge, M. E. Weinblatt, N. A. Shadick, etal. (2006). "Principal components analysis corrects for stratification ingenome-wide association studies." Nature Genetics 38(8): 904-909.
  • Pribyl, J. (1995). "A way of using markers for farm animal selection."ZIVOCISNA VYROBA 40: 375-375.
  • Pollinger, J. P., C. D. Bustamante, A. Fledel-Alon, S. Schmutz, M. M. Gray, etal. (2005). "Selective sweep mapping of genes with large phenotypic effects."Genome Research 15(12): 1809-1819.
  • Platt, S. A. and C. A. Sanislow (1988). "Norm-of-reaction: Definition andmisinterpretation of animal research." Journal of Comparative Psychology102(3): 254.
  • Pickrell, J. K., G. Coop, J. Novembre, S. Kudaravalli, J. Z. Li, et al. (2009)."Signals of recent positive selection in a worldwide sample of humanpopulations." Genome Research 19(5): 826-837.
  • Pickrell, J. K. and J. K. Pritchard (2012). "Inference of population splits andmixtures from genome-wide allele frequency data." PLoS Genetics 8(11):e1002967.
  • Perusse, L. and C. Bouchard (1999). "Genotype?Environment Interaction inHuman Obesity." Nutrition Reviews 57(5): 31-38.
  • Perez?Enciso, M. (2014). "Genomic relationships computed from either nextgenerationsequence or array SNP data." Journal of Animal Breeding andGenetics.
  • Pearson, T. A. and T. A. Manolio (2008). "How to interpret a genome-wideassociation study." JAMA: the Journal of the American Medical Association299(11): 1335-1344.
  • Park, B., N. Kim, C. Lee and I. Hwang (2007). "Effect of fiber type onpostmortem proteolysis in longissimus muscle of Landrace and Korean nativeblack pigs." Meat Science 77(4): 482-491.
  • Ottman, R. (1996). "Gene?environment interaction: definitions and studydesigns." Preventive Medicine 25(6): 764.
  • Oltenacu, P. A. and B. Algers (2005). "Selection for increased production andthe welfare of dairy cows: are new breeding goals needed?" AMBIO: AJournal of the Human Environment 34(4): 311-315.
  • Oleksyk, T. K., M. W. Smith and S. J. O'Brien (2010). "Genome-wide scansfor footprints of natural selection." Philosophical Transactions of the RoyalSociety B: Biological Sciences 365(1537): 185-205.
  • Oleksyk, T. K., K. Zhao, M. Francisco, D. A. Gilbert, S. J. O'Brien, et al.(2008). "Identifying selected regions from heterozygosity and divergenceusing a light-coverage genomic dataset from two human populations." PLoSOne 3(3): e1712.
  • Ojeda, A., L.-S. Huang, J. Ren, A. Angiolillo, I.-C. Cho, et al. (2008)."Selection in the making: a worldwide survey of haplotypic diversity around acausative mutation in porcine IGF2." Genetics 178(3): 1639-1652.
  • Ogorevc, J., T. Kunej, A. Razpet and P. Dovc (2009). "Database of cattlecandidate genes and genetic markers for milk production and mastitis."Animal Genetics 40(6): 832-851.
  • Nowacka-Woszuk, J., I. Szczerbal, H. Fijak-Nowak and M. Switonski (2008)."Chromosomal localization of 13 candidate genes for human obesity in thepig genome." Journal of Applied Genetics 49(4): 373-377.
  • Norton, H. L., R. A. Kittles, E. Parra, P. McKeigue, X. Mao, et al. (2007)."Genetic evidence for the convergent evolution of light skin in Europeans andEast Asians." Molecular Biology and Evolution 24(3): 710-722.
  • Nelson, T. E. (1983). "Abnormality in calcium release from skeletalsarcoplasmic reticulum of pigs susceptible to malignant hyperthermia."Journal of Clinical Investigation 72(3): 862.
  • Nekrutenko, A. and J. Taylor (2012). "Next-generation sequencing datainterpretation: enhancing reproducibility and accessibility." Nature ReviewsGenetics 13(9): 667-672.
  • Nei, M. and W.-H. Li (1979). "Mathematical model for studying geneticvariation in terms of restriction endonucleases." Proceedings of the NationalAcademy of Sciences 76(10): 5269-5273.
  • Nart, P., H. Thompson, D. Barrett, S. Armstrong and A. McPhaden (2004)."Clinical and pathological features of dilated cardiomyopathy in Holstein-Friesian cattle." Veterinary Record 155(12): 355-361.
