The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (FLH1 and FLH2), VanRaden (FVR1 and FVR2), Yang and colleagues (FYA1 and FYA2), marker homozygosity (FHOM), runs of homozygosity (FROH) and estimates based on pedigree (FPED) in comparison with estimates obtained from IBD measures (FIBD). If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with FIBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with FIBD is generally obtained by FLH1 and the best estimator of ΔID is FYA2. The estimators FVR2 and FLH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with FIBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (FHOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (FROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (FPED) show a lower correlation with FIBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations. When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with FIBD and provide good estimates of ΔID. When base population allele frequencies are unknown, FLH1 is the marker frequency-based estimator that is most correlated with FIBD, and FYA2 provides the most accurate estimates of ΔID. Estimates from FROH are also very precise in most scenarios. The estimators FVR2 and FLH2 have the poorest performances.

中文翻译：

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基于标记的近亲繁殖和近亲繁殖衰退估计量的比较

全基因组标记数据的可用性允许估计近亲繁殖系数（F，同一性概率，IBD），进而估计近亲繁殖衰退率（ΔID）。我们通过计算机模拟研究了在随机交配、父母贡献均衡和人工选择的种群下计算种群中的 F 和 ΔID 时基于分子标记的最流行的近亲繁殖估计量的准确性。我们评估了 Li 和 Horvitz（FLH1 和 FLH2）、VanRaden（FVR1 和 FVR2）、Yang 及其同事（FYA1 和 FYA2）、标记纯合性 (FHOM)、纯合子运行 (FROH) 和基于谱系的估计 (FPED) 描述的估计量与从 IBD 措施 (FIBD) 获得的估计值进行比较。如果作为计算近亲繁殖参考的基础种群的等位基因频率已知，则所有基于标记等位基因频率的估计量都与 FIBD 高度相关，并提供平均 ΔID 的准确估计。如果基群等位基因频率未知，并且使用当前频率进行估计，则与 FIBD 的最大相关性通常由 FLH1 获得，而 ΔID 的最佳估计量是 FYA2。在大多数情况下，估计器 FVR2 和 FLH2 的性能最差。基本种群等位基因频率等于 0.5 的假设导致对平均近亲繁殖系数的估计非常有偏差，但它们与 FIBD 高度相关并且给出了相对较好的 ΔID 估计。直接从标记纯合性 (FHOM) 获得的估计值大大高估了 ΔID。基于纯合子运行 (FROH) 的估计提供了近亲繁殖和 ΔID 的准确估计。最后，基于系谱 (FPED) 的估计显示与 FIBD 的相关性低于分子估计，但提供了相当准确的 ΔID 估计。对猪群数据的分析支持了模拟的主要发现。当基本种群等位基因频率已知时，所有基于标记等位基因频率的近亲繁殖系数估计通常显示与 FIBD 高度相关，并提供对 ΔID 的良好估计。当基础群体等位基因频率未知时，FLH1 是与 FIBD 最相关的基于标记频率的估计量，而 FYA2 提供最准确的 ΔID 估计。在大多数情况下，FROH 的估计也非常精确。估计器 FVR2 和 FLH2 的性能最差。