Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska st, 33, 60-637 Poznan, Poland.
Genet Sel Evol. 2011 Jun 21;43(1):23. doi: 10.1186/1297-9686-43-23.
The predictive ability of genomic estimated breeding values (GEBV) originates both from associations between high-density markers and QTL (Quantitative Trait Loci) and from pedigree information. Thus, GEBV are expected to provide more persistent accuracy over successive generations than breeding values estimated using pedigree-based methods. The objective of this study was to evaluate the accuracy of GEBV in a closed population of layer chickens and to quantify their persistence over five successive generations using marker or pedigree information.
The training data consisted of 16 traits and 777 genotyped animals from two generations of a brown-egg layer breeding line, 295 of which had individual phenotype records, while others had phenotypes on 2,738 non-genotyped relatives, or similar data accumulated over up to five generations. Validation data included phenotyped and genotyped birds from five subsequent generations (on average 306 birds/generation). Birds were genotyped for 23,356 segregating SNP. Animal models using genomic or pedigree relationship matrices and Bayesian model averaging methods were used for training analyses. Accuracy was evaluated as the correlation between EBV and phenotype in validation divided by the square root of trait heritability.
Pedigree relationships in outbred populations are reduced by 50% at each meiosis, therefore accuracy is expected to decrease by the square root of 0.5 every generation, as observed for pedigree-based EBV (Estimated Breeding Values). In contrast the GEBV accuracy was more persistent, although the drop in accuracy was substantial in the first generation. Traits that were considered to be influenced by fewer QTL and to have a higher heritability maintained a higher GEBV accuracy over generations. In conclusion, GEBV capture information beyond pedigree relationships, but retraining every generation is recommended for genomic selection in closed breeding populations.
基因组估计育种值（GEBV）的预测能力源自高密度标记与 QTL（数量性状位点）之间的关联以及系谱信息。因此，与使用基于系谱的方法估计的育种值相比，GEBV 预计在连续几代中具有更高的持续性准确性。本研究的目的是评估封闭层鸡群体中 GEBV 的准确性，并使用标记或系谱信息量化其在连续五代中的持久性。
训练数据由两代棕色蛋鸡系谱中的 16 个性状和 777 只基因型动物组成，其中 295 只有个体表型记录，而其他动物则有 2738 只非基因型亲属的表型记录，或累积了多达五代的类似数据。验证数据包括五个后续世代的表型和基因型鸟类（平均每个世代 306 只）。鸟类被 23356 个分离 SNP 基因分型。使用基因组或系谱关系矩阵和贝叶斯模型平均方法的动物模型用于训练分析。准确性评估为验证中 EBV（估计育种值）与表型之间的相关性除以性状遗传力的平方根。
在外交种群中，系谱关系每减数分裂减少 50%，因此，正如基于系谱的 EBV 所观察到的那样，准确性预计每代下降 0.5 的平方根。相比之下，GEBV 的准确性更持久，尽管在第一代中准确性大幅下降。被认为受较少 QTL 影响且具有更高遗传力的性状在几代中保持更高的 GEBV 准确性。总之，GEBV 捕获了超越系谱关系的信息，但建议在封闭繁殖群体中进行基因组选择时，每代都要重新训练。
