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Development of SSRs

 
 
The combination of next generation sequencing with a validated in-house bioinformatics pipeline to mine for promising marker candidates allows straight-forward microsatellite (Simple Sequence Repeats, SSR) marker development. The approach can be applied for any species and allows the identification of SSR markers within a short time span of 2 months. ecogenics delivers well-characterized markers and provides you with all information needed to publish the markers in a primer note or in a public database.
 
 

Workflow

 
A typical workflow for the development of SSRs is shown in the figure below. Please note that our modular development process allows various entry and output options. Whether you wish to outsource the entire development of SSRs or only parts of it, is up to you to decide.
 
 
SSR Development, Microsatellite Marker Development

Products

SSR-enriched Sequencing Data

The simplest way to profit from our marker development pipeline!
 
With 1 µg of genomic DNA we will produce the library for next generation sequencing. After sequencing, we will analyse the output with our validated in-house bioinformatics pipeline to provide you the designed primers for the best 300 in silico validated microsatellite candidates.
You can then directly order the respective primers and screen the loci for polymorphisms in a set of individuals of your species under study.
 

Polymorphy Tested Markers

The most cost-effective way to get your markers!
 
Let us perform the cumbersome work of testing the SSR loci for polymorphisms. We will screen 48 SSR loci for 7 unrelated individuals of your target species. Results of the screening include the testing of the functionality of the PCR primers and the number of alleles found in the 7 individuals. Besides detailed assay description, customers receive 100 µM stock solutions of the primers of each locus tested, with the forward primers carrying a FAM label.
 

Guaranteed Polymorphic Markers

The most efficient way to speed up your lab work!
 
Guaranteed polymorphic markers, our prime product, are ready-to-use markers that exhibit at least 4 alleles among 15 samples of unrelated individuals representing the species of interest (assuming diploid species). Most customers choosing this option appreciate the unprecedented speed of this product from the time point of the order to delivery (6 to 10 weeks).
Most successful studies in population genetics involve 12 to 20 microsatellite markers of moderate polymorphy. ecogenics developed the required markers for numerous species, involving all kind of taxa. Editors of all relevant journals know ecogenics and trust our work.
Besides detailed assay description, customers receive 100 µM stock solutions of the primers used for all loci, with the forward primers carrying a FAM label.
 
In case your plan is to genotype a larger number of samples with the newly developed markers, it may be more cost-effective to multiplex the markers. In this context we would like to draw your attention to our SSR Multiplexing Service.
 

Results

 
Depending on the project the following results are delivered:

SSR-enriched Sequencing Data

 
  • the raw data for the project (fastq, fasta and qual files)
  • SSR-enriched sequencing data (300 best loci)
 
 
Figure 1: Table including the 300 best in-silico validated microsatellite candidates incl. motif and length of the SSR marker, a possible primer design as well as the stitched read resulting from next-generations sequencing.
 

Polymorphy Tested Markers

 
  • a marker development project summary
  • the raw data for the project (fastq, fasta and qual files)
  • SSR-enriched sequencing data (300 best loci)
  • Results of the polymorphism screening incl. primers for 48 loci
  • stock solutions of the labelled and unlabelled primers (100 µM)
 
 
Figure 2: Example of electropherograms for 3 SSR markers tested on 7 individuals resulting from a polymorphism screening. Based on the result of the polymorphism screening researchers can then select the candidate loci for their project.
 

Guaranteed Polymorphic Markers

 
  • Read&Go brochure containing detailed information on the ordered SSR markers, the corresponding PCR protocols and a picture of the electropherogram for all the developed guaranteed polymorphic markers
  • the raw data for the project (fastq, fasta and qual files)
  • SSR-enriched sequencing data (300 best loci)
  • stock solutions of the labelled and unlabelled primers (100 µM)

 

 
 
Figure 3: Example for a primer certificate of a guaranteed polymorphic markers. As well as the electropherograms the researcher will also receive a Read & Go brochure with the PCR protocol used.