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10. MARKER EFFICIENCY
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random selection of different sequences. Similarly, to population genetic and mapping studies,
the surprisingly good results were obtained with random markers including AFLP, ISJ
and RAPD. Conversely, the organelle DNA and STS markers derived from cereals tend
to produce biases. The present data confirm that the best resolution is obtained if many
different sequences are used together. The consensus tree based on almost 3000 molecular
markers mirrors very well evolutionary relationships within Poaceae. However, it seems
unrealistic to employ so many markers in routine evolutionary analyses in which tens and
hundreds species are sampled. To this point, markers based on bacterial genes seem to
offer a good alternative. Their trees are very alike those based on multiple markers but their
development needs less efforts.
B-SAP - a new approach for phylogenetic studies
The idea is based on using primers complementary to bacterial genes to amplify plant
DNA and reveal polymorphism. For the first time B-SAP was tested using several representatives
of Poaceae (Polok 2005; Zielinski and Polok 2005). Several primer categories can be
used, however the best results, transferable among many taxa are received through using
primers complementary to the M. tuberculosis KatG gene encoding catalase-peroxidase and
primers complementary to IS6110 element from the same species. The revealed markers are
dominant i.e., the presence of a band is dominant over its lack. They are characterized by
low polymorphism within species, however great differences are observed at the interspecific
level. The mapping studies demonstrated that katG markers are linked with peroxidase and
some other enzymes, thus confirming that they are related with coding sequences, presumably
of bacterial origin. By contrary, markers derived from IS6110 behave alike transposons.
What is more, all bacteria-derived markers are rarely distorted in comparison with the others.
The percentage of bands that deviated from the expected Mendelian ratios is below the
mean for the whole genome. Therefore, it is reasonable to incorporate them in mapping studies
as well as in phylogenetic applications. We propose to use them in phylogenetic studies
to resolve deeper evolutionary relationships as well as species specific markers. Because
they are based on bacterial sequences, we propose to ascertain them as Bacteria Specific
Amplification Polymorphism (B-SAP) with a gene name if necessary.