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]
 

Merged Linkage Map

Merging Carrot Linkage Groups based on Conserved Dominant AFLP Markers in F2 Populations
Carlos A. F. Santos, Philipp W. Simon
J. Amer. Soc. Hort. Sci. 129(2):211-217. 2004


Abstract Markers were placed on linkage groups, ordered, and merged for two unrelated F2 populations of carrot (Daucus carota L.). Included were 277 and 242 dominant AFLP markers and 10 and eight co-dominant markers assigned to the nine linkage groups of Brasilia × HCM and B493 × QAL F2 populations, respectively. The merged linkage groups were based on two co-dominant markers and 28 conserved dominant AFLP markers (based upon sequence and size) shared by both populations. The average marker spacing was 4.8 to 5.5 cM in the four parental coupling phase maps. The average marker spacing in the six merged linkage groups was 3.75 cM with maximum gaps among linkage groups ranging from 8.0 to 19.8 cM. Gaps of a similar size were observed with the linkage coupling phase maps of the parents, indicating that linkage group integration did not double the bias which comes with repulsion phase mapping. Three out of nine linkage groups of carrot were not merged due to the absence of common markers. The six merged linkage groups incorporated similar numbers of AFLP fragments from the four parents, further indicating no significant increase in bias expected with repulsion phase linkage. While other studies have merged linkage maps with shared AFLPs of similar size, this is the first report to use shared AFLPs with highly conserved sequence to merge linkage maps in carrot. The genome coverage in this study is suitable to apply quantitative trait locus analysis and to construct a cross-validated consensus map of carrot, which is an important step toward an integrated map of carrot.


Fig. 1. Six merged linkage groups for Brasilia × HCM and B493 × QAL F2 populations of carrot. AFLP fragments with / (e.g. AAGCTC239-Q/B) and two pair base sizes (e.g. GAGCTT235/271) represent a conserved AFLP fragment between the two populations and a co-dominant AFLP, respectively.
The map data for these maps (manually entered from the figures) is available as Mergedmap.txt

1 2 3 4 5 6

Table 1. Heterogeneity test (H) for recombination fraction (θ) per linkage group among common molecular markers used to merge linkage groups between the Brasilia (Bsb) × HCM and B493 × QAL F2 carrot populations (P).