  • Mutch, D. M. and K. Clement (2006). "Unraveling the genetics of humanobesity." PLoS Genetics 2(12): e188.
  • Murray, C., E. Huerta-Sanchez, F. Casey and D. G. Bradley (2010). "Cattledemographic history modelled from autosomal sequence variation."Philosophical Transactions of the Royal Society B: Biological Sciences365(1552): 2531-2539.
  • Murcray, C. E., J. P. Lewinger and W. J. Gauderman (2009). "Geneenvironmentinteraction in genome-wide association studies." AmericanJournal of Epidemiology 169(2): 219-226.
  • Moreno-Estrada, A., K. Tang, M. Sikora, T. Marques-Bonet, F. Casals, et al.(2009). "Interrogating 11 fast-evolving genes for signatures of recent positiveselection in worldwide human populations." Molecular Biology and Evolution26(10): 2285-2297.
  • Moller, M. J., R. Chaudhary, E. Hellmen, B. Hoyheim, B. Chowdhary, et al.(1996). "Pigs with the dominant white coat color phenotype carry aduplication of the KIT gene encoding the mast/stem cell growth factorreceptor." Mammalian Genome 7(11): 822-830.
  • Miller, C. T., S. Beleza, A. A. Pollen, D. Schluter, R. A. Kittles, et al. (2007)."< i> cis</i>-Regulatory Changes in< i> Kit Ligand</i> Expression andParallel Evolution of Pigmentation in Sticklebacks and Humans." Cell 131(6):1179-1189.
  • Miettinen, P. J., J. Ustinov, P. Ormio, R. Gao, J. Palgi, et al. (2006)."Downregulation of EGF receptor signaling in pancreatic islets causesdiabetes due to impaired postnatal β-cell growth." Diabetes 55(12): 3299-3308.
  • Meyre, D., J. Delplanque, J. C. Chevre, C. Lecoeur, S. Lobbens, et al. (2009)."Genome-wide association study for early-onset and morbid adult obesityidentifies three new risk loci in European populations." Nature Genetics 41(2):157-159.
  • Mercade, A., J. Estelle, M. Perez?Enciso, L. Varona, L. Silio, et al. (2006)."Characterization of the porcine acyl?CoA synthetase long?chain 4 gene andits association with growth and meat quality traits." Animal Genetics 37(3):219-224.
  • Memisoglu, A., F. B. Hu, S. E. Hankinson, J. A. E. Manson, I. De Vivo, et al.(2003). "Interaction between a peroxisome proliferator-activated receptor γgene polymorphism and dietary fat intake in relation to body mass." HumanMolecular Genetics 12(22): 2923-2929.
  • Meissner, A. and B. E. Bernstein (2009). Sequencing the Epigenome.Epigenomics, Springer: 19-35.
  • Medzhitov, R., D. S. Schneider and M. P. Soares (2012). "Disease tolerance asa defense strategy." Science 335(6071): 936-941.
  • McTavish, E. J. B. (2013). "Estimating population histories using singlenucleotidepolymorphisms sampled throughout genomes."
  • McQuillan, R., A.-L. Leutenegger, R. Abdel-Rahman, C. S. Franklin, M.Pericic, et al. (2008). "Runs of Homozygosity in European Populations." TheAmerican Journal of Human Genetics 83(3): 359-372.
  • McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, et al. (2010)."The Genome Analysis Toolkit: a MapReduce framework for analyzing nextgenerationDNA sequencing data." Genome Research 20(9): 1297-1303.
  • Masuo, K., H. Mikami, T. Ogihara and M. L. Tuck (2001). "Weight reductionand pharmacologic treatment in obese hypertensives." American Journal ofHypertension 14(6): 530-538.
  • Manolio, T. A., L. D. Brooks and F. S. Collins (2008). "A HapMap harvest ofinsights into the genetics of common disease." The Journal of ClinicalInvestigation 118(5): 1590-1605.
  • Manolio, T. A., F. S. Collins, N. J. Cox, D. B. Goldstein, L. A. Hindorff, et al.(2009). "Finding the missing heritability of complex diseases." Nature461(7265): 747-753.
  • Maier, L. A. (2002). "Genetic and exposure risks for chronic berylliumdisease." Clinics in chest medicine 23(4): 827.
  • Maier, L. A. (2002). "Genetic and exposure risks for chronic berylliumdisease." Clinics in Chest Medicine 23(4): 827-839.
