Institute of Animal Breeding and Husbandry, Christian-Albrechts University of Kiel, 24098 Kiel, Germany.
Genetics. 2010 Jun;185(2):655-70. doi: 10.1534/genetics.110.115774. Epub 2010 Apr 9.
Information from cosegregation of marker and QTL alleles, in addition to linkage disequilibrium (LD), can improve genomic selection. Variance components linear models have been proposed for this purpose, but accommodating dominance and epistasis is not straightforward with them. A full-Bayesian analysis of a mixture genetic model is favorable in this respect, but is computationally infeasible for whole-genome analyses. Thus, we propose an approximate two-step approach that neglects information from trait phenotypes in inferring ordered genotypes and segregation indicators of markers. Quantitative trait loci (QTL) fine-mapping scenarios, using high-density markers and pedigrees of five generations without genotyped females, were simulated to test this strategy against an exact full-Bayesian approach. The latter performed better in estimating QTL genotypes, but precision of QTL location and accuracy of genomic breeding values (GEBVs) did not differ for the two methods at realistically low LD. If, however, LD was higher, the exact approach resulted in a slightly higher accuracy of GEBVs. In conclusion, the two-step approach makes mixture genetic models computationally feasible for high-density markers and large pedigrees. Furthermore, markers need to be sampled only once and results can be used for the analysis of all traits. Further research is needed to evaluate the two-step approach for complex pedigrees and to analyze alternative strategies for modeling LD between QTL and markers.
除连锁不平衡（LD）外，标记和 QTL 等位基因的共分离信息也可以改进基因组选择。为此已经提出了方差分量线性模型，但用这些模型直接容纳显性和上位性并不容易。混合遗传模型的全贝叶斯分析在这方面是有利的，但对于全基因组分析来说计算上是不可行的。因此，我们提出了一种近似的两步方法，该方法在推断有序基因型和标记的分离指标时忽略了来自性状表型的信息。使用高密度标记和五代无基因型雌性的系谱模拟了 QTL 精细定位场景，以比较这种策略与精确的全贝叶斯方法。后者在估计 QTL 基因型方面表现更好，但在实际低 LD 下，两种方法的 QTL 位置精度和基因组育种值（GEBV）的准确性没有差异。然而，如果 LD 更高，精确方法会导致 GEBV 的准确性略有提高。总之，两步方法使混合遗传模型在高密度标记和大型系谱中具有计算可行性。此外，仅需对标记进行一次采样，并且结果可用于分析所有性状。需要进一步研究两步方法在复杂系谱中的应用，并分析替代模型 QTL 和标记之间 LD 的策略。
