In the process of SSR fingerprinting 68 CIMMYT and other inbred lines (note above), we have found that often we can define clearly separate "morphs" or clusters of bands defined by migration distance. The small-scale shifts in numbers of SSR repeats that are expected in SSR fingerprinting can be seen, but easily defined morphs are clearly a major feature. Given this situation, we need to designate morph identifiers in such a format that labs can compare results, and future improvements in definition and understanding will be easily incorporated into the system.
The results of classification and sorting of estimated migration distances for the p-phi114 SSR probe at the oec17 locus (bin 7.02) illustrate a simple situation. We have accepted the HyperBlot analysis which, for a set of bands ranging ca. 133-199 bp, provides 3 morphs, with bands of ca. 133 to 144 bp, 163 to 176 bp and 199 bp. It is rather easy to name these by their mean sizes: phi114-a139, phi114-a170 and phi114-a199 (the "a" means agarose). Like species definitions, even though, as one studies more materials, there can be changes in the balance of readings for a morph, it should be best to maintain the original designations as long as sensible.
How can we avoid having to completely redesignate the morphs if, with better resolution, we were to subdivide morphs here defined? If polyacrylamide gels were used, one might just name a new series of morphs starting with "p", plus the more narrowly defined size estimates. On the other hand, a slash and a letter could be appended to the present morph designations. Letters could be chosen which indicate relative sizes and anticipate the discovery of more submorphs. phi114-a137 might end up with three submorphs, phi114-a137/b, phi114-a137/e and phi114-a137/h, while phi114-a169 might be divided into phi114-a169/k, --/n, --/q and --/t. Such subdivisions need to made with the possible number of microsatellite repeat motifs in mind. With phi114 this would be tough -- between the primer sites there are three repeat motifs in GenBank accession Z26824: (CCG)3, (TGCC)4 and (TA)4, so there are a great many possible permutations.
We hope this note elicits some constructive discussion before a wide range of methods appears
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