16.marker.14-17

The B493 × QAL F2 population was used for mapping STS markers. B493 is a dark orange USDA inbred carrot and QAL is a white wild carrot (D. carota var. carota). The population evaluated was derived from crossing a single B493 plant with a single QAL plant in Madison, WI, in 1989. A single F1 plant was self-pollinated to produce the F2 generation used for mapping. A total of 183 F2 plants grown in field conditions in 1998 were included in the study.

Genotype data for the putative carotenoid structural genes was added to the map data generated by Santos (2001), which consisted mostly of AFLP markers. MAPMAKER 3.0 was used for map construction. Dominant markers from a single parent linked in coupling were used in conjunction with all codominant markers. The two-point command was used to establish linkage groups at a LOD of 4.0. One or two codominant markers per group were assigned as anchor loci in the initialization file. Markers were assigned to linkage groups using the assign command. Three-point analysis was then performed for each linkage group followed by the order command to develop a framework map. Remaining markers were added using the place command. Markers that still remained unplaced were added using the try command. The linkage group numbering of Santos (2001) and Santos and Simon (2002, 2004) was retained.

Separate maps for each parent of the cross were generated consisting of a mixture of only codominant and coupling phase dominant markers. This map corresponds to the B493 parent.

A genetic linkage map was constructed using a set of 159 F2 progeny from the cross between the wild (QAL) and the cultivated (line B493) carrot. Details concerning the production of the mapping population, plant cultivation, DNA extraction, and identification of AFLP, SCAR, SSR and gene specific markers were reported previously (Santos and Simon, 2002, 2004; Just, 2004).

Polymorphic DcMTD products were used to saturate the existing genetic linkage map of the F2 population QAL × B493 (Santos and Simon, 2002; Just, 2004). Separate maps were constructed for each parent to avoid problems related to the use of repulsion phase dominant markers, as described previously (Santos and Simon, 2004). This map corresponds to the B493 parent. The maps were constructed with MAPMAKER 3.0 (Lander et al., 1987). Dominant markers from a single parent linked in coupling were used in conjunction with all codominant markers. The ‘two point’ command was used to establish linkage groups at LOD=4.0. Three point analysis was then performed for each linkage group followed by the ‘order’ command. Remaining markers were added using the ‘try’ command. To test whether the mapped DcMTD markers were evenly distributed among the nine linkage groups, we used a χ² test for goodness of fit, where the expected number of markers per linkage group was estimated from the proportion of the linkage group length related to the total length of the corresponding map.