engleski

Are autozygosity estimates from imputed genotypes reliable?

Estimates of the inbreeding coefficient based on runs of homozygosity (FROH) are widely used in population genetics and livestock studies. The accuracy of FROH estimates is determined in part by the density of the genotyping chip. Compared with high density (HD) chips, low density (LD) chips tend to overestimate FROH in shorter homozygous segments. It is unclear whether imputation of genotypes from LD to HD would reduce or eliminate this overestimation. Our goal was to determine whether FROH calculations based on imputed LD genotypes are accurate. To this end, FROH estimates were determined for Nelore cows using HD or LD imputed genotypes (FROH_HD and FROH_LDimp). Our results showed that LD imputed genotypes reduced but did not eliminate differences between estimates. Differences were observed in both directions, with under- and overestimates of FROH. This suggests that imputation errors can either disrupt or generate homozygous segments.

Runs Of Homozygosity ; Imputed genotypes ; Inbreeding

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