Microsatellite Genotyping Service

CD Genomics has extensive experience in providing support for the selection and design of microsatellite markers for a wide range of plant and animal species. Besides microsatellite genotyping, we also provide genotyping by sequencing (GBS) method, which saves time and resources.

Introduction to Microsatellite Genotyping

Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have been popular markers due to their high polymorphism. Genotyping is an accurate, cost-effective, and fast approach to distinguish microsatellite alleles, boosted by successive technical advances, including multiplexing PCR and next-generation sequencing technologies. The complete workflow for microsatellite genotyping includes acquisition of sequencing data, SSR selection, primer design, primer validation, multiplexing PCR, and capillary gel electrophoresis coupled with fluorescence-based detection, as well as data analysis.

The PCR reaction is performed with fluorescent dye-labeled primers, then the PCR fragments can be analyzed on a capillary DNA sequencing machine, and the data is analyzed using GeneMapper^TM software. By taking advantage of multiplexing by fragment size and dye color, and the ability of automated fluorescent genetic analyzer machines to autoload 16 samples at a time from 96-well or even 384-well microtiter plates, high-throughput marker analysis can be designed. This service has been applied to a wide variety of species and can accommodate any species for which microsatellite markers are available.

Advantages of microsatellites as genetic markers:

• Universal and polymorphic
• Locus-specific (in contrast to multi-locus markers such as minisatellites)
• Codominant (heterozygotes can be distinguished from homozygotes)
• PCR-based (only requires tiny amounts of tissue and works on degraded DNA)
• Multiple applications (from individual identification to fine-scale phylogenies)

Applications of microsatellite genotyping

The vast amount of data emerging for thousands of microsatellite markers across organisms makes microsatellite genotyping a widely accepted tool for:

• Linkage analysis of co-segregation
• Diagnosis and identification of human diseases
• Forensic identification and relatedness testing
• Cell line identification
• Population studies

Workflow of microsatellite genotyping

CD Genomics adopts advanced platforms (ABI 3730xl DNA Analyzer) and strategies (multiplexing PCR) to provide a fast and accurate microsatellite genotyping service and bioinformatics analysis. Our highly experienced expert team executes quality management, following every procedure to ensure confident and unbiased results. The rough workflow is outlined below.

Service Specifications

	Sample Requirement Tissue samples, or already extracted DNA, or PCR products DNA amount ≥ 50 μl, DNA concentration ≥ 10 ng/μl, OD260/280=1.8~2.0 PCR products with high specificity All DNA samples are validated for purity and quantity
	Multiplexing PCR and Genotyping SSR selection from sequence data Primer design and validation Multiplexing PCR Capillary gel electrophoresis with ABI 3730xl DNA Analyzer
	Data Analysis Sizing precision Allele calling and binning Clustering analysis Measuring and reporting error rates Genetic diversity and population studies More upon request

CD Genomics provides full microsatellite genotyping service package, including designing and ordering fluorescently labeled primer pairs, primer validation, microsatellite genotyping, as well as data analysis. We can tailor this pipeline to your research interest. If you have additional requirements or questions, please feel free to contact us.