Reliability of pedigree-based and genomic evaluations in selected populations.
Reliability of pedigree-based and genomic evaluations in selected populations.
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DOI：
10.1186/s12711-015-0145-1
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发表时间：
2015-08-14
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影响因子：
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通讯作者：
Hickey JM
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作者：
Gorjanc G;Bijma P;Hickey JM
可靠性是育种中的一个重要参数。它测量估计育种值（EBV）的精度，因此，对这些EBV选择的潜在反应。EBV的精确度通常通过将EBV的预测误差方差（PEV）与基础群体加性遗传方差（基础PEV可靠性）相关联来测量，而对选择的响应潜力通常通过EBV与选择候选者的育种值（BV）之间的平方相关（选择的可靠性）来测量。虽然这两项措施对非政府组织人口是等效的，但对选定人口则不等效。本研究的目的是量化选择对这两个可靠性指标的影响，并显示这如何影响基于谱系或基因组评估的育种计划的比较。模拟了随机和最佳线性无偏预测（BLUP）选择的两种情况，其中仅使用系谱、系谱和表型、全基因组标记基因型和表型或仅使用全基因组标记基因型来估计选择候选者的EBV。将这些EBV的基础PEV可靠性与相应的选择可靠性进行比较。评估了实现的遗传选择强度，以量化对不同类型EBV的选择潜力，从而验证可靠性的差异。最后，不同的基本过程的贡献加性遗传方差和可靠性的变化进行了量化。模拟结果表明，对于选定的人群，基本PEV可靠性大大高估了EBV选择的可靠性，EBV选择主要基于来自父母一代的旧信息，与基于谱系的预测一样。对这种EBV的选择得到了非常低的实现遗传选择强度，证实了对雄性和雌性选择候选物进行基因分型的高估和重要性。当考虑到由于布尔默效应、选择和近交而导致的加性遗传方差的减少时，这两种可靠性措施相匹配。对于选择的人群，基于全基因组信息的EBV比通过比较不同类型EBV之间的基础PEV可靠性所建议的更有价值。这意味着，全基因组标记信息被低估选定的人口和基因分型未表型的女性选择候选人应重新考虑。本文的在线版本（doi：10.1186/s12711-015-0145-1）包含补充材料，可供授权用户使用。
Reliability is an important parameter in breeding. It measures the precision of estimated breeding values (EBV) and, thus, potential response to selection on those EBV. The precision of EBV is commonly measured by relating the prediction error variance (PEV) of EBV to the base population additive genetic variance (base PEV reliability), while the potential for response to selection is commonly measured by the squared correlation between the EBV and breeding values (BV) on selection candidates (reliability of selection). While these two measures are equivalent for unselected populations, they are not equivalent for selected populations. The aim of this study was to quantify the effect of selection on these two measures of reliability and to show how this affects comparison of breeding programs using pedigree-based or genomic evaluations. Two scenarios with random and best linear unbiased prediction (BLUP) selection were simulated, where the EBV of selection candidates were estimated using only pedigree, pedigree and phenotype, genome-wide marker genotypes and phenotype, or only genome-wide marker genotypes. The base PEV reliabilities of these EBV were compared to the corresponding reliabilities of selection. Realized genetic selection intensity was evaluated to quantify the potential of selection on the different types of EBV and, thus, to validate differences in reliabilities. Finally, the contribution of different underlying processes to changes in additive genetic variance and reliabilities was quantified. The simulations showed that, for selected populations, the base PEV reliability substantially overestimates the reliability of selection of EBV that are mainly based on old information from the parental generation, as is the case with pedigree-based prediction. Selection on such EBV gave very low realized genetic selection intensities, confirming the overestimation and importance of genotyping both male and female selection candidates. The two measures of reliability matched when the reductions in additive genetic variance due to the Bulmer effect, selection, and inbreeding were taken into account. For populations under selection, EBV based on genome-wide information are more valuable than suggested by the comparison of the base PEV reliabilities between the different types of EBV. This implies that genome-wide marker information is undervalued for selected populations and that genotyping un-phenotyped female selection candidates should be reconsidered. The online version of this article (doi:10.1186/s12711-015-0145-1) contains supplementary material, which is available to authorized users.