  • Liu, L., B. Harris, M. Keehan and Y. Zhang (2009). "Genome scan for thedegree of white spotting in dairy cattle." Animal Genetics 40(6): 975-977.
  • Li, R., W. Fan, G. Tian, H. Zhu, L. He, et al. (2009). "The sequence and denovo assembly of the giant panda genome." Nature 463(7279): 311-317.
  • Li, M., S. Tian, L. Jin, G. Zhou, Y. Li, et al. (2013). "Genomic analysesidentify distinct patterns of selection in domesticated pigs and Tibetan wildboars." Nature Genetics 45(12): 1431-1438.
  • Li, M., S. Tian, C. K. Yeung, X. Meng, Q. Tang, et al. (2014). "Wholegenomesequencing of Berkshire (European native pig) provides insights intoits origin and domestication." Scientific Reports 4.
  • Li, J., H. Y. J. Li, H. Li, T. Ning, X. Pan, et al. (2010). "Artificial selection ofthe melanocortin receptor 1 gene in Chinese domestic pigs duringdomestication." Heredity 105(3): 274-281.
  • Levy, D., G. B. Ehret, K. Rice, G. C. Verwoert, L. J. Launer, et al. (2009)."Genome-wide association study of blood pressure and hypertension." NatureGenetics 41(6): 677-687.
  • Leve, L. D., D. C. R. Kerr, D. Shaw, X. Ge, J. M. Neiderhiser, et al. (2010)."Infant pathways to externalizing behavior: evidence of Genotype Environment interaction." Child Development 81(1): 340-356.
  • Lemay, D. G., D. J. Lynn, W. F. Martin, M. C. Neville, T. M. Casey, et al.(2009). "The bovine lactation genome: insights into the evolution ofmammalian milk." Genome Biology 10(4): R43.
  • Lee, K. T., M. J. Byun, K. S. Kang, E. W. Park, S. H. Lee, et al. (2011)."Neuronal genes for subcutaneous fat thickness in human and pig areidentified by local genomic sequencing and combined SNP association study."PLoS One 6(2): e16356.
  • Larkin, D. M., H. D. Daetwyler, A. G. Hernandez, C. L. Wright, L. A. Hetrick,et al. (2012). "Whole-genome resequencing of two elite sires for the detectionof haplotypes under selection in dairy cattle." Proceedings of the NationalAcademy of Sciences 109(20): 7693-7698.
  • Langmead, B. and S. L. Salzberg (2012). "Fast gapped-read alignment withBowtie 2." Nature Methods 9(4): 357-359.
  • Lander, E. S. (2011). "Initial impact of the sequencing of the human genome."Nature 470(7333): 187-197.
  • Lamason, R. L., M.-A. P. Mohideen, J. R. Mest, A. C. Wong, H. L. Norton, etal. (2005). "SLC24A5, a putative cation exchanger, affects pigmentation inzebrafish and humans." Science 310(5755): 1782-1786.
  • Kulyte, A., M. Ryden, N. Mejhert, E. Dungner, E. Sjolin, et al. (2011)."MTCH2 in human white adipose tissue and obesity." Journal of ClinicalEndocrinology & Metabolism 96(10): E1661-E1665.
  • Kucerova, J., A. Matejicek, O. Jandurova, P. Sorensen, E. Nemcova, et al.(2006). "Milk protein genes CSN1S1, CSN2, CSN3, LGB and their relation togenetic values of milk production parameters in Czech Fleckvieh." CzechJournal of Animal Science 51(6): 241.
  • Krzywinski, M., J. Schein, ?. Birol, J. Connors, R. Gascoyne, et al. (2009)."Circos: an information aesthetic for comparative genomics." GenomeResearch 19(9): 1639-1645.
  • Kosiol, C., T. Vina?, R. R. da Fonseca, M. J. Hubisz, C. D. Bustamante, et al.(2008). "Patterns of positive selection in six mammalian genomes." PLoSGenetics 4(8): e1000144.
  • Kong, A., V. Steinthorsdottir, G. Masson, G. Thorleifsson, P. Sulem, et al.(2009). "Parental origin of sequence variants associated with complexdiseases." Nature 462(7275): 868-874.
  • Kirin, M., R. McQuillan, C. S. Franklin, H. Campbell, P. M. McKeigue, et al.(2010). "Genomic runs of homozygosity record population history andconsanguinity." PLoS One 5(11): e13996.
  • Kimura, M. (1985). The neutral theory of molecular evolution, CambridgeUniversity Press.
