ARS | Publication request: Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 16, 2012
Publication Date: November 1, 2012
Citation: Miller, J.M., Kijas, J.W., Heaton, M.P., McEwan, J.C., Coltman, D.W. 2012. Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species. Molecular Ecology Resources. 12(6):1145-1150. doi:10.1111/1755-0998.12017.

Interpretive Summary: DNA marker development is the foundation from which all molecular ecology studies build. Advancing sequencing technology has facilitated development of large panels of DNA markers. However, most of these marker sets are developed for humans, lab animals, or domestic animals and not wildlife species. We tested marker sets for cattle, sheep, and horse and found that they all worked well in a wide-range of wild-species and gave meaningful results that were consistent across all three marker sets. This is important because it allows wildlife researchers to make use of these well-developed genomic tools. Thus, these marker sets and technologies can provide critical scientific resources in a vast and diverse array of wild-species.

Technical Abstract: Recent advances in technology facilitated development of large sets of genetic markers for many taxa, though most often model or domestic organisms. Cross-species application of genomic technologies may allow for rapid marker discovery in wild relatives of taxa with well developed resources. We investigated cross-species application of three commercially available SNP chips (the OvineSNP50, BovineSNP50, and EquineSNP50 BeadChips) as a function of divergence time between the domestic source species and wild target species. Across all three chips we observed a consistent linear decrease in call rate (~1.5% per million years), while retention of polymorphisms showed an exponential decay. These results will allow researchers to predict the expected amplification rate and polymorphism of cross-species application for their taxa of interest, as well as provide a resource for estimating divergence times.