Demeure Olivier, Bacciu Nicola, Filangi Olivier, Le Roy Pascale
INRA, UMR 598 Génétique Animale, F-35000 Rennes, France .
BMC Proc. 2010 Mar 31;4 Suppl 1(Suppl 1):S10. doi: 10.1186/1753-6561-4-s1-s10.
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.
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.
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.
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.
新的分子技术允许利用密集遗传图谱进行高通量基因分型以进行QTL定位。因此，针对连锁不平衡的连锁分析模型的意义可能会受到质疑。由于这两种策略对标记密度、实验设计结构、连锁不平衡程度和QTL效应非常敏感，我们建议研究这些参数对QTL检测的影响。
使用三种连锁不平衡模型和一种连锁分析模型对第13届QTLMAS研讨会模拟数据集进行分析。使用QTLMAP进行区间作图、多变量分析以及QTL之间的相互作用分析。
连锁分析模型鉴定出13个QTL，其中10个定位在模拟的18个QTL附近，另外三个位置被错误地定位为含有一个QTL。通过区间作图分析鉴定出的大多数QTL没有被任何连锁不平衡模型清楚地检测到。此外，QTL效应在整个过程中不断变化，而这在连锁不平衡模型中未被观察到。
我们的结果表明，对于这样的标记密度，区间作图策略仍然优于仅使用连锁不平衡。虽然实验设计结构赋予了两种方法很大的功效，但标记密度和信息性明显影响QTL检测的连锁不平衡效率。
