QTL detection for a medium density SNP panel: comparison of different LD and LA methods

BMC Proceedings

Pascale Le Roy¹  Olivier Filangi¹  Nicola Bacciu¹  Olivier Demeure¹ 

[1]Agrocampus-Ouest, UMR Génétique Animale, F-35000 Rennes, France

Others  :  1129505
DOI  :  10.1186/1753-6561-4-S1-S10

【 摘 要 】

Background

New molecular technologies allow high throughput genotyping for QTL mapping with dense genetic maps. Therefore, the interest of linkage analysis models against linkage disequilibrium could be questioned. As these two strategies are very sensitive to marker density, experimental design structures, linkage disequilibrium extent and QTL effect, we propose to investigate these parameters effects on QTL detection.

Methods

The XIIIth QTLMAS workshop simulated dataset was analysed using three linkage disequilibrium models and a linkage analysis model. Interval mapping, multivariate and interaction between QTL analyses were performed using QTLMAP.

Results

The linkage analysis models identified 13 QTL, from which 10 mapped close of the 18 which were simulated and three other positions being falsely mapped as containing a QTL. Most of the QTLs identified by interval mapping analysis are not clearly detected by any linkage disequilibrium model. In addition, QTL effects are evolving during the time which was not observed using the linkage disequilibrium models.

Conclusions

Our results show that for such a marker density the interval mapping strategy is still better than using the linkage disequilibrium only. While the experimental design structure gives a lot of power to both approaches, the marker density and informativity clearly affect linkage disequilibrium efficiency for QTL detection.

【 授权许可】

   
2010 Demeure et al; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Coster A, Bastiaansen J, Calus M, Maliepaard C, Bink M: QTLMAS 2009: Simulated Dataset. BMCProc 2010, 4(Suppl 1):S3.
• [2]SAS Institute: User's guide: statistics. SAS Publishing; 1982.
• [3]Elsen JM, Filangi O, Gilbert H, Legarra A, Le Roy P, Moreno C: QTLMap : a software for the detection of QTL in full and half sib families. Proceedings of the EAAP Annual Meeting: 2009.
• [4]Le Roy P, Elsen JM, Boichard D, Mangin B, Bidanel JP, Goffinet B: An algorithm for QTL detection in mixture of full and half sib families:. 6th World Congress on Genetics Applied to Livestock Production, Armidale 1998.
• [5]Elsen JM, Mangin B, Goffinet B, Boichard D, Le Roy P: Alternative models for QTL detection in livestock. I. General introduction. Genet Sel Evol 1999, 31:213-224. BioMed Central Full Text
• [6]Elsen JM, Filangi O, Gilbert H, Le Roy P, Moreno C: A fast algorithm for estimating transmission probabilities in QTL detection designs with dense maps. Genet Sel Evol 1999, 41:50. BioMed Central Full Text
• [7]Gilbert H, Le Roy P: Methods for detection of multiple linked QTL applied to a mixture of full and half sib families. Genet Sel Evol 2007, 39:139-158. BioMed Central Full Text
• [8]Harrel FE, Davis CE: A new distribution-free quantile estimator. Biometrika 1982, 69:635-640.
• [9]Sorensen D, Gianola D: Likelihood, Bayesian and MCMC Methods in Quantitative Genetics. Springer; 2002.