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Summary:
Procedures have been established to construct genetic (linkage) maps in farm animals using large numbers of AFLP markers, or a combination of AFLP - and microsatellite markers. These procedures take into account the complexities that result from the pedigree structures commonly encountered in these species, where marker information typically originates from multiple families. The procedures involve deriving zygosity of AFLP markers (co-dominant scoring) with high confidence and identification (elimination) of markers which complicate the mapping procedure. Framework markers may be needed to establish linkage groups, depending on the pedigree structure and the available number of co-informative meisoses.
Methods have been established to identify AFLP markers for monogenic traits and QTL using the combination of bulked segregant analysis and AFLP typing. This approach does not require a pedigree structure and can be used without prior sequence information. These advantages, together with the high multiplex capacity of the AFLP technology, make this procedure attractive for use in farm animal species, for example in commercial breeding populations.
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