Abstract
The genetic contribution with respect to autosomal genes has been widely used to evaluate the genetic diversity of a target population. Here, we developed a method to calculate the genetic contribution with respect to genes on sex chromosomes and mitochondrial DNA through pedigree analysis. To demonstrate the performance, we applied the methods for calculating genetic contributions to example pedigree data. To verify the results of genetic contribution calculations, we performed gene-dropping simulations mimicking flows of genes on autosomes, X and Y chromosomes, and mitochondrial DNA, and then compared the results from the simulation with the corresponding genetic contributions. To investigate the effect of pedigree error, we compared the results of genetic contribution calculations using pedigree data with and without errors. The results of gene-dropping simulation showed good agreement with the results of the genetic contribution calculation. The effect of pedigree errors on the calculation of genetic contribution depended on the error rate. Since the patterns of the genetic contributions of such genes might be different from those on autosomes, the novel approach could provide new information on the genetic composition of populations. The results are expected to contribute to the development of methods for sustainable breeding and population management.
Highlights
The genetic contribution with respect to autosomal genes has been widely used to evaluate the genetic diversity of a target population
It was expected that there was no effect on calculating GCMI,A when sires were replaced because mitochondrial DNA is assumed to be maternally inherited, and that replacement of dams did not affect GCYI,A because females do not have the Y chromosome. These results indicate that pedigree errors could affect the results of genetic contribution calculations, and the effect might depend on error rate and the kinds of errors
This study developed the novel method to calculate the genetic contributions with respect to genes on sex chromosomes and mitochondrial DNA
Summary
The genetic contribution with respect to autosomal genes has been widely used to evaluate the genetic diversity of a target population. We developed a method to calculate the genetic contribution with respect to genes on sex chromosomes and mitochondrial DNA through pedigree analysis. Existing theories assume the use of 100% accurate pedigree data, low but nonzero pedigree error rates, partly due to human errors, have been reported (e.g., [17,18,19]). This indicates the importance of investigating the effect of pedigree error on evaluation of genetic diversity (e.g., [20,21,22]). Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations
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