Untitled

10. MARKER EFFICIENCY
10.1. INTRODUCTION
It is not overstatement to say that any genetic analysis would be impossible without
genetic markers, whether morphological or molecular. They lend themselves to a wide variety
of methodological approaches depending on the particular problem and research goals.
Their generic applications include population, and evolutionary genetics as well as many
aspects of applied genetics including genome mapping, analysis of quantitative traits, gene
isolation and many others. Isozymes introduced in the mid 1960s, were the first markers that
provided insights into microevolutionary processes but also they became useful as a marker
system in the analysis of experimental crosses. Invention of the polymerase chain reaction
(PCR) revolutionized molecular biology and has stimulated many new methods of genetic
marker acquisition. These new methods that have been emerging in between eventually gain
wide popularity. But, usually, after a period of enthusiasm, a wave of interest has focused on
others newly introduced methods. Typically, the earlier methods have not been abandoned
however, their usage sometimes have been limited. The example involves protein electrophoresis
that remains a simple and useful method, although opinions that it is old fashioned
and should be abandoned do exist. Nevertheless, the easy interpretation of electrophoretic
patterns (zymograms) and codominance favour it in comparison with many DNA markers.
Similarly, a lot of objections are elevated for different PCR-based techniques. Consider RAPD
markers that are thought to be irreproducible and not highly polymorphic despite many valuable
results obtained through their usage. Examples include the first genetic map of Lolium
(Hayward et al. 1998), and molecular phylogeny of the grass genus Brachypodium (Catalan
et al. 1995). In the latter studies RAPD markers proved to be more efficient than RFLPs.
In deciding which marker system is the best for a given application several key factors
should be considered. The level of polymorphism, the availability of plant material necessary
for the analysis and the costs are among the most important. There are many manuals and
guides how and when to use a given type of molecular markers. Although they offer quite
useful reviews for beginners they do not avoid popular opinions, not always grounded very
well and repeated over and over again. The issue is exactly in what is meant by own experience.
In the present work a huge amount of different laboratory techniques has been addressed
at different levels of analyses from genetic diversity studies, phylogenetic analyses
and mapping. These data enabled to estimate the usefulness, efficiency and limitation of
different types of markers in variety genetic analyses. This chapter summarizes the results
obtained for Lolium with regard to marker efficiency and costs. It also proposes the most