Effects of missing marker and segregation distortion on QTL mapping in F2 populations
Effects of missing marker and segregation distortion on QTL mapping in F2 populations
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DOI：
10.1007/s00122-010-1372-z
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发表时间：
2010-06
影响因子：
5.4
通讯作者：
Luyan Zhang;Shiquan Wang;Huihui Li;Q. Deng;A. Zheng;Shuangcheng Li;Ping Li;Zhonglai Li;
中科院分区：
文献类型：
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作者：
Luyan Zhang;Shiquan Wang;Huihui Li;Q. Deng;A. Zheng;Shuangcheng Li;Ping Li;Zhonglai Li;
在实际的QTL定位群体中，标记缺失和分离失真是常见的现象。本研究的目的是通过计算机模拟研究这两个因素对QTL定位的影响。结果表明，检测能力随着缺失标记水平的增加而降低，并且错误发现率增加。缺失标记对较小效应QTL和较小群体的影响较大。缺失标记物的影响可以通过具有类似于标记物缺失率的减小的大小的群体来量化。对于偏分离，如果偏分离标记与QTL不紧密连锁，则对QTL定位没有显著影响;反之，偏分离标记的影响则取决于QTL的显性程度、3种标记类型的频率、偏分离标记与QTL的连锁距离以及定位群体的大小。有时，畸变会导致比非畸变更高的遗传方差，从而有利于连锁QTL的检测。为了更好地判断偏分离标记（SDM）对QTL检测能力的提高或降低，本文给出了偏分离和非偏分离条件下QTL解释的遗传方差比的计算公式。SDM效应随着与QTL连锁关系的松散而迅速降低。一般来说，标记畸变对QTL定位和效应估计的影响不大，在大规模作图群体中可以忽略不计。
Missing marker and segregation distortion are commonly encountered in actual quantitative trait locus (QTL) mapping populations. Our objective in this study was to investigate the impact of the two factors on QTL mapping through computer simulations. Results indicate that detection power decreases with increasing levels of missing markers, and the false discovery rate increases. Missing markers have greater effects on smaller effect QTL and smaller size populations. The effect of missing markers can be quantified by a population with a reduced size similar to the marker missing rate. As for segregation distortion, if the distorted marker is not closely linked with any QTL, it will not have significant impact on QTL mapping; otherwise, the impact of the distortion will depend on the degree of dominance of QTL, frequencies of the three marker types, the linkage distance between the distorted marker and QTL, and the mapping population size. Sometimes, the distortion can result in a higher genetic variance than that of non-distortion, and therefore benefits the detection of linked QTL. A formula of the ratio of genetic variance explained by QTL under distortion and non-distortion was given in this study, so as to easily determine whether the segregation distortion marker (SDM) increases or decreases the QTL detection power. The effect of SDM decreases rapidly as its linkage relationship with QTL becomes looser. In general, distorted markers will not have a great effect on the position and effect estimations of QTL, and their effects can be ignored in large-size mapping populations.