AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution

We exploited the AFLP technique to saturate a RFLP linkage map derived from a maize mapping population. By using two restriction enzyme, EcoRI and Pst I, differing in methylation sensitivity, both in combination with MseI, we detected 1568 bands of which 340 where polymorphic. These were added to the exitsing RFLP marker data to study the effects of incorporation of AFLPs p roduced by different restriction-enzyme combinations upon genetic maps. Add ition of the AFLP data resulted in greater genome coverage, both through li nking previously separate groups and the extension of other groups. The inc rease of the total map length was mainly caused by the addition of markers to telomeric regions, where RFLP markers were poorly represented. The perce ntage of informative loci was significantly different between the EcoRI and PstI assays. There was also evidence that PstI AFLP markers were more rand omly distributed across chromosomes and chromosome regions, while EcoRI AFL P markers clustered mainly at centomeric regions. The more-random ditsribut ion of PstI AFLP markers on the genetic map reported here may reflect a pre ferential localisation of the markers in the hypomethylated telomeric regio ns of the chromosomes.