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

This study demonstrates the relative ease of generating high-density linkag e maps using the AFLP(R) technology. Two high-density AFLP linkage maps of Zea mays L. were generated based on: (1) a B73 x Mo17 recombinant inbred po pulation and (2) a D32 x D145 immortalized F-2 population. Although AFLP te chnology is in essence a mono-allelic marker system, markers can be scored quantitatively and used to deduce zygosity. AFLP markers were generated usi ng the enzyme combinations EcoRI/MseI and PstI/MseI. A total of 1539 and 13 55 AFLP markers have been mapped in the two populations, respectively. Amon g the mapped PstI/MseI AFLP markers we have included fragments bounded by a methylated PstI site ((m)AFLP markers). Mapping these (m)AFLP markers show s that the presence of C-methylation segregates in perfect accordance with the primary target sequence, leading to Mendelian inheritance. Simultaneous mapping of PstI/MseI AFLP and PstI/MseI (m)AFLP markers allowed us to iden tify a number of epi-alleles, showing allelic variation in the CpNpG methyl ation 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 AF LP markers are predominantly single-locus markers. Changes in map order occ ur mainly in marker-dense regions. These marker-dense regions, representing clusters of mainly EcoRI/MseI AFLP and PstI/MseI (m)AFLP markers, colocali ze well with the putative centromeric regions of the maize chromosomes. In contrast, PstI/MseI markers are more uniformly distributed over the genome.