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Development of a web-based high-throughput marker design program: CAPS (cleaved amplified polymorphic sequence) Maker
Joo-Seok Park1,2, Yoram Choi1, Jin-Hyun Kim3
1Department of Applied Bioscience, Dong-A University, Saha-Gu Nakdong-Daero 550 beongil 37, Busan, 49315, Republic of Korea.
Plant Methods
|December 24, 2024
Summary
A new digital platform, CAPS Maker, streamlines the design of DNA markers for soybean breeding. This tool facilitates the development of improved soybean varieties with desirable traits by efficiently handling large genomic datasets.
Area of Science:
- Plant genetics
- Bioinformatics
- Crop science
Background:
- Genetic markers are essential for developing crops with improved agronomic traits.
- Next-generation sequencing (NGS) and bioinformatics tools accelerate marker development.
- Existing tools are limited to short sequences, hindering genome-wide marker design in large datasets.
Purpose of the Study:
- To develop an automated system for designing genome-wide molecular markers in soybean.
- To create a user-friendly platform for efficient marker development using big data.
Main Methods:
- Development of the CAPS Maker digital platform with a graphical interface.
- Integration of a 'SNP Browser' and 'Primer Table' for systematic marker design.
- Inclusion of internal programs, such as the eHT-PCR module, for primer pair design in complex genomes.
Main Results:
- The CAPS Maker platform was developed for designing cleaved amplified polymorphic sequence (CAPS) and derived CAPS (dCAPS) markers in soybeans.
- The platform features user-friendly tools for marker design and primer pair selection.
- Internal programs were incorporated to handle highly duplicated genomes.
Conclusions:
- The CAPS Maker platform's effectiveness and accuracy were validated experimentally.
- The platform enables breeders to easily design CAPS/dCAPS markers for developing new soybean cultivars.
- The CAPS Maker is accessible online for public use.
