SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Marklund, Stefan ^a   Carlborg, Örjan ^a,b  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHICKEN; CONTROLLED STUDY; DNA FLANKING REGION; DNA SEQUENCE; GENE FREQUENCY; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOTYPE; MICROCHROMOSOME; NONHUMAN; PREDICTION; SENSITIVITY ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BREEDING; DNA MICROARRAY; GENETICS; GENOME; METHODOLOGY;

ANIMALS; BREEDING; CHICKENS; DNA; GENE FREQUENCY; GENETIC VARIATION; GENOME; GENOTYPE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 78649330039     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-665     Document Type: Article

References (15)

1. Darvasi A, Soller M. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 1995, 141:1199-1207. 1206841, 8582624.
2. Karlsson EK, Baranowska I, Wade CM, Salmon Hillbertz NHC, Zody MC, Anderson N, Biagi TM, Pattersson N, Rosengren Pielberg G, Kulbokas EJ, Comstock KE, Keller ET, Mesirov JP, von Euler H, Kämpe O, Hedhammar T, Lander ES, Andersson G, Andersson L, Lindblad-Toh K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 2007, 39:1321-1328. 10.1038/ng.2007.10, 17906626.
3. Koudandé OD, Iraqi F, Thomson PC, Teale AJ, van Arendonk JA. Strategies to optimize marker-assisted introgression of multiple unlinked QTL. Mamm Genome 2000, 11:145-150. 10.1007/s003350010028, 10656930.
4. Flaherty L. Congenic strains. The Mouse in Biomedical Research 1981, 1:215-222. New York, Academic Press, Foster HL, Small JD, Fox JG.
5. Dunnington EA, Siegel PB. Long-term divergent selection for eight-week body weight in white Plymouth rock chickens. Poult Sci 1996, 75(10):1168-1179.
6. Jacobsson L, Park HB, Wahlberg P, Fredriksson R, Perez-Enciso M, Siegel PB, Andersson L. Many QTLs with minor additive effects are associated with a large difference in growth between two selection lines in chickens. Genet Res Camb 2005, 86:115 -125.
7. Carlborg T, Jacobsson L, Åhgren P, Siegel P, Andersson L. Epistasis and the release of genetic variation during long-term selection. Nat Genet 2006, 38(4):418-420. 10.1038/ng1761, 16532011.
8. Chicken (Gallus gallus) May 2006 assembly v 2.1/galGal3. Genome Sequencing Center at the Washington University School of Medicine in St. Louis, MO, USA (WUSTL)., http://genome.wustl.edu/pub/organism/Other_Vertebrates/Gallus_gallus/assembly/Gallus_gallus-2.1
9. Rubin CJ, Zody MC, Eriksson J, Meadows JR, Sherwood E, Webster MT, Jiang L, Ingman M, Sharpe T, Ka S, Hallböök F, Besnier F, Carlborg T, Bed'hom B, Tixier-Boichard M, Jensen P, Siegel P, Lindblad-Toh K, Andersson L. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 2010, 464:587-591. 10.1038/nature08832, 20220755.
10. Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, Yang H. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms International Chicken Polymorphism Map Consortium. Nature 2004, 432:717-22. 10.1038/nature03156, 2263125, 15592405.
11. Axelsson E, Webster MT, Smith NG, Burt DW, Ellegren H. Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res 2005, 15:120-125. 10.1101/gr.3021305, 540272, 15590944.
12. Megens HJ, Crooijmans RP, Bastiaansen JW, Kerstens HH, Coster A, Jalving R, Vereijken A, Silva P, Muir WM, Cheng HH, Hanotte O, Groenen MA. Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken. BMC Genet 2009, 10:86. 10.1186/1471-2156-10-86, 2803787, 20021697.
13. International Chicken Genome Sequencing Consortium Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 2004, 432:695-716. Erratum in: Nature. 2005 433:777, 10.1038/nature03154, 15592404, International Chicken Genome Sequencing Consortium.
14. Python Software Foundation. , http://www.python.org
15. R Foundation for Statistical Computing. , http://www.r-project.org