Development of a web-based high-throughput marker design program: CAPS (cleaved amplified polymorphic sequence) Maker.

Background: Genetic markers are crucial for breeding crops with desired agronomic traits, and their development can be expedited using next-generation sequencing (NGS) and bioinformatics tools. Numerous tools have been developed to design molecular markers, enhancing the convenience, accuracy, and efficiency of molecular breeding. However, these tools primarily focus on genetic variants within short user-input sequences, despite the availability of extensive omics data for genomic variants. To design molecular markers encompassing a vast number of genetic variants at the genome-wide scale in soybean, an automatic system capable of handling NGS-based big data is necessary.

Results: In this study, we developed a robust digital platform, the CAPS Maker, for designing cleaved amplified polymorphic sequence (CAPS)/derived CAPS (dCAPS) markers in soybeans. This platform simplifies the systematic design of genomic markers with a user-friendly graphical interface, featuring a 'SNP Browser' and 'Primer Table', along with internal programs (e.g., the eHT-PCR module) to design unique primer pairs for highly duplicated genomes like soybean.

Conclusions: The CAPS Maker's efficiency and reliability were experimentally verified by comparing its marker predictions with actual experimental results. Consequently, breeders can easily design CAPS/dCAPS markers using the CAPS Maker platform to develop new soybean cultivars with beneficial agronomic traits. This platform is freely accessible at https://tgil.donga.ac.kr/CAPSMaker .