Zhao H, Nettleton D, Soller M, Dekkers J C M
Department of Animal Science, 239 Kildee Hall, Iowa State University, Ames, IA 50011, USA.
Genet Res. 2005 Aug;86(1):77-87. doi: 10.1017/S001667230500769X.
Effectiveness of marker-assisted selection (MAS) and quantitative trait loci (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTL depends on the extent of LD and how it declines with distance in a population. Because marker-QTL LD cannot be observed directly, the objective of this study was to evaluate alternative measures of observable LD between multi-allelic markers as predictors of usable LD of multi-allelic markers with presumed biallelic QTL. Observable LD between marker pairs was evaluated using eight existing measures and one new measure. These consisted of two pooled and standardized measures of LD between pairs of alleles at two markers based on Lewontin's LD measure, two pooled measures of squared correlations between alleles, one standardized measure using Hardy-Weinberg heterozygosities, and four measures based on the chi-square statistic for testing for association between alleles at two loci. In simulated populations with a range of LD generated by drift and a range of marker polymorphism, marker-marker LD measured by a standardized chi-square statistic (denoted chi(2')) was found to be the best predictor of useable marker-QTL LD for a group of multi-allelic markers. Estimates of the level and decline of marker-marker LD with distance obtained from chi(2') were linearly and highly correlated with usable LD of those markers with QTL across population structures and marker polymorphism. Corresponding relationships were poorer for the other marker-marker LD measures. Therefore, when LD is generated by drift, chi(2') is recommended to quantify the amount and extent of usable LD in a population for QTL mapping and MAS based on multi-allelic markers.
利用标记与数量性状基因座（QTL）之间全群体连锁不平衡（LD）进行标记辅助选择（MAS）和QTL定位的有效性，取决于LD的程度以及它在群体中随距离的衰减情况。由于标记-QTL的LD无法直接观测，本研究的目的是评估多等位基因标记间可观测LD的替代指标，作为多等位基因标记与假定双等位基因QTL可用LD的预测指标。使用8种现有指标和1种新指标评估标记对之间的可观测LD。这些指标包括基于Lewontin的LD指标的两个关于两个标记上等位基因对间LD的合并和标准化指标、两个等位基因间平方相关性的合并指标、一个使用哈迪-温伯格杂合度的标准化指标，以及四个基于卡方统计量用于检验两个位点上等位基因间关联性的指标。在由遗传漂变产生一系列LD以及一系列标记多态性的模拟群体中，发现用标准化卡方统计量（记为chi(2')）测量的标记-标记LD是一组多等位基因标记可用标记-QTL LD的最佳预测指标。从chi(2')获得的标记-标记LD水平及其随距离衰减的估计值，与跨群体结构和标记多态性的那些具有QTL的标记的可用LD呈线性且高度相关。对于其他标记-标记LD指标，相应的关系则较差。因此，当LD由遗传漂变产生时，建议使用chi(2')来量化群体中用于基于多等位基因标记的QTL定位和MAS的可用LD的数量和范围。
