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Updated: Mar 15, 2026
Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
Published on: November 5, 2020
Development and Characterization of 15 Polymorphic Dinucleotide Microsatellite Markers for Tule Elk Using HiSeq3000
Benjamin N Sacks1, Zachary T Lounsberry2, Tatyana Kalani2
1From 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.
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.
