Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers

This study demonstrates the relative ease of generating high-density linkage maps using the AFLP® technology. Two high-density AFLP linkage maps of Zea mays L. were generated based on: (1) a B73 × Mo17 recombinant inbred population and (2) a D32 × D145 immortalized F2 population. Although AFLP technology is in essence a mono-allelic marker system, markers can be scored quantitatively and used to deduce zygosity. AFLP markers were generated using the enzyme combinations EcoRI/MseI and PstI/MseI. A total of 1539 and 1355 AFLP markers have been mapped in the two populations, respectively. Among the mapped PstI/MseIAFLP markers we have included fragments bounded by a methylated PstI site (mAFLP markers). Mapping these mAFLP markers shows that the presence of C-methylation segregates in perfect accordance with the primary target sequence, leading to Mendelian inheritance. Simultaneous mapping of PstI/MseIAFLP and PstI/MseI mAFLP markers allowed us to identify a number of epi-alleles, showing allelic variation in the CpNpG methylation only. However, their frequency in maize is low. Map comparison shows that, despite some rearrangements, most of the AFLP markers that are common in both populations, map at similar positions. This would indicate that AFLP markers are predominantly single-locus markers. Changes in map order occur mainly in marker-dense regions. These marker-dense regions, representing clusters of mainly EcoRI/MseI AFLP and PstI/MseI mAFLP markers, co- localize well with the putative centromeric regions of the maize chromosomes. In contrast, PstI/MseImarkers are more uniformly distributed over the genome.