The Institute for Genetics and Bioinformatics, University of New England, Armidale, NSW 2351, Australia.
J Anim Breed Genet. 2010 Jun;127(3):199-206. doi: 10.1111/j.1439-0388.2009.00836.x.
Some individual genetic markers show strong and apparently consistent effects on trait merit and are taken as causative mutations that can be used directly as fixed effects in marker-assisted selection programs. If the effect of such a marker is seen to decrease over time, key reasons include epistasis, where the effect depends on genetic background, and recombination, where the marker is in fact not causative, and strong linkage disequilibrium between the marker and the causative QTL is breaking down. This paper presents a method to detect the latter scenario, including calculation of the probability of a recombinant haplotype for each gamete contributing to each individual in a pedigree. This method requires only pedigree, phenotypes and genotypic information on the single marker. Missing marker genotypes are handled by the method, but with diminishing power. For biallelic markers, strong QTL effects are needed for the method to be of clear value. Given suitable results, breeders may chose to eliminate certain individuals from the breeding program in order to continue using the single genetic marker under high linkage disequilibrium with the causative QTL. Alternatively, other linked markers might be sought that can be used individually or in haplotype tests to restore strong LD for marker-assisted selection.
一些个体遗传标记表现出对性状优势的强烈且明显一致的影响，被视为可直接用作标记辅助选择计划中固定效应的因果突变。如果这样的标记的效果随着时间的推移而降低，关键原因包括上位性，即效应取决于遗传背景，以及重组，即标记实际上不是因果关系，并且标记与因果 QTL 之间存在强烈的连锁不平衡正在瓦解。本文提出了一种检测后一种情况的方法，包括计算每个配子对系谱中每个个体的重组单倍型的概率。该方法仅需要系谱、表型和单个标记的基因型信息。该方法处理缺失的标记基因型，但功效会降低。对于双等位基因标记，需要强 QTL 效应才能使该方法具有明显的价值。如果得到合适的结果，育种者可能会选择从育种计划中淘汰某些个体，以便继续在与因果 QTL 高度连锁的情况下使用单个遗传标记。或者，可以寻找其他连锁标记，这些标记可以单独使用或在单倍型测试中用于恢复标记辅助选择的强 LD。
