A comparative assessment of ISSR, RAPD, IRAP, & REMAP molecular markers in Zingiber officinale germplasm characterization

• RAPD, ISSR, IRAP, & REMAP marker systems could discriminate all the accessions with varied efficiency of polymorphism (83.6–88.2%) in 194 ginger germplasm.
• The core collection was broadly classified into two major clusters.
• Comparison of the techniques enabled generating a common index, reflecting the degree of DNA polymorphism generated in each case.
• The study demonstrated REMAP and RAPD employing rice SSR markers are the markers of choice in ginger germplasm genetic diversity assessment.
• The information will help in crop selection, efficient management and conservation of ginger genetic resources.

One hundred and ninety four collection of ginger germplasm were genetically evaluated using four PCR based markers employing 7 ISSR, 9 rice-SSR, 6 IRAP pairs and 25 combinations of REMAP primers. Each marker technique could discriminate the accessions with varied efficiency of polymorphism (83.6–88.2%). The resolving power and marker index were estimated to be maximum in REMAP (5.24 & 4.18) and minimum in IRAP (3.92 & 3.25) techniques. The combined data matrices of RAPD-ISSR and retrotransposon displayed similar polymorphism 87.03% and 87.5%, respectively. All the four techniques broadly classified the germplasm into two major clusters. Correlations between combined similarity matrices of the two techniques to the individual matrices were high (0.90–0.97). Comparison of the techniques helped in generating a common index, reflecting the degree of DNA polymorphism generated in each case. The study demonstrated REMAP and RAPD, employing rice-SSR markers, are the markers of choice in ginger germplasm genetic diversity assessment. The information will help in crop selection, efficient management and conservation of ginger genetic resources.