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.