Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  Zhang, Hui ^a,b   Hu, Xiaoxiang ^c   Wang, Zhipeng ^a,b   Zhang, Yuandan ^d   Wang, Shouzhi ^a,b   Wang, Ning ^a,b   Ma, Li ^e   Leng, Li ^a,b   Wang, Shengwen ^e   Wang, Qigui ^a,b   Wang, Yuxiang ^a,b   Tang, Zhiquan ^a,b   Li, Ning ^c   Da, Yang ^e   Li, Hui ^a,b  

^a AGRO ENVIRONMENTAL PROTECTION INSTITUTE   (China)

^b NORTHEAST AGRICULTURAL UNIVERSITY   (China)

^c CHINA AGRICULTURAL UNIVERSITY   (China)

^d UNIVERSITY OF NEW ENGLAND   (Australia)

^e UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABDOMINAL FAT; ABDOMINAL FAT CONTENT; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CAST GENE; CHICKEN; CHROMOSOMAL LOCALIZATION; CHROMOSOME; CHROMOSOME 1; CHROMOSOME 11; CHROMOSOME 15; CHROMOSOME 2; CHROMOSOME 20; CHROMOSOME 26; CHROMOSOME 4; CHROMOSOME 5; CHROMOSOME ANALYSIS; CHROMOSOME Z; ELL2 GENE; ERAP1 GENE; FAT CONTENT; FBN2 GENE; GENE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; MALE; MAR 03 GENE; NONHUMAN; PC1 GENE; PROMOTER REGION; SELECTION SIGNATURE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SLC12A2 GENE;

ABDOMINAL FAT; ANIMALS; BASE SEQUENCE; CHICKENS; CHROMOSOME MAPPING; GENE FREQUENCY; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; LINKAGE DISEQUILIBRIUM; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROPROTEIN CONVERTASE 1;

EID: 84863814398     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040736     Document Type: Article

References (35)

1. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
2. Zhao J, Bradfield JP, Zhang H, Sleiman PM, Kim CE, et al. (2011) Role of BMI-Associated Loci Identified in GWAS Meta-Analyses in the Context of Common Childhood Obesity in European Americans. Obesity (Silver Spring) doi:10.1038/oby.2011.237.
3. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nat Genet 42: 937-948.
4. Thorleifsson G, Walters GB, Gudbjartsson DF, Steinthorsdottir V, Sulem P, et al. (2009) Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. Nat Genet 41: 18-24.
5. Willer CJ, Speliotes EK, Loos RJ, Li S, Lindgren CM, et al. (2009) Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nat Genet 41: 25-34.
6. Morgan AR, Han DY, Thompson JM, Mitchell EA, Ferguson LR, (2011) Analysis of MMP2 promoter polymorphisms in childhood obesity. BMC Res Notes 4: 253.
7. Han DH, Kim SK, Kang S, Choe BK, Kim KS, et al. (2008) Matrix Metallopeptidase 2 Gene Polymorphism is Associated with Obesity in Korean Population. Korean J Physiol Pharmacol 12: 125-129.
8. Benzinou M, Creemers JW, Choquet H, Lobbens S, Dina C, et al. (2008) Common nonsynonymous variants in PCSK1 confer risk of obesity. Nat Genet 40: 943-945.
9. Choquet H, Stijnen P, Creemers JW, (2011) Genetic and Functional Characterization of PCSK1. Methods Mol Biol 768: 247-253.
10. Kilpeläinen TO, Bingham SA, Khaw KT, Wareham NJ, Loos RJ, (2009) Association of variants in the PCSK1 gene with obesity in the EPIC-Norfolk study. Hum Mol Genet 18: 3496-3501.
11. Chang YC, Chiu YF, Shih KC, Lin MW, Sheu WH, et al. (2010) Common PCSK1 haplotypes are associated with obesity in the Chinese population. Obesity (Silver Spring) 18: 1404-1409.
12. NCBI website. Available:http://www.ncbi.nlm.nih.gov. Accessed 2011 Aug 22.
13. Parikh RM, Joshi SR, Menon PS, Shah NS, (2007) Index of central obesity - A novel parameter. Med Hypotheses 68: 1272-1275.
14. Méthot J, Houle J, Poirier P, (2010) Obesity: how to define central adiposity? Expert Rev Cardiovasc Ther 8: 639-644.
15. Nones K, Ledur MC, Ruy DC, Baron EE, Melo CM, et al. (2006) Mapping QTLs on chicken chromosome 1 for performance and carcass traits in a broiler x layer cross. Animal Genetics 37: 95-100.
16. Havenstein GB, Ferket PR, Scheideler SE, Rives DV, (1994) Carcass composition and yield of 1991 vs 1957 broilers when fed "typical" 1957 and 1991 broiler diets. Poult Sci 73: 1795-1804.
17. Kessler AM, Snizek PN Jr, Brugalli I, (2000) Manipulação da quantidade de gordura na carcaça de frangos In: Anais da Conferência APINCO de Ciência e Tecnologia Avícolas. APINCO, Campinas, SP, Brazil Press.
18. Chambers JR, (1990) Genetics of growth and meat production in chickens. In Poultry breeding and genetics Edited by: Crawford RD. Amsterdam: Elsevier Press.
19. Rubin CJ, Zody MC, Eriksson J, Meadows JRS, Sherwood E, et al. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-591.
20. Sabeti PC, Varilly P, Fry B, Lohmueller J, Elizabeth Hostetter E, et al. (2007) The International HapMap Consortium: Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
21. Flori L, Fritz S, Jaffrézic F, Boussaha M, Gut I, et al. (2009) The genome response to artificial selection: a case study in dairy cattle. PLoS One 4: e6595.
22. Johansson AM, Pettersson ME, Siegel PB, Carlborg Ö, (2010) Genome-Wide Effects of Long-Term Divergent Selection. PLoS Genet 6(11): e1001188 doi:10.1371/journal.pgen.1001188.
23. Barrett JC, Fry B, Maller J, Daly MJ, (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
24. Sabeti PC, Reich DE, Higgins JM, Levine HZ, Richter DJ, et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
25. Scheet P, Stephens M, (2006) A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
26. Ma L, Runesha HB, Dvorkin D, Garbe JR, Da Y, (2008) Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies. BMC Bioinformatics 9: 315.
27. Mao Y, London NR, Ma L, Dvorkin D, Da Y, (2006) Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model. Physiol Genomics 28: 46-52.
28. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81: 559-575.
29. Ensembl website. Available:http://useast.ensembl.org/index.html. Accessed 2011 Aug 24.
30. Mutch DM, Clément K, (2006) Unraveling the genetics of human obesity. PLoS Genet 2: e188 doi:10.1371/journal.pgen.0020188.
31. UCSC website. Available:http://genome.ucsc.edu. Accessed 2011 Aug 18.
32. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, et al. (2002) The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
33. Ikeobi CO, Woolliams JA, Morrice DR, Law A, Windsor D, et al. (2002) Quantitative trait loci affecting fatness in the chicken. Anim Genet 33: 428-435.
34. Zhou H, Mitchell AD, McMurtry JP, Ashwell CM, Lamont SJ, (2005) Insulin-like growth factor-I gene polymorphism associations with growth, body composition, skeleton integrity, and metabolic traits in chickens. Poult Sci 84: 212-219.
35. Animal QTLdb website. Available:http://www.genome.iastate.edu/cgi-bin/QTLdb/index. Accessed 2011 Aug 29.