An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines

G3: Genes, Genomes, Genetics

Volumn 1, Issue 1, 2011, Pages 57-64

  Crooks, Lucy ^a   Nettelblad, Carl ^a   Carlborg, Örjan ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

Hidden markov model; Interval mapping; Line origin probabilities; Outbred line cross; SNP chip

Indexed keywords

EID: 84866175167     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.111.000109     Document Type: Article

References (18)

1. Broman, K. W., H. Wu, S. Sen, and G. A. Churchill, 2003 R/qtl: QTL mapping in experimental crosses. Bioinformatics., 19: 889-890.
2. Corva, P. M., and J. F. Medrano, 2001 Quantitative trait loci (QTLs) mapping for growth traits in the mouse: a review. Genet. Sel. Evol., 33: 105-132.
3. Frary, A., T. C. Nesbitt, A. Frary, S. Grandillo, E. Van Der Knaap et al., 2000 fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science., 289: 85-88.
4. Groenen, M. A. M., P. Wahlberg, M. Foglio, H. H. Cheng, H.-J. Megens et al., 2009 A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res., 19: 510-519.
5. Haley, C. S., S. A. Knott, and J.-M. Elsen, 1994 Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics., 136: 1195-1207.
6. Hocking, P. M., 2005 Review of QTL mapping results in chickens. Worlds Poult. Sci. J., 61: 215-226.
7. Kerje, S., Ö. Carlborg, L. Jacobsson, K. Schütz, C. Hartmann et al., 2003 The twofold difference in adult size between the red junglefowl and White Leghorn chickens is largely explained by a limited number of QTLs. Anim. Genet., 34: 264-274.
8. Lander, E. S., and D. Botstein, 1989 Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics., 121: 185-199.
9. Lander, E. S., and P. Green, 1987 Construction of multilocus genetic linkage maps in humans. Proc. Natl. Acad. Sci., USA 84: 2363-2367.
10. Long, A. D., R. F. Lyman, A. H. Morgan, C. H. Langley, and T. F. C. Mackay, 2000 Both naturally occurring insertions of transposable elements and intermediate frequency polymorphisms at the achaete-scute complex are associated with variation in bristle number in Drosophila melanogaster. Genetics., 154: 1255-1269.
11. Mackay, T. F. C., 2001 Quantitative trait loci in Drosophila. Nat. Rev. Genet., 2: 11-20.
12. Maloof, J. N., 2003 QTL for plant growth and morphology. Curr. Opin. Plant Biol., 6: 85-90.
13. Nettelblad, C., S. Holmgren, L. Crooks, and Ö. Carlborg, 2009 cnF2freq: efficient determination of genotype and haplotype probabilities in outbred populations using Markov models, pp. 307-319 in Bioinformatics and Computational Biology, 1st International Conference BICoB, April 8- 10, New Orleans, edited by S. Rajasekaran. Springer-Verlag, Berlin, Heidelberg.
14. Rabiner, L. R., 1989 A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE., 77: 257-286.
15. Rothschild, M. F., Z.-L. Hu, and Z. Jiang, 2007 Advances in QTL mapping in pigs. Int. J. Biol. Sci., 3: 192-197.
16. RÖnnegård, L., F. Besnier, and Ö. Carlborg, 2008 An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs. Genetics., 178: 2315-2326.
17. Seaton, G., J. Hernandez, J.-A. Grunchec, I. White, J. Allen et al., 2006 GridQTL: a grid portal for QTL mapping of compute intensive datasets, Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, August 13-18, Belo Horizonte, MG, Brasil.
18. Van Laere, A.-S., M. Nguyen, M. Braunschwieg, C. Nezer, C. Collette et al., 2003 A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature., 425: 832-836.