| Summary: | Premise of the study: Microsatellite primers were developed for Nootka cypress (<i>Callitropsis nootkatensis</i>) to provide quantitative measures for gene conservation that can assist in guiding management decisions for a species experiencing climate-induced decline.
Methods and Results: Using multiplexed massively parallel sequencing, we identified 136,785 microsatellite-containing sequences from 489,625 Illumina paired-end 80-bp reads. After stringent filtering, we selected 144 primer pairs and screened variation at these loci in five populations of <i>C. nootkatensis</i>. Loci show between three and 36 dinucleotide repeats per locus, with an average of 13. Screening of these markers in the Pacific Northwest relative <i>Chamaecyparis lawsoniana</i> demonstrated no marker transferability. This finding highlights the narrow taxonomic utility of microsatellite markers in <i>Callitropsis</i>.
Conclusions: These microsatellites show high polymorphism and can be used for routine screening of natural variation in <i>Callitropsis nootkatensis</i>, and will be particularly helpful in identifying clones and inbred relatives at the stand-level.
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