  • Kim, Y. and R. Nielsen (2004). "Linkage disequilibrium as a signature ofselective sweeps." Genetics 167(3): 1513-1524.
  • Kim, T., K. Kim, B. Choi, D. Yoon, G. Jang, et al. (2005). "Genetic structureof pig breeds from Korea and China using microsatellite loci analysis."Journal of Animal Science 83(10): 2255-2263.
  • Kim, J., T. Lee, T.-H. Kim, K.-T. Lee and H. Kim (2012). "An integratedapproach of comparative genomics and heritability analysis of pig and humanon obesity trait: evidence for candidate genes on human chromosome 2."BMC Genomics 13(1): 711.
  • Kim, D., P. Seong, S. Cho, J. Kim, J. Lee, et al. (2009). "Fatty acidcomposition and meat quality traits of organically reared Korean native blackpigs." Livestock Science 120(1): 96-102.
  • Kijas, J. W., J. A. Lenstra, B. Hayes, S. Boitard, L. R. P. Neto, et al. (2012)."Genome-wide analysis of the world's sheep breeds reveals high levels ofhistoric mixture and strong recent selection." PLoS Biology 10(2): e1001258.
  • Kiełbasa, S. M., R. Wan, K. Sato, P. Horton and M. C. Frith (2011). "Adaptiveseeds tame genomic sequence comparison." Genome Research 21(3): 487-493.
  • Kent, W. J. (2002). "BLAT?the BLAST-like alignment tool." GenomeResearch 12(4): 656-664.
  • Kelley, J. L., J. Madeoy, J. C. Calhoun, W. Swanson and J. M. Akey (2006)."Genomic signatures of positive selection in humans and the limits of outlierapproaches." Genome Research 16(8): 980-989.
  • Kahn, S. E., R. L. Hull and K. M. Utzschneider (2006). "Mechanisms linkingobesity to insulin resistance and type 2 diabetes." Nature 444(7121): 840-846.
  • Johannes, F., V. Colot and R. C. Jansen (2008). "Epigenome dynamics: aquantitative genetics perspective." Nature Reviews Genetics 9(11): 883-890.
  • Johannes, F., E. Porcher, F. K. Teixeira, V. Saliba-Colombani, M. Simon, et al.(2009). "Assessing the impact of transgenerational epigenetic variation oncomplex traits." PLoS Genetics 5(6): e1000530.
  • Jeong, J., E. Kwon, S. Im, K. Seo and M. Baik (2012). "Expression of fatdeposition and fat removal genes is associated with intramuscular fat contentin longissimus dorsi muscle of Korean cattle steers." Journal of AnimalScience 90(6): 2044-2053.
  • Jayasooriya, A. P., M. L. Mathai, L. L. Walker, D. P. Begg, D. A. Denton, et al.(2008). "Mice lacking angiotensin-converting enzyme have increased energyexpenditure, with reduced fat mass and improved glucose clearance."Proceedings of the National Academy of Sciences 105(18): 6531-6536.
  • Ioannidis, J. P. A., E. E. Ntzani and T. A. Trikalinos (2004)."'Racial'differences in genetic effects for complex diseases." Nature Genetics36(12): 1312-1318.
  • Hwang, I., B. Park, S. Cho, J. Kim, Y. Choi, et al. (2004). "Identification ofmuscle proteins related to objective meat quality in Korean native black pig."ASIAN AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 17(11):1599-1607.
  • Hunter, D. J. (2005). "Gene?environment interactions in human diseases."Nature Reviews Genetics 6(4): 287-298.
  • Hudson, R. R. (2002). "Generating samples under a Wright?Fisher neutralmodel of genetic variation." Bioinformatics 18(2): 337-338.
  • Hubisz, M. J., D. Falush, M. Stephens and J. K. Pritchard (2009). "Inferringweak population structure with the assistance of sample group information."Molecular Ecology Resources 9(5): 1322-1332.
  • Huang, Y., Y. Li, D. W. Burt, H. Chen, Y. Zhang, et al. (2013). "The duckgenome and transcriptome provide insight into an avian influenza virusreservoir species." Nature Genetics 45(7): 776-783.
  • Huang, D. W., Brad T Sherman and R. A. Lempicki (2008). "Systematic andintegrative analysis of large gene lists using DAVID bioinformaticsresources." Nature Protocols 4(1): 44-57.
  • Huang, D. W., B. T. Sherman and R. A. Lempicki (2009). "Systematic andintegrative analysis of large gene lists using DAVID bioinformaticsresources." Nature Protocols 4(1): 44-57.
