Abstract We exploited the AFLP technique to saturate a RFLP linkage map derived from a maize mapping popu- lation. By using two restriction enzyme, EcoRI and PstI, 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 AF- LPs produced by different restriction-enzyme combina- tions upon genetic maps. Addition of the AFLP data re- sulted in greater genome coverage, both through linking previously separate groups and the extension of other groups. The increase of the total map length was mainly caused by the addition of markers to telomeric regions, where RFLP markers were poorly represented. The per- centage of informative loci was significantly different between the EcoRI and PstI assays. There was also evi- dence that PstI AFLP markers were more randomly dis- tributed across chromosomes and chromosome regions, while EcoRI AFLP markers clustered mainly at centom- eric regions. The more-random ditsribution of PstI AFLP markers on the genetic map reported here may reflect a preferential localisation of the markers in the hypometh- ylated telomeric regions of the chromosomes. Key words Genetic map · Linkage analysis · AFLP · Methylation sensitivity · Codominant markers · Zea mays L. Introduction Extensive genome mapping based on DNA restriction fragment length polymorphism (RFLP) markers has been accomplished in many crop species (O’Brien 1993). These maps and their associated technology have been used successfully for a number of applications in genetic research and breeding, including gene tagging, evolu- tionary studies, marker-aided selection, and the analysis of quantitative trait loci (QTLs; for a review see Lee 1995, and references therein). However, RFLP analysis is an expensive and time-consuming technology and may not provide detailed coverage throughout the genome, which is a prerequisite for QTL analyses. The development of the polymerase chain reaction (PCR; Saiki et al. 1988) has expanded the repertoire and efficiency of available DNA marker systems, which in- clude the AFLP method (Vos et al. 1995). The advantage of the AFLP assay over other DNA marker techniques includes the detection of a larger number of polymor- phisms from a single PCR reaction within a very short period of time, and the requirement for small amounts of DNA, thus reducing expenses and expediting the con- struction of high-density linkage maps. As described in many comparative studies AFLP is considered to be an efficient marker technology due to its high multiplex ra- tio (Powell et al. 1996; Pejic et al. 1998). The AFLP ap- proach has recently been used to rapidly create linkage maps in a variety of plant species (Maheswaran et al. 1997; Alonso-Blanco et al. 1998; Castiglioni et al. 1998; Lu et al. 1998). With the aim of exploiting AFLP markers in a maize genome-mapping program, we assayed the AFLP codom- inantly to test the distribution of these marker loci on the maize linkage groups, and to investigate enzyme combi- nations differing in sensitivity to DNA methylation. Communicated by F. Salamini P. Castiglioni · P. Ajmone-Marsan · R. van Wijk · M. Motto (✉) Istituto Sperimentale per la Cerealicoltura, Via Stezzano 24, 24100 Bergamo, Italy e-mail: isc1@spm.it, Fax: +39 035 316054 Present address: R. van Wijk, Keygene N.V., Agro Business Park 90, P.O. Box 216, 6700 AE Wageningen, The Netherlands Theor Appl Genet (1999) 99:425–431 © Springer-Verlag 1999 P. Castiglioni · P. Ajmone-Marsan · R. van Wijk M. Motto AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group ditsribution Received: 22 December 1998 / Accepted: 25 March 1999