Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602-2771, USA.
J Anim Sci. 2011 Sep;89(9):2673-9. doi: 10.2527/jas.2010-3555. Epub 2011 Mar 31.
Phenotypic data on BW and breast meat area were available on up to 287,614 broilers. A total of 4,113 birds were genotyped for 57,636 SNP. Data were analyzed by a single-step genomic BLUP (ssGBLUP), which accounts for all phenotypic, pedigree, and genomic information. The genomic relationship matrix (G) in ssGBLUP was constructed using either equal (0.5; GEq) or current (GC) allele frequencies, and with all SNP or with SNP with minor allele frequencies (MAF) below multiple thresholds (0.1, 0.2, 0.3, and 0.4) ignored. Additionally, a pedigree-based relationship matrix for genotyped birds (A(22)) was available. The matrices and their inverses were compared with regard to average diagonal (AvgD) and off-diagonal (AvgOff) elements. In A(22), AvgD was 1.004 and AvgOff was 0.014. In GEq, both averages decreased with the increasing thresholds for MAF, with AvgD decreasing from 1.373 to 1.020 and AvgOff decreasing from 0.722 to 0.025. In GC, AvgD was approximately 1.01 and AvgOff was 0 for all MAF. For inverses of the relationship matrices, all AvgOff were close to 0; AvgD was 2.375 in A(22), varied from 11.563 to 12.943 for GEq, and increased from 8.675 to 12.859 for GC as the threshold for MAF increased. Predictive ability with all GEq and GC was similar except that at MAF = 0.4, they declined by 0.01 for BW and improved by 0.01 for breast meat area. Compared with BLUP, EBV in the ssGBLUP were, on average, increased by up to 1 additive SD greater with GEq and decreased by 2 additive SD less with GC. Genotyped animals were biased upward with GEq and downward with GC. The biases and differences in EBV could be controlled by adding a constant to GC; they were eliminated with a constant of 0.014, which corresponds to AvgOff in A(22). Unbiased evaluation in the ssGBLUP may be obtained with GC scaled to be compatible with A(22). The reduction of SNP with small MAF has a small effect on the real accuracy, but it may falsely increase the estimated accuracies by inversion.
对多达 287614 只肉鸡的 BW 和胸肉面积的表型数据进行了分析。共有 4113 只鸡进行了 57636 个 SNP 的基因型分析。采用单步基因组 BLUP（ssGBLUP）进行数据分析，该方法考虑了所有表型、系谱和基因组信息。ssGBLUP 中的基因组关系矩阵（G）是使用相等（0.5；GEq）或当前（GC）等位基因频率构建的，同时忽略 SNP 或 SNP 中 MAF（0.1、0.2、0.3 和 0.4）较低的 SNP。此外，还提供了一个基于系谱的基因型鸟类关系矩阵（A(22)）。比较了这些矩阵及其逆矩阵的平均对角（AvgD）和非对角（AvgOff）元素。在 A(22)中，AvgD 为 1.004，AvgOff 为 0.014。在 GEq 中，随着 MAF 阈值的增加，这两个平均值都降低了，AvgD 从 1.373 降低到 1.020，AvgOff 从 0.722 降低到 0.025。在 GC 中，对于所有 MAF，AvgD 约为 1.01，AvgOff 为 0。对于关系矩阵的逆矩阵，所有 AvgOff 都接近 0；AvgD 在 A(22)中为 2.375，在 GEq 中从 11.563 到 12.943 不等，在 GC 中从 8.675 增加到 12.859，随着 MAF 阈值的增加而增加。除了 MAF = 0.4 时，所有 GEq 和 GC 的预测能力都相似，BW 下降 0.01，胸肉面积增加 0.01。与 BLUP 相比，ssGBLUP 中的 EBV 平均增加了 1 个加性 SD，GEq 增加了 1 个加性 SD，GC 减少了 2 个加性 SD。基因型动物的 GEq 呈上升趋势，GC 呈下降趋势。GC 中添加常数可以控制 EBV 的偏差和差异；用 0.014 的常数消除，与 A(22)中的 AvgOff 相对应。GC 调整到与 A(22)兼容后，ssGBLUP 中可能会获得无偏估计值。具有较小 MAF 的 SNP 的减少对实际准确性的影响很小，但通过反转可能会错误地增加估计的准确性。
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