Evaluation of AFLP for genetic mapping in Pinus radiata D-Don

Efficient construction of reasonable density genetic linkage maps is an essential component of QTL detection programmes. The AFLP technique has been used to produce genetic linkage maps in a range of species. We have developed protocols to generate reproducible AFLP profiles in Pinus radiata and have evaluated the inheritance and informativeness of AFLP markers in this important timber species. The large genome size of P. radiata necessitated increased levels of selection at both the pre-amplification and selective amplification steps of the AFLP protocol to generate reproducible AFLP profiles. Once optimised ca. 41.3 scorable AFLP bands were resolvable through denaturing gels, of which 48.4% were polymorphic in a screen of eight unrelated trees. This level of polymorphism is ca. three times higher than with RAPD markers. The total number of bands and the number of polymorphismic bands per PCR were ca. halved when AFLPs were electrophoresed on non-denaturing gels and stained with ethidium bromide. Using the protocols developed, AFLP is an efficient method for generating the DNA markers required for genetic linkage map construction in P. radiata.