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- Title
DNAMarkMaker: streamlining ARMS and CAPS marker development from resequencing data with NGS short reads.
- Authors
Tenta Segawa; Sorachi Saiga; Takata, Marina; Riki Kumazawa; Makishi Hara; Hiromoto Yamakawa; Hiroki Takagi
- Abstract
DNA markers serve as essential tools in breeding selection and genetic analysis. However, developing DNA markers can be time-consuming and labor-intensive due to the need to identify polymorphisms between culti‐ vars/lines and to design suitable primers. To address these challenges, we have developed DNAMarkMaker, a tool designed to automate the process of primer design for Amplification Refractory Mutation System (ARMS) and Cleaved Amplified Polymorphic Sequences (CAPS) markers, utilizing resequencing data. One key feature of DNAMarkMaker is its user-friendly graphical user interface (GUI), ensuring its accessibility and ease of use, even for researchers not well-versed in bioinformatics. We confirmed DNAMarkMaker’s applicability by developing DNA markers for rice, potato, and turnip—each representing distinct genome structures: homozygous diploid, heterozygous autotetraploid, and heterozygous diploid, respectively. DNAMarkMaker will contribute to the rapid and efficient development of DNA markers, accelerating breed‐ ing and genetic analysis in various crops.
- Subjects
GENETIC markers; GRAPHICAL user interfaces; NUCLEOTIDE sequencing; CAPS (Headgear); RESEARCH personnel
- Publication
Breeding Science, 2024, Vol 74, Issue 2, p73
- ISSN
1344-7610
- Publication type
Article
- DOI
10.1270/jsbbs.23048