Abstract
BackgroundThe most efficient method to maintain genetic diversity in populations under conservation programmes is to optimize, for each potential parent, the number of offspring left to the next generation by minimizing the global coancestry. Coancestry is usually calculated from genealogical data but molecular markers can be used to replace genealogical coancestry with molecular coancestry. Recent studies showed that optimizing contributions based on coancestry calculated from a large number of SNP markers can maintain higher levels of diversity than optimizing contributions based on genealogical data. In this study, we investigated how SNP density and effective population size impact the use of molecular coancestry to maintain diversity.ResultsAt low SNP densities, the genetic diversity maintained using genealogical coancestry for optimization was higher than that maintained using molecular coancestry. The performance of molecular coancestry improved with increasing marker density, and, for the scenarios evaluated, it was as efficient as genealogical coancestry if SNP density reached at least 3 times the effective population size.However, increasing SNP density resulted in reduced returns in terms of maintained diversity. While a benefit of 12% was achieved when marker density increased from 10 to 100 SNP/Morgan, the benefit was only 2% when it increased from 100 to 500 SNP/Morgan.ConclusionsThe marker density of most SNP chips already available for farm animals is sufficient for molecular coancestry to outperform genealogical coancestry in conservation programmes aimed at maintaining genetic diversity. For the purpose of effectively maintaining genetic diversity, a marker density of around 500 SNPs/Morgan can be considered as the most cost effective density when developing SNP chips for new species. Since the costs to develop SNP chips are decreasing, chips with 500 SNPs/Morgan should become available in a short-term horizon for non domestic species.
Highlights
The most efficient method to maintain genetic diversity in populations under conservation programmes is to optimize, for each potential parent, the number of offspring left to the generation by minimizing the global coancestry
The aims of this study were to (i) investigate, through computer simulations, how Ne and single nucleotide polymorphism (SNP) density affect the performance of molecular coancestry to maintain genetic diversity when used in the optimization of contributions; and (ii) determine the minimum SNP density required to maintain at least the same genetic diversity with molecular coancestry than with genealogical coancestry
This study investigated the effect of effective population size (Ne) and marker density (d) on the efficiency of molecular coancestry when used in the optimization of contributions aimed at minimizing the loss of genetic diversity
Summary
The most efficient method to maintain genetic diversity in populations under conservation programmes is to optimize, for each potential parent, the number of offspring left to the generation by minimizing the global coancestry. Recent studies showed that optimizing contributions based on coancestry calculated from a large number of SNP markers can maintain higher levels of diversity than optimizing contributions based on genealogical data. Management of populations under conservation programmes are usually aimed at maintaining the maximum possible genetic diversity (usually measured as expected and observed heterozygosity and sometimes as allelic diversity) and avoiding high levels of inbreeding. This can be achieved by optimizing contributions of potential parents through the minimization of their global coancestry [4,5,6]. Recently de Cara et al [8] showed that with high-density panels of markers, the expected and observed heterozygosities maintained were higher using molecular coancestry than genealogical coancestry
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