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Updated: Jun 11, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.

Tenta Segawa¹, Sorachi Saiga¹, Marina Takata¹

¹Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.

Breeding Science

|October 2, 2024

Summary

DNAMarkMaker automates DNA marker development for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers. This tool accelerates genetic analysis and crop breeding by simplifying primer design.

Keywords:

ARMS CAPS DNA marker Next-generation sequencing SNP

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Published on: March 22, 2018

Area of Science:

Plant genetics
Bioinformatics
Molecular breeding

Background:

DNA markers are crucial for crop breeding and genetic analysis.
Developing DNA markers is often time-consuming and labor-intensive, requiring polymorphism identification and primer design.

Purpose of the Study:

To develop DNAMarkMaker, an automated tool for designing primers for ARMS and CAPS DNA markers.
To streamline the DNA marker development process using resequencing data.

Main Methods:

Developed DNAMarkMaker with a user-friendly graphical user interface (GUI).
Utilized resequencing data for automated primer design.
Tested the tool on rice, potato, and turnip with diverse genome structures.

Main Results:

DNAMarkMaker successfully automated primer design for ARMS and CAPS markers.
The tool demonstrated applicability across different plant species and ploidy levels.
Facilitated marker development for homozygous diploid, heterozygous autotetraploid, and heterozygous diploid genomes.

Conclusions:

DNAMarkMaker significantly accelerates the development of DNA markers.
The tool enhances efficiency in crop breeding and genetic analysis.
DNAMarkMaker is accessible to researchers with varying bioinformatics expertise.