Comparative AFLP mapping in two hexaploid oat populations

Amplified fragment length polymorphisms (AFLPs) can be used to quickly deve lop linkage maps in plant species and are especially useful for crops with large genomes Like oat (Avena sativa L., 2n=6x=42). High reproducibility an d consistency are crucial if AFLP linkage maps are employed for comparative mapping. We mapped AFLP markers in combination with restriction fragment l ength polymorphism (RFLP) markers in two recombinant inbred populations of hexaploid oat in two laboratories to test the consistency of AFLP markers i n a polyploid crop. Eight primer combinations produced 102 and 121 scoreabl e AFLP markers in the respective populations. In a population from the cros s Kanota x Ogle, AFLP markers were placed onto a RFLP reference map consist ing of 32 Linkage groups. Nineteen linkage groups from another population f rom the cross Kanota x Marion were assigned to the reference map using AFLP and RFLP markers homologous to those used in the Kanota x Ogle cross. Repr oducibility of AFLP assays was high in both laboratories and between labora tories. The AFLP markers were well-distributed across the genome in both po pulations. Many AFLP markers tended to extend the distance between adjacent RFLP markers in linkage analysis. Of the 27 polymorphic AFLPs common in bo th populations, 20 mapped to homologous linkage groups, 4 were unlinked in at least one population, and 3 mapped to different linkage groups in the tw o crosses. We believe that 1 of the 3 markers that mapped to a different Li nkage group in the two populations mapped to homoeologous Linkage groups. T he linkage map of hexaploid oat is not yet complete, and genomic rearrangem ents such as translocations exist among cultivars and are likely to account for the remaining two non-syntenous mapping results. AFLPs provide not onl y a fast and powerful tool for mapping but could be useful in characterizin g genomic structural variations among germplasms in hexaploid oat.