A SNP resource for studying North American moose

Authors: KALBFLEISCH, THEODORE - University Of Louisville; MURDOCH, BRENDA - University Of Idaho; Smith, Timothy - Tim; MURDOCH, JAMES - University Of Vermont; Heaton, Michael - Mike; MCKAY, STEPHANIE - University Of Vermont

Submitted to: F1000Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/5/2018
Publication Date: 1/10/2018
Citation: Kalbfleisch, T.S., Murdoch, B.M., Smith, T.P.L., Murdoch, J.D., Heaton, M.P., Mckay, S.D. 2018. A SNP resource for studying North American moose. F1000Research. 7(40):1-17. https://doi.org/10.12688/f1000research.13501.1.
DOI: https://doi.org/10.12688/f1000research.13501.1

Interpretive Summary: Large wild herbivores like moose provide resources and income to rural communities and can have significant impacts on land use and landscape conditions. Consequently, substantial effort is put into local and regional management of moose populations throughout most of their range in North America. However, effective science-based management of wild populations could be improved with better tools for identifying individuals and assessing the genetic structure of populations. Recent advances in DNA technology transferred from cattle and sheep, have made it feasible to develop a new set of genetic tools designed specifically for North American moose populations. Here, we used the existing reference genomes of cattle and sheep, together with newly generated moose DNA sequences derived from the entire moose genome, to identify 317 DNA markers in moose. These highly-informative genetic variants are predicted to be useful for developing DNA-based genetic tests to support wildlife conservation and forensic activities. These include identifying animals, tracing diseased or illegally harvested animals, determining parentage, estimating relatedness, and tracking the flow of genes in and out of populations. Detailed information regarding these moose DNA markers is free, publicly available, and suitable for use on a variety of popular DNA-testing systems. The availability of these multi-use “parentage” SNP markers provides a starting point for developing DNA-based tests for commercial use in North American moose.

Technical Abstract: Background: Moose (Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data. Methods: WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively. Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs. Results: Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively. The reads clustered at genomic segments where sequence identity between these species was greater than 95%. In these segments, average mapped read depth was approximately 19-fold. Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species. Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east. A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design. Conclusion: All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating relatedness in North American moose.