Theor Appl Genet (1998) 97 : 960—967  Springer-Verlag 1998 J. M. Bradeen · P. W. Simon Conversion of an AFLP fragment linked to the carrot Y 2 locus to a simple, codominant, PCR-based marker form Received: 16 February 1998 / Accepted: 7 April 1998 Abstract Recent advances have expanded the potential usefulness of molecular techniques for plant genetic research. AFLP is a powerful technique, allowing rapid and reliable analysis of multiple, potentially poly- morphic sites in a single experiment. Because AFLP technology requires no a priori knowledge of genome structure or preparation of molecular probes, it is im- mediately useful for a wide variety of plant species. However, because AFLP markers are dominant, costly, and technologically demanding, the technique has lim- ited application for large-scale, locus-specific uses. In carrot, the ½ 2 locus controls carotene accumulation in the root xylem core. Although carrot is an important source of dietary carotene, little is known about the regulation and biosynthesis of carotenes in carrot. We identified six AFLP fragments linked to the ½ 2 locus through a combination of F  mapping and bulked segregant analysis. We have developed a procedure for generating simple, codominant, PCR-based markers from dominant AFLP fragments using a ½ 2 -linked AFLP fragment as a model. Our converted marker requires only a simple PCR followed by standard agarose gel electrophoresis. It is rapid, simple, reliable, comparatively inexpensive, codominant, and non-radio- active. Conversion of AFLP fragments to forms better adapted to large-scale, locus-specific applica- tions greatly expands the usefulness of this molecular technique. Key words AFLP · Bulked segregant analysis · Daucus carota · Inverse PCR · Marker conversion Communicated by G. Wenzel J. M. Bradeen · P. W. Simon ( ) USDA-ARS Vegetable Research Crops Unit and Department of Horticulture, University of Wisconsin—Madison, 1575 Linden Drive, Madison, WI 53706, USA E-mail: psimon@facstaff.wisc.edu Fax: #1-608-262-4743 Introduction With recent improvements in marker technologies, mo- lecular maps have been developed for a wide variety of important agronomic and horticultural crops (Davis and Yu 1997; Hallde´ n et al. 1996; Jiang et al. 1997; King et al. 1998; Mudge et al. 1996; Paillard et al. 1996) and genes conditioning disease and insect resistance, yield, plant architecture, and other important traits have been mapped and/or cloned (Cai et al. 1997; Lu et al. 1996; Sourdille et al. 1996; Veldboom and Lee 1996; Warburton et al. 1996). Yet despite increasing marker availability for many species, molecular biology re- mains largely inaccessible for locus-specific applica- tions requiring the characterization of large plant populations, and marker-aided selection is frequently little more than theory. This is due in part to the fact that markers used to generate linkage or genetic maps are frequently poorly adapted to other, larger scale uses. Markers that are useful must allow rapid charac- terization of hundreds or thousands of individuals with a minimal input of resources, including money and skilled labor. They must also be reliable with low error rates and typically should be codominant. Finally, in most instances, the markers must be non-radioactive. The Amplified Fragment Length Polymorphism (AFLP; Vos et al. 1995; Zabeau and Vos 1993) is growing in popularity. Combining the specificity of restriction enzyme analysis with the ease and specificity of the polymerase chain reaction (PCR), this technique requires no genomic or cDNA library construction and no specific a priori knowledge of the plant genome. The technique is rapid and reliable, allowing the researcher to simultaneously evaluate 50 or more potential poly- morphisms on a single polyacrylamide gel. For plant researchers the technique offers quick linkage map con- struction and rapid identification of markers linked to genes of interest. Limitations to the large-scale, locus- specific application of AFLP include the requirement