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10. MARKER EFFICIENCY
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a map is used for QTL mapping high resolution is necessary. The other strategy is employed
if a single gene should be mapped. Then BSA (Bulk Segregant Analysis) can be used to find
as many markers as possible in a given region. Once markers are found a detailed map for
that region is constructed. For species comparisons there is always a choice between high
resolution of a single map and mapping in many cross combinations. It is possible to use only
selected sequences or isoezymes in a case of preliminary species comparisons. The use of
common sets of DNA probes to detect and map homologous sequences across different species
has revealed a high degree of conservation in species belonging to the same family. The
extended comparative relationships facilitate the transfer of genetic knowledge from wellstudied
crops to other species. Unfortunately, the use of common DNA probes or STS markers
is not free of problems. Own results have demonstrated that STS markers derived from
cereals are completely useless in genome mapping of Lolium owing to low polymorphism or
inability to amplify a single PCR product. Similar results were also obtained for STS markers
derived from Medicago truncatula and applied for genetic mapping of stiff straw in Pisum
sativum (K. Polok, unpublished results). All primers are not able either to amplify a discrete
band or they do not reveal polymorphism between parents, cultivars and mutants. Surprisingly,
it is easier to obtain reproducible results using primers derived from bacterial genes
than those from close relatives. Because bacteria-derived markers tend to be linked with
enzymes it seems reasonable to incorporate them in maps as potential markers of genes as
well as potential markers for interspecific comparisons. Comparisons of the utility of different
marker categories as indicated by the number of primers needed for a map construction in
Lolium and the number of polymorphic loci between parents demonstrate the relatively high
utility of RAPDs and ISJs. Unexpectedly, quite poor performance is observed for AFLP that
are thought to be the most reliable and informative markers for genetic mapping (Table 10.3).
Unfortunately, own results do not confirm this view, also because they tend to group and they
are underrepresented as markers linked or flanking QTLs. This feature may seriously limit
their utility for mapping quantitative traits. Perhaps it is the reason for difficulties in alignment
of most Lolium maps based on AFLPs.
The SSR markers are highly polymorphic and they are useful in mapping studies. The
disadvantage is the effort needed for their development in each species and relatively high