A comparison of marker-based estimators of inbreeding and inbreeding depression

Background: 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 (& UDelta;ID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and & UDelta;ID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (F-LH1 and F-LH2), VanRaden (F-VR1 and F-VR2), Yang and colleagues (F-YA1 and F-YA2), marker homozygosity (F-HOM), runs of homozygosity (F-ROH) and estimates based on pedigree (F-PED) in comparison with estimates obtained from IBD measures (F-IBD). Results: 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 F-IBD and provide accurate estimates of the mean & UDelta;ID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with F-IBD is generally obtained by F-LH1 and the best estimator of & UDelta;ID is F-YA2. The estimators F-VR2 and F-LH2 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 F-IBD and give relatively good estimates of & UDelta;ID. Estimates obtained directly from marker homozygosity (F-HOM) substantially overestimated & UDelta;ID. Estimates based on runs of homozygosity (F-ROH) provide accurate estimates of inbreeding and & UDelta;ID. Finally, estimates based on pedigree (F-PED) show a lower correlation with F-IBD than molecular estimators but provide rather accurate estimates of & UDelta;ID. An analysis of data from a pig population supports the main findings of the simulations. Conclusions: When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with F-IBD and provide good estimates of & UDelta;ID. When base population allele frequencies are unknown, F-LH1 is the marker frequency-based estimator that is most correlated with F-IBD, and F-YA2 provides the most accurate estimates of & UDelta;ID. Estimates from F-ROH are also very precise in most scenarios. The estimators F-VR2 and F-LH2 have the poorest performances.

Automated summary

This study investigates the accuracy of estimators of inbreeding based on molecular markers in different mating systems and artificially selected populations. The results show that when the allele frequencies of the base population are known, all estimators based on marker allele frequencies provide accurate estimates of inbreeding coefficients and inbreeding depression. When the allele frequencies are unknown, F-LH1 is the most correlated estimator with the actual values, and F-YA2 provides the most accurate estimates of inbreeding depression.