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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Published on: October 5, 2018

Bioinformatics: identification of markers from next-generation sequence data.

Pradeep Ruperao¹, David Edwards

¹School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.

Methods in Molecular Biology (Clifton, N.J.)

|November 7, 2014

Summary

Next-generation sequencing (NGS) advances plant genomics by enabling large-scale discovery of genetic markers like simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) for breeding and research.

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Area of Science:

Genomics
Plant Science
Bioinformatics

Background:

Next-generation sequencing (NGS) has transformed plant genomics.
New software tools facilitate large-scale genetic marker discovery and validation.
Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) are key genetic markers.

Purpose of the Study:

To discuss tools for genome assembly.
To focus on the discovery of SSR and SNP markers.
To highlight the importance of these markers in plant genetics and breeding.

Main Methods:

Review of NGS technologies and associated software.
Focus on methodologies for SSR marker discovery.
Focus on methodologies for SNP marker discovery.

Main Results:

NGS enables efficient, large-scale identification of SSR and SNP markers.
SSRs are valuable for germplasm characterization, genetic mapping, and QTL identification.
SNPs are abundant and frequent throughout plant genomes, offering broad utility.

Conclusions:

NGS technology and bioinformatics tools are crucial for modern plant genomics.
SSR and SNP markers are essential for advancing plant genetics and breeding programs.
This work provides insights into marker discovery tools and their applications.