Pair F2 θ LOD Chi-square Linkage
group
P H
AACCAT218-4/B × AGGCTA108-4/H Bsb × HCM 0.3033 1.42 3.70   LG1
B493 × QAL 0.1340 14.47 1.69 5.39* LG1
AACCAT218-4/B × GAGCAC444-4/H Bsb × HCM 0.2005 9.02 0.07   LG1
B493 × QAL 0.2401 2.36 0.19 0.26 NS LG1
AACCAT218-4/B × DCDRTSG Bsb × HCM 0.0658 23.19 1.26   LG1
B493 × QAL 0.1230 16.49 1.05 2.30NS LG1
AACCAT218-4/B × GATCTC181-4/H Bsb × HCM 0.1937 2.47 0.17   LG1
B493 × QAL 0.1561 12.14 0.04 0.22NS LG1
AGGCTA108-4/H × DCDRTSG Bsb × HCM 0.3194 2.01 7.43   LG1
B493 × QAL 0.1044 18.73 5.70 13.12** LG1
AGGCTA108-4/H × GAGCAC444-4/H Bsb × HCM 0.0928 19.58 1.21   LG1
B493 × QAL 0.1704 8.57 1.43 2.64 NS LG1
AGGCTA108-4/H × GATCTC181-4/H Bsb × HCM 0.0722 16.43 2.24   LG1
B493 × QAL 0.0133 32.85 2.67 4.91* LG1
GAGCAC444-4/H × GATCTC181-4/H Bsb × HCM 0.0658 23.15 0.87   LG1
B493 × QAL 0.1229 11.44 1.04 1.91 NS LG1
GAGCAC444-4/H × DCDRTSG Bsb × HCM 0.1870 9.79 1.95   LG1
B493 × QAL 0.3247 2.01 2.49 4.44* LG1
DCDRTSG × GATCTC181-4/H Bsb × HCM 0.2902 2.77 5.19   LG1
B493 × QAL 0.1102 17.07 4.11 9.30** LG1
GGACAA222-4/B × GGGCAT282-4/H Bsb × HCM 0.2551 1.95 4.45   LG2
B493 × QAL 0.0805 18.82 2.14 6.59* LG2
GGACAA222-4/B × AAGCAG075-4/H Bsb × HCM 0.3509 0.85 0.80   LG2
B493 × QAL 0.2561 4.58 0.43 1.23 NS LG2
GGGCAT282-4/H × GGACAG272-4/H Bsb × HCM 0.3339 1.05 0.08   LG2
B493 × QAL 0.3676 1.09 0.05 0.13 NS LG2
GGGCAT282-4/H × AAGCAG075-4/H Bsb × HCM 0.2824 3.23 0.15   LG2
B493 × QAL 0.2435 4.85 0.15 0.31 NS LG2
AAGCAG075-4/H × GGACAG272-4/H Bsb × HCM 0.2334 4.64 1.51   LG2
B493 × QAL 0.1304 12.07 1.39 2.91 NS LG2
GGACAG259-4/B × ACACAA142-4/H Bsb × HCM 0.2477 1.68 0.39   LG3
B493 × QAL 0.1834 8.08 0.15 0.54 NS LG3
GGACAG259-4/B × AGCCAA136-Q/H Bsb × HCM 0.3835 0.53 0.84   LG3
B493 × QAL 0.2584 2.56 0.83 1.67 NS LG3
ACACAA142-4/H × AGCCAA136-Q/H Bsb × HCM 0.3984 0.67 0.98   LG3
B493 × QAL 0.2564 2.54 1.66 2.64 NS LG3
AACCAT100-4/H × AAGCAG097-4/B Bsb × HCM 0.2256 1.97 0.86   LG4
B493 × QAL 0.1434 15.03 0.22 1.09 NS LG4
AACCAT100-4/H × GGGCAT119-Q/H Bsb × HCM 0.3308 1.83 0.01   LG4
B493 × QAL 0.3224 2.13 0.01 0.01 NS LG4
AAGCAG097-4/B × GGGCAT119-Q/H Bsb × HCM 0.3200 1.20 0.27   LG4
B493 × QAL 0.2527 2.80 0.24 0.51 NS LG4
AACCAT202-4/B × ACACAA106-Q/B Bsb × HCM 0.0979 15.43 0.23   LG5
B493 × QAL 0.0000 4.82 2.80 3.04 NS LG5
AACCAT202-4/B × ACACTT153-4/H Bsb × HCM 0.2567 2.01 0.01   LG5
B493 × QAL 0.2465 5.22 0.00 0.01 NS LG5
AACCAT202-4/B × GGGCAA229-4/H Bsb × HCM 0.4136 0.34 0.01   LG5
B493 × QAL 0.4228 0.35 0.01 0.01 NS LG5
ACACAA106-Q/B × ACACTT153-4/H Bsb × HCM 0.2442 2.34 0.02   LG5
B493 × QAL 0.2206 2.33 0.03 0.05 NS LG5
ACACAA106-Q/B × GGGCAA229-4/H Bsb × HCM 0.3395 0.99 0.74   LG5
B493 × QAL 0.4418 0.21 0.44 1.18 NS LG5
ACACTT153-4/H × GGGCAA229-4/H Bsb × HCM 0.2869 3.56 0.81   LG5
B493 × QAL 0.2033 7.23 0.86 1.66 NS LG5
AGCCTT206-Q/H × GATCTC386-4/B Bsb × HCM 0.3503 0.70 1.10   LG6
B493 × QAL 0.1834 3.10 1.35 2.45 NS LG6
AGCCTT206-Q/H × Scar-AFLP3 Bsb × HCM 0.2191 5.37 0.14   LG6
B493 × QAL 0.1915 11.62 0.08 0.22 NS LG6
AGCCTT206-Q/H × ACACAA319-4/H Bsb × HCM 0.1808 8.08 0.59   LG6
B493 × QAL 0.0000 5.21 5.62 6.21* LG6
AGCCTT206-Q/H × GGGCAT165-Q/H Bsb × HCM 0.1420 10.27 0.20   LG6
B493 × QAL 0.1157 20.08 0.13 0.32 NS LG6
AGCCTT206-Q/H × GGTCTT350-4/H Bsb × HCM 0.1524 9.16 0.40   LG6
B493 × QAL 0.0000 4.52 4.11 4.51* LG6
AGCCTT206-Q/H × GGGCAA289-Q/H Bsb × HCM 0.1637 7.87 0.35   LG6
B493 × QAL 0.1260 18.61 0.2 0.55 NS LG6
GATCTC386-4/B × Scar-AFLP3 Bsb × HCM 0.0552 24.71 0.01   LG6
B493 × QAL 0.0605 22.45 0.01 0.03 NS LG6
GATCTC386-4/B × ACACAA319-4/H Bsb × HCM 0.1539 4.21 0.90   LG6
B493 × QAL 0.2445 4.69 0.38 1.27 NS LG6
GATCTC386-4/B × GGGCAT165-Q/H Bsb × HCM 0.2374 2.35 0.42   LG6
B493 × QAL 0.1519 4.39 0.46 0.88 NS LG6
GATCTC386-4/B × GGTCTT350-4/H Bsb × HCM 0.3220 1.02 3.51   LG6
B493 × QAL 0.1389 11.45 1.75 5.25* LG6
GATCTC386-4/B × GGGCAA289-Q/H Bsb × HCM 0.2729 1.45 0.69   LG6
B493 × QAL 0.1553 4.04 0.69 1.38 NS LG6
Scar-AFLP3 × ACACAA319-4/H Bsb × HCM 0.1736 10.66 0.10   LG6
B493 × QAL 0.1990 8.03 0.11 0.21 NS LG6
Scar-AFLP3 × GGGCAT165-Q/H Bsb × HCM 0.1531 10.35 0.50   LG6
B493 × QAL 0.1108 20.52 0.36 0.86 NS LG6
Scar-AFLP3 × GGTCTT350-4/H Bsb × HCM 0.1608 9.03 1.48   LG6
B493 × QAL 0.0808 19.12 1.40 2.88 NS LG6
Scar-AFLP3 × GGGCAA289-Q/H Bsb × HCM 0.1144 12.55 0.16   LG6
B493 × QAL 0.0927 23.33 0.10 0.27 NS LG6
ACACAA319-4/H × GGGCAT165-Q/H Bsb × HCM 0.0667 20.16 4.03   LG6
B493 × QAL 0.2557 2.64 5.85 9.88** LG6
ACACAA319-4/H × GGTCTT350-4/H Bsb × HCM 0.1573 10.17 0.03   LG6
B493 × QAL 0.1439 11.52 0.03 0.06 NS LG6
ACACAA319-4/H × GGGCAA289-Q/H Bsb × HCM 0.1252 13.08 0.58   LG6
B493 × QAL 0.2139 3.21 1.12 1.70 NS LG6
GGGCAT165-Q/H × GGTCTT350-4/H Bsb × HCM 0.0790 16.74 0.27   LG6
B493 × QAL 0.0000 5.92 2.65 2.95 NS LG6
GGGCAT165-Q/H × GGGCAA289-Q/H Bsb × HCM 0.0713 17.34 0.14   LG6
B493 × QAL 0.0555 29.74 0.09 0.24 NS LG6
GGTCTT350-4/H × GGGCAA289-Q/H Bsb × HCM 0.0713 17.34 0.14   LG6
B493 × QAL 0.055 29.74 0.09 0.24 NS LG6

