The PlantPathMarks (PPMdb) portal is an extensive website providing interactive and convenient access and mapping to thousands of pathways-based primers/markers in 82 plant genomes. Here, we also developed a novel approach called the Pathway Gene-set Mining (PGM). Besides, new marker systems were developed based on their pathways-based mapping of developed markers. The systems were named Pathway Microsatellites-Targeted Markers (PMTM) and Pathway Genes-Targeted Markers (PGTM); as a kind of annotation-based marker. In the PlantPathMarks hub, 9894 marker-panels (comprising 2,690,742 markers) were developed across eighty-two plant genomes. This huge number of markers includes 1,999,187 PMTM and 691,555 PGTM markers