State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany.
Theor Appl Genet. 2011 Sep;123(5):847-58. doi: 10.1007/s00122-011-1631-7. Epub 2011 Jun 17.
Association mapping (AM) is a powerful approach to dissect the genetic architecture of quantitative traits. The main goal of our study was to empirically compare several statistical methods of AM using data of an elite maize breeding program with respect to QTL detection power and possibility to correct for population stratification. These models were based on the inclusion of cofactors (Model A), cofactors and population effect (Model B), and SNP effects nested within populations (Model C). A total of 930 testcross progenies of an elite maize breeding population were field-evaluated for grain yield and grain moisture in multi-location trials and fingerprinted with 425 SNP markers. For grain yield, population stratification was effectively controlled by Model A. For grain moisture with a high ratio of variance among versus within populations, Model B should be applied in order to avoid potential false positives. Model C revealed large differences among allele substitution effects for trait-associated SNPs across multiple plant breeding populations. This heterogeneous SNP allele substitution effects have a severe impact for genomic selection studies, where SNP effects are often assumed to be independent of the genetic background.
关联作图（AM）是解析数量性状遗传结构的一种强大方法。我们的研究主要目的是使用一个优秀的玉米育种计划的数据，从 QTL 检测能力和校正群体分层的可能性方面，对 AM 的几种统计方法进行实证比较。这些模型基于包含协变量（模型 A）、协变量和群体效应（模型 B）以及 SNP 效应嵌套在群体内（模型 C）。一个优秀的玉米育种群体的 930 个测验交后代在多个地点的试验中进行了田间产量和籽粒水分的评估，并利用 425 个 SNP 标记进行了指纹图谱分析。对于产量，模型 A 有效地控制了群体分层。对于群体间方差与群体内方差比值较高的籽粒水分，为避免潜在的假阳性，应采用模型 B。模型 C 揭示了跨多个植物育种群体的与性状相关的 SNP 等位基因替代效应之间的巨大差异。这种不均匀的 SNP 等位基因替代效应对基因组选择研究有严重影响，在这些研究中，通常假设 SNP 效应与遗传背景无关。