**, * and NS significant at the p-values of 1%, 5% and non-significant, respectively, by chi-square test


Supplementary Table A. List of the two co-dominant markers and 28 conserved dominant AFLP markers used for merging the maps, and the corresponding map location of these markers in the previously published B493×QAL and BSB×HCM maps

Marker NameMerged GroupB493×QAL
Location
BSB×HCM
Location
DCDRTSG 1@57.6 LG1LG1
Scar-AFLP3 6@63.4 LG6LG6
AACCAT100-4/H not in merged mapLG4LG4
AACCAT202-4/B5@11.8 LG5LG5
AACCAT218-4/B1@63.7 LG1LG1
AACCAT315-Q/Hnot in merged mapnot mappedLG8
AAGCAG075-4/Hnot in merged mapLG2LG2
AAGCAG097-4/Bnot in merged mapLG4not mapped
AAGCAG134-Q/Bnot in merged mapLG7LG7
AAGCTC186-Q/H3@65.1
&6@ 8.0
LG3   LG6
AAGCTC239-Q/B1@19.8 LG1LG8
ACACAA106-Q/Bnot in merged mapLG5LG5
ACACAA142-4/Hnot in merged mapnot mappedLG3
ACACAA319-4/Hnot in merged mapLG6LG6
ACACTT153-4/Hnot in merged mapLG5LG5
AGCCAA136-Q/H3@21.0 LG3LG3
AGCCTT206-Q/H6@38.9 LG6LG6
AGGCTA108-4/Hnot in merged mapLG1LG1
GAGCTT203-4/Bnot in merged mapnot mappedLG8
GATCTC181-4/Hnot in merged mapLG1LG1
GATCTC386-4/Bnot in merged mapLG6LG6
GGACAA222-4/B2@40.0 LG2LG2
GGACAG259-4/Bnot in merged mapLG3LG3
GGACAG272-4/Hnot in merged mapnot mappednot mapped
GGGCAA229-4/Hnot in merged mapLG5LG5
GGGCAA289-Q/H6@53.3 LG6LG6
GGGCAA477-4/H1@48.5 LG1   LG7
GGGCAT119-Q/H4@59.3 LG4LG4
GGGCAT165-Q/H6@49.0 LG6LG6
GGGCAT282-4/Hnot in merged mapLG2LG2
GGTCTT350-4/Hnot in merged mapLG6LG6
Others not used
GGACAA272-Q/B LG2not scored
(shown as GGACAA272-Q in map)
GAGCAC444-4/H LG1LG1