Zhao H, Nettleton D, Dekkers J C M
Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA.
Genet Res. 2007 Feb;89(1):1-6. doi: 10.1017/S0016672307008634.
Effectiveness of marker-assisted selection (MAS) and quantitative trait locus (QTL) mapping using population-wide linkage disequilibrium (LD) between markers and QTLs depends on the extent of LD and how it declines with distance between markers and QTLs in a population. Marker-QTL LD can be predicted from LD between markers. Our previous work evaluated LD measures between multi-allelic markers as predictors of usable LD of multi-allelic markers with QTLs. Since single nucleotide polymorphisms (SNPs) are the current marker of choice for high-density genotyping and LD-mapping of QTLs, the objective of this study was to use LD between multi-allelic markers to predict LD among biallelic SNPs or between SNPs and QTLs. Observable LD between multi-allelic markers was evaluated using nine measures. These included 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. The standardized chi-square measure that best predicted usable LD between multi-allelic markers and QTLs, based on our previous work, overestimated usable SNP-SNP or SNP-QTL LD. Instead, three other measures were found to be good predictors of usable SNP-SNP or SNP-QTL LD when LD is generated by drift. Therefore, the LD measure between multi-allelic markers that is best for predicting usable LD in a population depends on the type of markers (i.e. multi-allelic or biallelic) that will eventually be used for QTL mapping or MAS.
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如何随标记与QTL之间的距离而衰减。标记-QTL LD可以从标记之间的LD预测得到。我们之前的工作评估了多等位基因标记之间的LD度量，作为多等位基因标记与QTL可用LD的预测指标。由于单核苷酸多态性（SNP）是当前用于QTL高密度基因分型和LD定位的首选标记，本研究的目的是利用多等位基因标记之间的LD来预测双等位基因SNP之间或SNP与QTL之间的LD。使用九种度量评估了多等位基因标记之间可观察到的LD。这些度量包括基于Lewontin的LD度量的两个合并和标准化的两个标记上等位基因对之间LD的度量、两个等位基因之间平方相关性的合并度量、一个使用哈迪-温伯格杂合度的标准化度量，以及四个基于卡方统计量用于检验两个位点上等位基因之间关联性的度量。基于我们之前的工作，能最佳预测多等位基因标记与QTL之间可用LD的标准化卡方度量，高估了可用的SNP-SNP或SNP-QTL LD。相反，当LD由漂变产生时，发现其他三种度量是可用的SNP-SNP或SNP-QTL LD的良好预测指标。因此，对于预测群体中可用LD而言，多等位基因标记之间最佳的LD度量取决于最终将用于QTL定位或MAS的标记类型（即多等位基因或双等位基因）。
