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.2
Marker Table

Return to B493×QAL map main page

Raw Data

The data used in making this map might be 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 here

Map Data

Text files with the linkage map data:

Linkage map construction

(From the publication)

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 (Lander et al. 1987) 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.

Old Marker Information

Marker Information for AFLPs and other previously mapped markers is here

New Marker Information

MarkerProtocolMap location
IPIProtocol MK000030 Not mapped
GGPS1Protocol MK000031 Not mapped
GGPS2 (GGPPS)Protocol MK000032 B493 lg 2 @ 95.8/111.7; QAL lg 2 @ 92.5/145.1
PSY1Protocol MK000033 B493 lg 3 @ 0.0/113.9; QAL lg 3 @ 2.0/109.5
PSY2Protocol MK000034 B493 lg 8 @ 55.0/97.2; QAL lg 8 @ 134.4/186.2
CRTISOProtocol MK000035 B493 lg 6 @ 23.1/136.0; QAL lg 6 @ 14.8/99.0
PDSProtocol MK000036 B493 lg 2 @ 111.7/111.7; QAL lg 2 @ 118.0/145.1
ZDS1Protocol MK000037 B493 lg 4 @ 12.2/104.9; QAL lg 4 @ 19.7/74.8
ZDS2Protocol MK000038 B493 lg 5 @ 53.9/105.4; QAL lg 5 @ 88.4/115.8
LCYBProtocol MK000039 B493 lg 3 @ 62.2/113.9; QAL lg 3 @ 76.1/109.5
CCS (CYC-B)(LCYB2)Protocol MK000040 B493 lg 3 @ 9.4/113.9; QAL lg 3 @ 14.2/109.5
LCYEProtocol MK000041 B493 lg 9 @ 76.6/149.5; QAL lg 9 @ 61.8/114.3
CHXB1Protocol MK000042 B493 lg 3 @ 58.7/113.9; QAL lg 3 @ 72.6/109.5
CHXB2Protocol MK000043 B493 lg 6 @ 43.9/136.0; QAL lg 6 @ 39.3/99.0
CHXB3Protocol MK000044 B493 lg 6 @ 45.2/136.0; QAL lg 6 @ 40.5/99.0 (not on figure but in map file)
CHXEProtocol MK000045 B493 lg 2 @ 64.6/111.7; QAL lg 2 @ 68.7/145.1
ZEPProtocol MK000046 B493 lg 5 @ 57.0/105.4; QAL lg 5 @ 92.7/115.8
VDEProtocol MK000047 B493 lg 6 @ 25.2/136.0; QAL lg 6 @ 17.1/99.0
NCED1Protocol MK000048 B493 lg 2 @ 21.9/111.7; QAL lg 2 @ 16.8/145.1
NCED2Protocol MK000049 B493 lg 2 @ 70.1/111.7; QAL lg 2 @ 74.9/145.1
NCED3Protocol MK000050 B493 lg 6 @ 35.1/136.0; QAL lg 6 @ 25.4/99.0
CCD1Protocol MK000051 B493 lg 3 @ 20.6/113.9; QAL lg 3 @ 29.0/109.5
CCD2Protocol MK000052 B493 lg 1 @ 145.4/242.2; QAL lg 1 @ 68.9/96.6
CCD3Protocol MK000053 B493 lg 3 @ 20.6/113.9; QAL lg 3 @ 29.0/109.5
Y2MarkProtocol MK000002 B493 lg 5 @ 94.8/105.4; QAL lg 5 @ 109.0/115.8

References

  1. Santos CAF (2001) Biometrical studies and quantitative trait loci associated with major products of the carotenoid pathway of carrot (Daucus carota L.). PhD Thesis. University of Wisconsin, Madison, WI
  2. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
  3. Santos CAF, Simon PW (2002) QTL analyses reveal clustered loci for accumulation of major provitamin A carotenes and lycopene in carrot roots. Mol Genet Genom 268:122–129
  4. Santos CAF, Simon PW (2004) Merging carrot linkage groups based on conserved dominant AFLP markers in F2 populations. J Am Soc Hortic Sci 129:211–217