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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Animal Health Genomics » Research » Publications at this Location » Publication #348567
Research Project: Genomic Intervention Strategies to Prevent and/or Treat Respiratory Diseases of Ruminants

Location: Animal Health Genomics

Title: Using cattle and sheep reference assemblies to develop genomic resources for North American moose

Author
item Heaton, Michael - Mike

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/2/2017
Publication Date: 1/2/2018
Citation: Heaton, M.P. 2018. Using cattle and sheep reference assemblies to develop genomic resources for North American moose [abstract]. International Plant & Animal Genome XXVI Conference, January 13-17, 2018, San Diego, California. Abstract W153. Available: https://plan.core-apps.com/pag_2018/abstracts

Interpretive Summary:

Technical Abstract: 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. 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. WGS data were generated for four individual moose from 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. 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 47,236 and 38,250 high-confidence SNPs were identified from cattle and sheep comparisons, respectively. 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.