Microsatellite Development

Microsatellite Development

CD Genomics now offers a next generation sequencing based method to develop microsatellite markers for your species of interest, to benefit the scientific community.


Microsatellites, also referred to as SSR, consist of a repeated motif with one to six Nucleotides, and they are ubiquitous in most eukaryotic genomes. Variations in the number of repetitions generate different alleles. SSR has high polymorphism, genomic specificity, abundance, and codominance. This makes them appropriate molecular markers for molecular-assisted breeding, molecular phylogenetics, and population genetics.

Next-generation sequencing (NGS) is recently used to develop microsatellite markers. Traditional methods depending on capillary sequencing are time-consuming and complex. Compared to traditional methods, NGS has the advantages of high-throughput, massively increasing output and low-cost. It can sufficiently analyze even non-model organisms. We utilized illumina NGS technology to produce millions of short fragment reads, which were screened with bioinformatics toolsets to identify primers that amplify polymorphic microsatellite loci.

The general workflow for microsatellite development is outlined below.

  • DNA library preparation and shotgun sequencing with Illumina platform.
  • Analysis of sequencing results with bioinformatics tools and identification of potential microsatellite loci for primer development.
  • Synthesis of primers and selection of microsatellite loci by testing on several individuals to assess amplification and polymorphism.
  • Analysis of individuals you would like us to genotype with only those selected primer pairs which amplified polymorphic loci.

We would screen at least 8 samples across up to 60 loci, attempt PCR optimization for all loci, finally we will do our best to identify 10 polymorphic loci, but we cannot guarantee because some population don't have ‘normal’ level of polymorphism.

Sample Requirements

We can start working by using either isolated DNA or tissue sample. If you are sending tissue samples, please make sure that they have been properly preserved for DNA isolation (ethanol, silica gel, frozen, or another suitable preservation method).

Sample Requirements

To start microsatellite development for your species of interest, we ideally require 1 µg high molecular weight DNA. Please submit any QC data (either copy of Gel Electrophoresis picture or Qubit measurements) for the sample. Depending on the specifics of your project, we may need additional DNA samples representing the population of interest to assess the polymorphy and functionality of marker candidates.


  • The original sequencing data
  • Experimental results
  • Data analysis report

CD Genomics is dedicated to provide you with ready-to-use guaranteed, tested, polymorphic SSRs, and we have no legal right to any of your SSR markers. If you have additional requirements or questions, please feel free to contact us.

For Research Use Only. Not for use in diagnostic procedures.
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! For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment.
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