  • Hu, Z.-L. and J. M. Reecy (2007). "Animal QTLdb: beyond a repository."Mammalian Genome 18(1): 1-4.
  • Houpt, K. A., T. R. Houpt and W. G. Pond (1979). "The pig as a model for thestudy of obesity and of control of food intake: a review." The Yale Journal ofBiology and Medicine 52(3): 307.
  • Hotta, K., M. Nakamura, T. Nakamura, T. Matsuo, Y. Nakata, et al. (2009)."Association between obesity and polymorphisms in SEC16B, TMEM18,GNPDA2, BDNF, FAIM2 and MC4R in a Japanese population." Journal ofHuman Genetics 54(12): 727-731.
  • Hirschhorn, J. N. (2009). "Genomewide association studies--illuminatingbiologic pathways." New England Journal of Medicine 360(17): 1699.
  • Herbert, A., N. P. Gerry, M. B. McQueen, I. M. Heid, A. Pfeufer, et al. (2006)."A common genetic variant is associated with adult and childhood obesity."Science 312(5771): 279-283.
  • He, K., Q. Wang, Z. Wang and Y. Pan (2013). "Association study betweengene polymorphisms in PPAR signaling pathway and porcine meat qualitytraits." Mammalian Genome 24(7-8): 322-331.
  • Hayes, B., A. Chamberlain, S. Maceachern, K. Savin, H. McPartlan, et al.(2009). "A genome map of divergent artificial selection between Bos taurusdairy cattle and Bos taurus beef cattle." Animal Genetics 40(2): 176-184.
  • Haudry, A., A. Cenci, C. Ravel, T. Bataillon, D. Brunel, et al. (2007)."Grinding up wheat: a massive loss of nucleotide diversity sincedomestication." Molecular Biology and Evolution 24(7): 1506-1517.
  • Han, S.-H., K.-Y. Shin, S.-S. Lee, M.-S. Ko, D. K. Jeong, et al. (2010). "SINEindel polymorphism of AGL gene and association with growth and carcasstraits in Landrace Jeju black pig F2 population." Molecular Biology Reports37(1): 467-471.
  • Hamosh, A., A. F. Scott, J. S. Amberger, C. A. Bocchini and V. A. McKusick(2005). "Online Mendelian Inheritance in Man (OMIM), a knowledgebase ofhuman genes and genetic disorders." Nucleic Acids Research 33(suppl 1):D514-D517.
  • Hamblin, M. T., E. E. Thompson and A. Di Rienzo (2002). "Complexsignatures of natural selection at the Duffy blood group locus." The AmericanJournal of Human Genetics 70(2): 369-383.
  • Haase, B., S. Brooks, T. Tozaki, D. Burger, P. A. Poncet, et al. (2009). "Sevennovel KIT mutations in horses with white coat colour phenotypes." AnimalGenetics 40(5): 623-629.
  • Guo, S., J. Zhang, H. Sun, J. Salse, W. J. Lucas, et al. (2013). "The draftgenome of watermelon (Citrullus lanatus) and resequencing of 20 diverseaccessions." Nature Genetics 45(1): 51-58.
  • Grossman, S. R., I. Shylakhter, E. K. Karlsson, E. H. Byrne, S. Morales, et al.(2010). "A composite of multiple signals distinguishes causal variants inregions of positive selection." Science 327(5967): 883-886.
  • Groenen, M. A., A. L. Archibald, H. Uenishi, C. K. Tuggle, Y. Takeuchi, et al.(2012). "Analyses of pig genomes provide insight into porcine demographyand evolution." Nature 491(7424): 393-398.
  • Granka, J. M., B. M. Henn, C. R. Gignoux, J. M. Kidd, C. D. Bustamante, etal. (2012). "Limited evidence for classic selective sweeps in Africanpopulations." Genetics 192(3): 1049-1064.
  • Glantz, S. A. (2002). "Primer of biostatistics."185Goddard, M. (1992). "Optimal effective population size for the globalpopulation of black and white dairy cattle." Journal of Dairy Science 75(10):2902-2911.
  • Gillespie, J. H. (1991). The causes of molecular evolution, Oxford UniversityPress.
  • Gilad, Y., S. Rosenberg, M. Przeworski, D. Lancet and K. Skorecki (2002)."Evidence for positive selection and population structure at the human MAOAgene." Proceedings of the National Academy of Sciences 99(2): 862-867.
