Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Aug 14;3(8):apps.1500051.
doi: 10.3732/apps.1500051. eCollection 2015 Aug.

Characterization of 13 microsatellite markers for Calochortus gunnisonii (Liliaceae) from Illumina MiSeq sequencing

Ryan S Fuller  1 , Seth Frietze  1 , Mitchell E McGlaughlin  1
Affiliations

Characterization of 13 microsatellite markers for Calochortus gunnisonii (Liliaceae) from Illumina MiSeq sequencing

Ryan S Fuller et al. Appl Plant Sci. .

Abstract

Premise of the study: Microsatellite primers were designed for Calochortus gunnisonii (Liliaceae), a montane lily species of the central and southern Rocky Mountains, using next-generation DNA sequencing. The markers will be used to investigate population structure, genetic diversity, and demographic history.

Methods and results: Thirteen polymorphic microsatellite loci were isolated from C. gunnisonii using Illumina MiSeq next-generation DNA sequencing and bioinformatic screening. The mean number of alleles per locus ranged from 4.15 to 5.92 (avg. = 4.97). Observed and expected heterozygosity ranged from 0.077 to 0.871 and 0.213 to 0.782, respectively. The primers were also tested for cross-species amplification value with C. flexuosus, C. nuttallii, C. kennedyi var. kennedyi, and C. subalpinus.

Conclusions: These primers will be useful for genetic and evolutionary studies across C. gunnisonii's range within the southern and central Rocky Mountains. Furthermore, these markers have proven valuable for cross-species amplifications within Calochortus.

Keywords: Calochortus gunnisonii; Illumina; Liliaceae; MiSeq; microsatellites.

PubMed Disclaimer

References

    1. Bolger A. M., Lohse M., Usadel B. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114–2120. - PMC - PubMed
    1. Boutin-Ganache I., Raposo M., Raymond M., Deschepper C. F. 2001. M13-tailed primers improve the readability and usability of microsatellite analyses performed with two different allele-sizing methods. BioTechniques 31: 24–28. - PubMed
    1. Faircloth B. C. 2008. MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8: 92–94. - PubMed
    1. Fiedler P. L., Zebell R. K. 2012. Calochortus: Flora of North America online. Available at website http://www.efloras.org/florataxon.aspx?flora_id=1taxon_id=105173 [accessed 15 January 2014].
    1. Friar E. A. 2005. Isolation of DNA from plants with large amounts of secondary metabolites. Methods in Enzymology 395: 1–12. - PubMed

LinkOut - more resources