Development and Characterization of 15 Polymorphic Dinucleotide Microsatellite Markers for Tule Elk Using HiSeq3000

Benjamin N Sacks; Zachary T Lounsberry; Tatyana Kalani; Erin P Meredith; Cristen Langner

doi:10.1093/jhered/esw069

Development and Characterization of 15 Polymorphic Dinucleotide Microsatellite Markers for Tule Elk Using HiSeq3000

J Hered. 2016;107(7):666-669. doi: 10.1093/jhered/esw069. Epub 2016 Sep 16.

Authors

Benjamin N Sacks¹, Zachary T Lounsberry², Tatyana Kalani², Erin P Meredith², Cristen Langner²

Affiliations

¹ From the Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, One Shields Avenue/Old Davis Road, Davis, CA 95616 (Sacks, Lounsberry, and Kalani); Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 (Sacks); California Department of Fish and Wildlife, Sacramento, CA 95834 (Meredith); and California Department of Fish and Wildlife, Fresno, CA 93710 (Langner). bnsacks@ucdavis.edu.
² From the Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, One Shields Avenue/Old Davis Road, Davis, CA 95616 (Sacks, Lounsberry, and Kalani); Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA 95616 (Sacks); California Department of Fish and Wildlife, Sacramento, CA 95834 (Meredith); and California Department of Fish and Wildlife, Fresno, CA 93710 (Langner).

PMID: 27638816
DOI: 10.1093/jhered/esw069

Abstract

The tule elk (Cervus elaphus nannodes) experienced a severe bottleneck in the 1800s, resulting in low genetic diversity. There is a need for high-resolution genetic assays that can be used to differentiate individual elk, including close relatives, with high confidence. An efficient assay requires multiple markers both polymorphic and that can be amplified in concert with other markers in multiplex reactions. To develop such markers, we employed 150-bp paired-end whole genome shotgun sequencing on an Illumina HiSeq3000 platform to discover dinucleotide microsatellite markers. After preliminary screening of these markers, we selected and screened 15 candidate loci and 5 existing tetra nucleotide markers in 56 tule elk. We combined these markers in 2 multiplex reactions and report primer concentrations and PCR conditions enabling their efficient amplification.

Keywords: Cervus elaphus nannodes; HiSeq; Illumina; dinucleotide; microsatellite; tule elk.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Animals
Deer / classification*
Deer / genetics*
Female
Gene Frequency
Genotype
High-Throughput Nucleotide Sequencing
Male
Microsatellite Repeats*
Polymorphism, Genetic*

Associated data

Dryad/10.5061/dryad.j2654