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Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

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Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.

Subramaniam Geethanjali¹, Palchamy Kadirvel², Mahender Anumalla^3,4

¹Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India.

Plants (Basel, Switzerland)

|September 28, 2024

Summary

Simple sequence repeats (SSRs) are crucial genetic markers for plant breeding, offering high repeatability and adaptability. Advances in next-generation sequencing (NGS) enable efficient SSR discovery, even in crops with limited genomic resources.

Keywords:

SSR data mining genomic resources microsatellite databases microsatellites molecular markers primer designing simple sequence repeats

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Area of Science:

Plant genetics and breeding
Genomic research
Bioinformatics

Background:

DNA markers have evolved significantly over 50 years, from hybridization-based to sequence-based technologies.
Simple sequence repeats (SSRs) possess desirable traits like repeatability, codominance, and locus specificity, making them ideal for plant breeding.
Previous studies often overlooked SSR polymorphism and evolution due to limited data on chromosomal placement.

Purpose of the Study:

To review current methodologies for SSR marker development.
To highlight genomic resource databases and computational tools for SSR data mining and primer generation.
To serve as a comprehensive guide for researchers selecting SSR tools in genetic research and breeding programs.

Main Methods:

Leveraging next-generation sequencing (NGS) technologies for high-throughput SSR generation.
Utilizing bioinformatic approaches and tools for identifying SSRs in genomic sequences.
Developing primers for genotyping applications in plant breeding.

Main Results:

NGS enables rapid, cost-effective SSR production across diverse plant species.
Bioinformatic tools facilitate efficient SSR identification and primer design.
SSRs remain vital for orphan crops lacking extensive genomic resources.

Conclusions:

SSR markers are indispensable tools in modern plant breeding, particularly for genetic diversity and trait analysis.
The integration of NGS and bioinformatics has revolutionized SSR marker development and application.
This review provides a consolidated resource for optimizing SSR utilization in crop improvement programs.