Reliability of direct genomic values for animals with different relationships within and to the reference population
Reliability of direct genomic values for animals with different relationships within and to the reference population
复制标题
DOI：
10.3168/jds.2011-4338
复制
发表时间：
2012-01-01
影响因子：
3.5
通讯作者：
Calus, M. P. L.
中科院分区：
文献类型：
--
作者：
Pszczola, M.;Strabel, T.;Calus, M. P. L.
基因组选择的准确性取决于单核苷酸多态性效应预测的准确性和标记解释的遗传变异的比例。参考群体的设计与其家族结构有关，可能会影响基因组选择的准确性。本研究的目的是调查参考群体内的各种关系水平和评价动物与参考群体的不同关系水平对直接基因组育种值（DGV）可靠性的影响。在3个遗传力水平下计算评价动物的DGV可靠性，表示为估计育种值和真实育种值之间的平方相关。为了模仿一个难以测量或测量成本很高的特征，如甲烷排放量，参考群体保持较小，由具有自己表现记录的女性组成。模拟了反映奶牛种群结构的种群。四个选择的参考群体由第一代基因分型的所有女性组成。通过选择大小递减的父系半同胞家系，它们由高度（HR）、中度（MR）或低度（LR）相关动物组成，或由随机选择的动物（RND）组成。在这4个参考群体中，RND的平均关系最低。从连续3代基因分型动物中选择3组评价动物，从与参考群体相同的代开始。使用选择指数理论确定性地计算DGV预测的可靠性。随机选择的参考人群在参考人群中的平均关系最低。当参考群体内的平均关系降低时，平均可靠性增加，并且RND达到最高的平均可靠性（例如，从HR的0.53到RND的0.61，遗传力为0.30）。与参考人群的关系越高，可靠性值越高。在评价动物与参考群体的平均平方关系为0.005时，遗传力为0.30时的平均可靠性为0.49（HR）和0.63（RND）;遗传力为0.05时的平均可靠性为0.20（HR）和0.27（RND）;遗传力为0.01时的平均可靠性为0.07（HR）和0.09（RND）。当参考群体的代数增加时，观察到可靠性显著降低[例如，对于0.30的遗传力，从评估集I（与参考群体选自同一代）到II（比参考群体年轻一代）的降低对于HR为0.04，对于RND为0.07]。本研究表明了奶牛参考群体设计的重要性，并提出了基因组预测参考群体的优化设计。
Accuracy of genomic selection depends on the accuracy of prediction of single nucleotide polymorphism effects and the proportion of genetic variance explained by markers. Design of the reference population with respect to its family structure may influence the accuracy of genomic selection. The objective of this study was to investigate the effect of various relationship levels within the reference population and different level of relationship of evaluated animals to the reference population on the reliability of direct genomic breeding values (DGV). The DGV reliabilities, expressed as squared correlation between estimated and true breeding value, were calculated for evaluated animals at 3 heritability levels. To emulate a trait that is difficult or expensive to measure, such as methane emission, reference populations were kept small and consisted of females with own performance records. A population reflecting a dairy cattle population structure was simulated. Four chosen reference populations consisted of all females available in the first genotyped generation. They consisted of highly (HR), moderately (MR), or lowly (LR) related animals, by selecting paternal half-sib families of decreasing size, or consisted of randomly chosen animals (RND). Of those 4 reference populations, RND had the lowest average relationship. Three sets of evaluated animals were chosen from 3 consecutive generations of genotyped animals, starting from the same generation as the reference population. Reliabilities of DGV predictions were calculated deterministically using selection index theory. The randomly chosen reference population had the lowest average relationship within the reference population. Average reliabilities increased when average relationship within the reference population decreased and the highest average reliabilities were achieved for RND (e.g., from 0.53 in HR to 0.61 in RND for a heritability of 0.30). A higher relationship to the reference population resulted in higher reliability values. At the average squared relationship of evaluated animals to the reference population of 0.005, reliabilities were, on average, 0.49 (HR) and 0.63 (RND) for a heritability of 0.30; 0.20 (HR) and 0.27 (RND) for a heritability of 0.05; and 0.07 (HR) and 0.09 (RND) for a heritability of 0.01. Substantial decrease in the reliability was observed when the number of generations to the reference population increased [e.g., for heritability of 0.30, the decrease from evaluated set I (chosen from the same generation as the reference population) to II (one generation younger than the reference population) was 0.04 for HR, and 0.07 for RND]. In this study, the importance of the design of a reference population consisting of cows was shown and optimal designs of the reference population for genomic prediction were suggested.