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PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes
Morad M Mokhtar1, Achraf El Allali2, Mohamed-Elamir F Hegazy3
1African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
Scientific Reports
|October 30, 2021
Summary
The PlantPathMarks database (PPMdb) offers novel pathway-based markers for plant trait characterization. This resource aids researchers in identifying specific gene targets for plant breeding and molecular research.
Area of Science:
- Plant genomics
- Bioinformatics
- Molecular biology
Background:
- Developing efficient gene-targeting marker sets for plant trait characterization remains a challenge.
- Existing pathway mining databases often lack targeted marker sets for specific biological processes.
- This gap hinders precise gene function analysis and marker-assisted breeding.
Purpose of the Study:
- To introduce the PlantPathMarks database (PPMdb) as a comprehensive resource for pathway-based plant markers.
- To present novel marker systems: pathway gene-targeted markers (PGTMs) and pathway microsatellite-targeted markers (PMTMs).
- To facilitate efficient plant trait characterization and molecular research.
Main Methods:
- Developed a novel pathway gene set mining approach.
- Created two new marker systems: PGTMs and PMTMs.
- Integrated 2,690,742 markers across 82 plant genomes, mapping 165,378 enzyme-coding genes to 126 KEGG pathways.
Main Results:
- Established PPMdb, a user-friendly, web-based hub for plant pathway markers.
- Generated 9,894 marker panels, including 691,555 PGTMs and 1,999,187 PMTMs.
- Incorporated interactive visualization tools (Map Browse, JBrowse, Species Comparison) for marker analysis.
Conclusions:
- PPMdb provides a powerful, accessible tool for plant scientists and breeders.
- The novel PGTMs and PMTMs offer a new class of annotation-based markers.
- This resource is expected to significantly advance plant molecular marker research and trait characterization.
