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B493×QAL Linkage Map v.3 Marker Information Table

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Raw Data

The data used in making this map is in the following files:

• Excel file with data: TD_map_data.xls
• Input data file for analysis by MAPMAKER: map493.txt
• Input data file for analysis by MAPMAKER: mapQAL.txt

The most complete single file for 493×QAL, a consolidated copy with ALL data for ALL markers up to Darek's map, is 493xQAL-Complete.xls
(Note that the marker GGGCAA097-Q was still in this file twice, but now it contains two copies of GGGCAA097-Q[1])
This version created Nov 2007 has some errors in Darek's names indicated in red 493xQAL-MoreComplete.xls

Map Data

Text files with the linkage map data.
March 17, 2010: These files have notations added for the 6 errors in names as listed in the errata, and have been flipped when necessary to match the published map orientation:

• TD_493.map
• TD_QAL.map

Linkage map construction

(From the publication)

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). 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 ofmarkers per linkage group was estimated from the proportion of the linkage group length related to the total length of the corresponding map.

Old Marker Information

Marker Information for AFLPs and some other previously mapped markers is here

Carotenoid genes and Y2mark are here

New Marker Information

The Rs marker is described in procol MK000012

Table 1. Number of products amplified using the DcMaster Transposon Display system from the wild x cultivated F2 (QALxB493) carrot population with primers carrying different combinations of selective nucleotides

Transposon Display Markers

References

1. Santos, C.A.F., Simon, P.W., 2002. QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots. Mol. Genet. Genom. 268, 122–129.
2. Just,B.J., 2004. Genetic mapping of carotenoid pathway structural genes and major gene QTLs for carotenoid accumulation in wild and domesticated carrot (Daucus carota L.). University of Wisconsin–Madison, PhD dissertation.
3. Santos, C.A.F., Simon, P.W., 2004. Merging carrot linkage groups based on conserved dominant AFLP markers in F2 populations. J. Am. Soc. Hortic. Sci. 129, 211–217.
4. Lander, E.S., et al., 1987. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1, 174–181.