I am trying to select microsatellite markers from the database for assessing genetic diversity and DNA fingerprinting for germplasm. The database has consisted of Di-, Tri-, Tetra-, Penta- and Hexa-repeats along with the compound type of repeats. So what type of repeats are more potent as utilize in molecular analysis of germplasm. Whether I should choose perfect SSR markers or compound (imperfect) type or both? Kindly suggest to select the SSR markers.
Thank you
Regards
Chet Ram
Dear Chet Ram in my opinion, focus your attention in polymorphism, allelic richness, heterocigocity and discriminative power. Some authors suggest that imperfect markers would have a greater discriminative power, especially amongst individuals with a high kinship degree. About the number of repeated motifs, for some species it's known that mono and dinucleotides SSRs are more abundant; however, there's not unanimity regarding whether markers with more repeats be more discriminative.
Di- Repeats can be ignored and from tri nucleotide repeat onward should be used for the germplasm evaluation.
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