School of Mathematical Sciences, Beijing Normal University, Beijing, 100875, China.
Theor Appl Genet. 2010 Oct;121(6):1071-82. doi: 10.1007/s00122-010-1372-z. Epub 2010 Jun 10.
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.
在实际的数量性状基因座（QTL）定位群体中，缺失标记和分离失真很常见。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，随着缺失标记水平的增加，检测能力降低，假发现率增加。缺失标记对较小效应 QTL 和较小大小群体的影响更大。缺失标记的影响可以通过类似于标记缺失率的较小大小群体来量化。对于分离失真，如果失真标记与任何 QTL 不紧密连锁，则不会对 QTL 定位产生重大影响；否则，失真的影响将取决于 QTL 的显性程度、三种标记类型的频率、失真标记与 QTL 之间的连锁距离以及定位群体的大小。有时，失真会导致比非失真更高的遗传方差，从而有利于检测连锁 QTL。本研究给出了失真和非失真条件下由 QTL 解释的遗传方差比的公式，以便于确定分离失真标记（SDM）是否增加或降低了 QTL 的检测能力。随着 SDM 与 QTL 的连锁关系变得越来越松，其效应会迅速降低。一般来说，失真标记不会对 QTL 的位置和效应估计产生重大影响，在较大的定位群体中可以忽略它们的影响。