  • Fuller, T., S. Sarkar and D. Crews (2005). "The use of norms of reaction toanalyze genotypic and environmental influences on behavior in mice andrats." Neuroscience & Biobehavioral Reviews 29(3): 445-456.
  • Fujii, J., K. Otsu, F. Zorzato, S. de Leon, V. K. Khanna, et al. (1991)."Identification of a mutation in porcine ryanodine receptor associated withmalignant hyperthermia." Science 253(5018): 448-451.
  • Frazer, K. A., S. S. Murray, N. J. Schork and E. J. Topol (2009). "Humangenetic variation and its contribution to complex traits." Nature ReviewsGenetics 10(4): 241-251.
  • Frayling, T. M., N. J. Timpson, M. N. Weedon, E. Zeggini, R. M. Freathy, etal. (2007). "A common variant in the FTO gene is associated with body massindex and predisposes to childhood and adult obesity." Science 316(5826):889-894.
  • Fontanesi, L., G. Galimberti, D. Calo, R. Fronza, P. Martelli, et al. (2012)."Identification and association analysis of several hundred single nucleotidepolymorphisms within candidate genes for back fat thickness in Italian LargeWhite pigs using a selective genotyping approach." Journal of Animal Science90(8): 2450-2464.
  • Fontanesi, L., E. Scotti, L. Buttazzoni, S. Dall’Olio, A. Bagnato, et al. (2010)."Confirmed association between a single nucleotide polymorphism in theFTO gene and obesity-related traits in heavy pigs." Molecular BiologyReports 37(1): 461-466.
  • Fontanesi, L., E. Scotti, L. Buttazzoni, R. Davoli and V. Russo (2009). "Theporcine fat mass and obesity associated (FTO) gene is associated with fatdeposition in Italian Duroc pigs." Animal Genetics 40(1): 90-93.
  • Flori, L., S. Fritz, F. Jaffrezic, M. Boussaha, I. Gut, et al. (2009). "Thegenome response to artificial selection: a case study in dairy cattle." PLoSOne 4(8): e6595.
  • Fan, B., Z. Q. Du and M. F. Rothschild (2009). "The fat mass and obesityassociated(FTO) gene is associated with intramuscular fat content and growthrate in the pig." Animal Biotechnology 20(2): 58-70.
  • Falconer, D. S., T. F. Mackay and R. Frankham (1996). "Introduction toQuantitative Genetics (4th edn)." Trends in Genetics 12(7): 280.
  • Falconer, D. S., T. F. C. Mackay and R. Frankham (1996). "Introduction toQuantitative Genetics (4th edn)." Trends in Genetics 12(7): 280.
  • Excoffier, L., G. Laval and S. Schneider (2005). "Arlequin (version 3.0): anintegrated software package for population genetics data analysis."Evolutionary Bioinformatics Online 1: 47.
  • Ewing, G. and J. Hermisson (2010). "MSMS: a coalescent simulationprogram including recombination, demographic structure and selection at asingle locus." Bioinformatics 26(16): 2064-2065.
  • Eichler, E. E., J. Flint, G. Gibson, A. Kong, S. M. Leal, et al. (2010). "Missingheritability and strategies for finding the underlying causes of complexdisease." Nature Reviews Genetics 11(6): 446-450.
  • Ebrahim, S., S. Kinra, L. Bowen, E. Andersen, Y. Ben-Shlomo, et al. (2010)."The effect of rural-to-urban migration on obesity and diabetes in India: across-sectional study." PLoS Medicine 7(4): e1000268.
  • Durnin, J. and J. Womersley (1974). "Body fat assessed from total bodydensity and its estimation from skinfold thickness: measurements on 481 menand women aged from 16 to 72 years." British Journal of Nutrition 32(01):77-97.
  • Du, Z. Q., B. Fan, X. Zhao, R. Amoako and M. F. Rothschild (2008)."Association analyses between type 2 diabetes genes and obesity traits inpigs." Obesity 17(2): 323-329.
  • Dick, D. M. (2011). "Gene-environment interaction in psychological traits anddisorders." Annual Review of Clinical Psychology 7: 383.
  • Dennis Jr, G., B. T. Sherman, D. A. Hosack, J. Yang, W. Gao, et al. (2003)."DAVID: database for annotation, visualization, and integrated discovery."Genome Biology 4(5): P3.
  • Dempfle, A., A. Scherag, R. Hein, L. Beckmann, J. Chang-Claude, et al.(2008). "Gene?environment interactions for complex traits: definitions,methodological requirements and challenges." European Journal of HumanGenetics 16(10): 1164-1172.
