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Related Experiment Video

Updated: Feb 6, 2026

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications

Published on: November 5, 2020

Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species.

Hantao Qin^1,2, Guoqian Yang^2,3, Jim Provan⁴

¹Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.

Plant Diversity

|August 31, 2018

Summary

This study developed new polymorphic microsatellite markers for the endangered yew species Taxus florinii using ddRAD-seq data. These markers are valuable for future population genetics and conservation efforts.

Keywords:

Endangered species Microsatellite MiddRAD-seq Next-generation sequencing Taxus florinii

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Area of Science:

Population Genetics
Molecular Ecology
Conservation Genetics

Background:

Microsatellites are crucial polymorphic markers for genetic studies.
Next-generation sequencing data, particularly RAD-seq, offers potential for microsatellite discovery.
The endangered yew species, Taxus florinii, requires robust genetic markers for conservation.

Purpose of the Study:

To develop novel polymorphic microsatellite loci for Taxus florinii.
To assess the utility of ddRAD-seq data for microsatellite ascertainment in this species.
To provide genetic markers for future population genetics and speciation studies of T. florinii.

Main Methods:

Employed ddRAD-seq data from ten individuals of Taxus florinii.
Bioinformatically identified microsatellite motifs and assessed polymorphism.
Designed and validated primer pairs for PCR amplification and screening in two populations.

Main Results:

Identified 2993 unique microsatellite loci from ddRAD-seq data, with 526 (18%) exhibiting polymorphism.
Successfully designed and validated 16 polymorphic microsatellite loci.
Characterized loci in 24 individuals, revealing 2-10 alleles per locus and high expected heterozygosity (mean=0.530).

Conclusions:

ddRAD-seq is an effective method for mining polymorphic microsatellite loci in Taxus florinii.
The developed microsatellite markers are suitable for population genetics and speciation research.
These markers will aid in the conservation and management of the endangered yew species.