How many markers are enough? Factors influencing parentage testing in different livestock populations

Summary
Reliability of parentage test panels is usually based on its power to exclude wrong parentage assignments based on allele frequencies. We evaluated the rates of false exclusions and inclusions in parentage assignments, and how these results are affected by allele frequencies, panel sizes and the number of allowed mismatches. We also evaluated the reliability of parentage testing by comparing populations with distinct genetic backgrounds using pure and composite families of cattle and sheep. Allowing for 1% genotype mismatches in true parent–offspring relations provided the best compromise between false‐positive and false‐negative assignments. Pure breeds needed at least 200–210 single‐nucleotide polymorphism (SNP) markers to correctly assign relations, but between 700 and 890 markers to avoid assigning incorrect relationships. Composite breeds needed between 220 (sheep) and 500 (cattle) markers for correct assignment; 680 (cattle) to 4400 (sheep) SNPs were needed to eliminate false‐positive assignments. Allowing 0% genotype mismatches decreased false‐positive but increased false‐negative assignments, whilst a higher threshold of 2% showed the opposite effects. Panels with high minor allele frequencies (0.35–0.45) provided the best chance for correct parentage resolutions requiring fewer markers. Further, we propose that a dynamic threshold would allow adapting to population specific error rates. A comparison to the performance of the official Interna...

Source: Journal of Animal Breeding and Genetics - August 1, 2015 Category: Genetics & Stem Cells Authors: E.M. Strucken, S.H. Lee, H.K. Lee, K.D. Song, J.P. Gibson, C. Gondro Tags: Original Article Source Type: research