  • Decker, J. E., J. C. Pires, G. C. Conant, S. D. McKay, M. P. Heaton, et al.(2009). "Resolving the evolution of extant and extinct ruminants with highthroughputphylogenomics." Proceedings of the National Academy ofSciences 106(44): 18644-18649.
  • Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks, et al. (2011). "Thevariant call format and VCFtools." Bioinformatics 27(15): 2156-2158.
  • Da Wei Huang, B. T. S. and R. A. Lempicki (2008). "Systematic andintegrative analysis of large gene lists using DAVID bioinformaticsresources." Nature Protocols 4(1): 44-57.
  • Cornes, B., P. Lind, S. Medland, G. Montgomery, D. Nyholt, et al. (2008)."Replication of the association of common rs9939609 variant of FTO withincreased BMI in an Australian adult twin population but no evidence for geneby environment (G E) interaction." International Journal of Obesity 33(1):75-79.
  • Consortium, B. H. (2009). "Genome-wide survey of SNP variation uncoversthe genetic structure of cattle breeds." Science 324(5926): 528-532.
  • Connelly, T. J., R. El-Hayek, M. Sukhareva and R. Coronado (1994). "Lthyroxineactivates the intracellular Ca2+ release channel of skeletal musclesarcoplasmic reticulum." Biochemistry and Molecular Biology International32(3): 441-448.
  • Comuzzie, A. G., J. E. Hixson, L. Almasy, B. D. Mitchell, M. C. Mahaney, etal. (1997). "A major quantitative trait locus determining serum leptin levelsand fat mass is located on human chromosome 2." Nature Genetics 15(3):273-276.
  • Comuzzie, A. G. and D. B. Allison (1998). "The search for human obesitygenes." Science 280(5368): 1374-1377.
  • Chung, E. and W. Kim (2005). "Association of SNP marker in IGF-I andMYF5 candidate genes with growth traits in Korean cattle." ASIANAUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 18(8): 1061.
  • Cho, Y. S., M. J. Go, Y. J. Kim, J. Y. Heo, J. H. Oh, et al. (2009). "A largescalegenome-wide association study of Asian populations uncovers geneticfactors influencing eight quantitative traits." Nature Genetics 41(5): 527-534.
  • Cho, I., H. Park, C. Yoo, G. Lee, H. Lim, et al. (2011). "QTL analysis of whiteblood cell, platelet and red blood cell?related traits in an F2 intercross betweenLandrace and Korean native pigs." Animal Genetics 42(6): 621-626.
  • Cheung, C. Y. Y., A. W. K. Tso, B. M. Y. Cheung, A. Xu, K. Ong, et al. (2010)."Obesity susceptibility genetic variants identified from recent genome-wideassociation studies: implications in a Chinese population." Journal of ClinicalEndocrinology & Metabolism 95(3): 1395-1403.
  • Chen, H., N. Patterson and D. Reich (2010). "Population differentiation as atest for selective sweeps." Genome Research 20(3): 393-402.
  • Cheah, K., A. Cheah, A. Crosland, J. Casey and A. Webb (1984)."Relationship between Ca< sup> 2+</sup> release, sarcoplasmic Ca< sup>2+</sup>, glycolysis and meat quality in halothane-sensitive and halothaneinsensitivepigs." Meat Science 10(2): 117-130.
  • Cassens, R. G. (2000). "Historical perspectives and current aspects of porkmeat quality in the USA." Food Chemistry 69(4): 357-363.
  • Cannon, J., J. Morgan, F. McKeith, G. Smith, S. Sonka, et al. (1996). "PORKCHAIN QUALITY AUDIT SURVEY: QUANTIFICATION OF PORKQUALITY CHARACTERISTICS1." Journal of Muscle Foods 7(1): 29-44.
  • CLAUSEN, J., D. KECK and W. HIESEY (1948). "Experimental studies onthe nature of species. III. Environresponses of climatic races of Achillea."Experimental studies on the nature of species. III. Environresponses ofclimatic races of Achillea.(Publ. 581).
  • Buczinski, S., A. Rezakhani and D. Boerboom (2010). "Heart disease in cattle:diagnosis, therapeutic approaches and prognosis." The Veterinary Journal184(3): 258-263.
  • Browning, S. R. and B. L. Browning (2007). "Rapid and accurate haplotypephasing and missing-data inference for whole-genome association studies byuse of localized haplotype clustering." American Journal of Human Genetics81(5): 1084.
