A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data

Area of Science:

• Genetics
• Molecular Biology
• Plant Science

Background:

• Microsatellites, also known as Simple Sequence Repetitions (SSRs), are vital molecular markers in plant genetics and ecology.
• Developing these markers, particularly for non-model species, can be challenging and time-consuming.

Purpose of the Study:

• To present a novel workflow for developing microsatellite markers utilizing genome skimming.
• To demonstrate the pipeline's efficiency in identifying and selecting microsatellite regions for marker development.

Main Methods:

• A sequential pipeline involving DNA sequence acquisition, microsatellite region identification, primer design, and candidate region selection.
• Application of the pipeline using Illumina sequencing data from the non-model tree species *Pterodon emarginatus*.

Main Results:

• The workflow successfully identified 4,382 microsatellite regions and designed 7,411 primer pairs for *P. emarginatus*.
• A large number of potential microsatellite regions were discovered, with 50 selected for high marker development potential and 29 organized for multiplex PCR.

Conclusions:

• The proposed pipeline offers a powerful, fast, and efficient method for large-scale microsatellite marker development.
• This approach is particularly beneficial for non-model plant species, accelerating genetic and ecological studies.