Sampling method for estimating neutral allele frequency in a pedigreed population
2012
Honda, Takeshi | Sasazaki, Shinji | Oyama, Kenji | Mukai, Fumio | Nomura, Tetsuro
The estimated allele frequency at neutral DNA marker loci is a fundamental parameter for establishing a conservation scheme for a set of livestock breeds. In this study, we propose a novel ‘minimum distance (MD) method’ for estimating neutral allele frequencies, which minimizes the error by the use of pedigree information. Using computer simulation and actual microsatellite data for a pedigreed cattle population, the performance of the proposed method was compared with that of conventional random sampling (RND). MD manifests a promising superiority to RND, irrespective of the sample size and the depth of pedigree. It is theoretically demonstrated that the error of the estimates depends on both the sample size and the distance of founder allele frequencies between the sampled and the non‐sampled individuals. MD samples individuals so as to minimize the latter source of estimation error.
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