  • Brotherstone, S. and M. Goddard (2005). "Artificial selection andmaintenance of genetic variance in the global dairy cow population."Philosophical Transactions of the Royal Society B: Biological Sciences360(1459): 1479-1488.
  • Briskey, E., L. Kastenchmidt, J. Forrest, G. Beecher, M. Judge, et al. (1966)."Biochemical aspects of post-mortem changes in porcine muscle." Journal ofAgricultural and Food Chemistry 14(3): 201-207.
  • Bovenhuis, H., J. A. Van Arendonk and S. Korver (1992). "Associationsbetween milk protein polymorphisms and milk production traits." Journal ofDairy Science 75(9): 2549-2559.
  • Bouchard, C. (2008). "Gene?environment interactions in the etiology ofobesity: defining the fundamentals." Obesity 16: S5-S10.
  • Botto, L. D. and M. J. Khoury (2001). "Commentary: facing the challenge ofgene-environment interaction: the two-by-four table and beyond." AmericanJournal of Epidemiology 153(10): 1016-1020.
  • Bochukova, E. G., N. Huang, J. Keogh, E. Henning, C. Purmann, et al. (2009)."Large, rare chromosomal deletions associated with severe early-onsetobesity." Nature 463(7281): 666-670.
  • Biswas, S. and J. M. Akey (2006). "Genomic insights into positive selection."Trends in Genetics 22(8): 437-446.
  • Bindea, G., B. Mlecnik, H. Hackl, P. Charoentong, M. Tosolini, et al. (2009)."ClueGO: a Cytoscape plug-in to decipher functionally grouped geneontology and pathway annotation networks." Bioinformatics 25(8): 1091-1093.
  • Below, J., E. Gamazon, J. Morrison, A. Konkashbaev, A. Pluzhnikov, et al.(2011). "Genome-wide association and meta-analysis in populations fromStarr County, Texas, and Mexico City identify type 2 diabetes susceptibilityloci and enrichment for expression quantitative trait loci in top signals."Diabetologia 54(8): 2047-2055.
  • Barrett, J. C. (2009). "Haploview: Visualization and analysis of SNP genotypedata." Cold Spring Harbor Protocols 2009(10): pdb. ip71.
  • Bamshad, M. and S. P. Wooding (2003). "Signatures of natural selection in thehuman genome." Nature Reviews Genetics 4(2): 99-111.
  • Ashburner, M., C. A. Ball, J. A. Blake, D. Botstein, H. Butler, et al. (2000)."Gene Ontology: tool for the unification of biology." Nature Genetics 25(1):25.
  • Aouizerat, B. E., E. Vittinghoff, S. L. Musone, L. Pawlikowska, P. Y. Kwok,et al. (2011). "GWAS for discovery and replication of genetic loci associatedwith sudden cardiac arrest in patients with coronary artery disease." BMCCardiovascular Disorders 11(1): 29.
  • Amaral, A. J., H.-J. Megens, R. P. Crooijmans, H. C. Heuven and M. A.Groenen (2008). "Linkage disequilibrium decay and haplotype block structurein the pig." Genetics 179(1): 569-579.
  • Albelda, S. M. and C. A. Buck (1990). "Integrins and other cell adhesionmolecules." The FASEB Journal 4(11): 2868-2880.
  • Akey, J. M., G. Zhang, K. Zhang, L. Jin and M. D. Shriver (2002)."Interrogating a high-density SNP map for signatures of natural selection."Genome Research 12(12): 1805-1814.
  • Agerholm, J., A. Basse and K. Christensen (1993). "Investigations on theoccurrence of hereditary diseases in the Danish cattle population 1989-1991."Acta Veterinaria Scandinavica 34(3): 245.
  • Adeyemo, A., N. Gerry, G. Chen, A. Herbert, A. Doumatey, et al. (2009). "Agenome-wide association study of hypertension and blood pressure in AfricanAmericans." PLoS Genetics 5(7): e1000564.
  • 200Yim, H.-S., Y. S. Cho, X. Guang, S. G. Kang, J.-Y. Jeong, et al. (2014)."Minke whale genome and aquatic adaptation in cetaceans." Nature Genetics46(1): 88-92.
  • 195Qanbari, S., E. Pimentel, J. Tetens, G. Thaller, P. Lichtner, et al. (2010). "Agenome?wide scan for signatures of recent selection in Holstein cattle."Animal Genetics 41(4): 377-389.
  • 190Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, et al. (2009). "Thesequence alignment/map format and SAMtools." Bioinformatics 25(16):2078-2079.