USDA ARS VCRU Data Server
This web site, https://www.vcru.wisc.edu/sdata, contains data from the laboratory of Philipp W. Simon, USDA-ARS Vegetable Crops Research Unit [Click here for our web page]
 

B493×QAL Linkage Map v.3 Marker Information Table

Return to B493×QAL v.3 map main page

Raw Data

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

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:

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

Selective nucleotides Number of amplicons Number of sequenced products
Total Polymorphic Total Specific
ACA 8 8 7 6
ACT 9 9 8 6
AGT 10 7 4 3
CTA 5 4 5 4
GTA 10 7 4 4
CAT 7 7 7 7
GAT 12 7 6 5
CTT 8 8 4 4
GTT 10 7 5 5
CAA 9 7 6 5
GAA 12 9 5 5
AGA 9 7 - -
CAG 8 6 - -
TCA 13 8 - -
TGT 8 5 - -
Total 138 106 61 54

Transposon Display Markers

MarkerProtocolMap Location
TD-ACA073MK000056LG9
TD-ACA081MK000056LG6
TD-ACA104MK000056LG3
TD-ACA111MK000056LG7
TD-ACA128MK000056LG6
TD-ACA143MK000056LG5
TD-ACA171MK000056LG6
TD-ACT069MK000056LG3
TD-ACT078MK000056LG5
TD-ACT082MK000056LG6
TD-ACT088MK000056LG9
TD-ACT099MK000056LG8
TD-ACT102MK000056LG4
TD-ACT121MK000056LG5
TD-AGA184MK000056LG2
TD-AGT063MK000056LG3
TD-AGT088MK000056LG1
TD-AGT154MK000056LG2
TD-AGT163MK000056LG7
TD-CAG120MK000056LG8
TD-CAG177MK000056LG6
TD-CAG235MK000056LG9
TD-CAT068MK000056LG2
TD-CAT171MK000056LG9
TD-CAT182MK000056LG4
TD-CAT213MK000056LG7
TD-CTA069MK000056LG4
TD-CTA075MK000056LG8
TD-CTA119MK000056LG8
TD-CTA261MK000056LG6
TD-CTT069MK000056LG5
TD-CTT082MK000056LG9
TD-CTT084MK000056LG1
TD-CTT102MK000056LG4
TD-CTT176MK000056LG8
TD-GAA120MK000056LG9
TD-GAA205MK000056LG7
TD-GAT069MK000056LG1
TD-GAT099MK000056LG2
TD-GAT101MK000056LG4
TD-GAT120MK000056LG5
TD-GTA076MK000056LG5
TD-GTA185MK000056LG2
TD-GTT068MK000056LG5
TD-GTT104MK000056LG2
TD-GTT138MK000056LG4
TD-GTT152MK000056LG2
TD-GTT158MK000056LG6
TD-TCA230MK000056LG5
TD-TGT063MK000056LG4
TD-TGT150MK000056LG2

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.