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A Novel Software and Method for the Efficient Development of Polymorphic SSR Loci Based on Transcriptome Data.

Ruizheng Tian¹, Cunhuan Zhang¹, Yixiao Huang¹

¹Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture and Rural Affairs, Yangling 712100, China.

|November 14, 2019

Summary

A new method and software (PSSRdt) efficiently identify polymorphic microsatellite markers from transcriptome data. This approach overcomes limitations of traditional methods, enabling rapid discovery of valuable genetic markers for research.

Keywords:

SSR method polymorphic transcriptomes

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

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Published on: June 21, 2018

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Developing polymorphic microsatellite loci without reference sequences is challenging and inefficient.
Simple sequence repeat (SSR) loci from expressed sequence tag (EST) databases often exhibit poor polymorphism.

Purpose of the Study:

To develop a novel software (PSSRdt) and an effective method for direct identification of polymorphic SSR loci.
To analyze diverse transcriptome data for efficient microsatellite marker discovery.

Main Methods:

A three-step method: raw data processing, PSSRdt application, and loci extraction/verification.
Utilizing transcriptome data from 44 pea aphid individuals.
Validation of selected SSR loci through genotyping.

Main Results:

Successfully identified 1940 potential polymorphic SSRs from combined transcriptome data.
Genotyping of 52 selected SSR loci revealed over 92% polymorphism.
73.1% of the validated loci demonstrated high polymorphism.

Conclusions:

The PSSRdt software and developed method offer an innovative approach for microsatellite development using RNA-seq data.
This provides a rapid pathway for discovering numerous polymorphic microsatellite loci.
Facilitates advancements in microsatellite research and genetic marker development.