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Brasilia 1252×B6274 RAPD Linkage Map Marker Information Table

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These maps were published in Characterization of the Meloidogyne javanica resistance locus employing molecular markers and isolation of candidate disease resistance loci in the carrot (Daucus carota L.) genome
by Leonardo Silva Boiteux, Ph.D. Thesis, 2000, University of Wisconsin-Madison
Chapter 6: Molecular Tagging of the Meloidogyne javanica Resistance Locus with Amplified Fragment Length Polymorphism (AFLP) Markers and Sequence Characterization of AFLP Loci in Carrot (Daucus carota)
or
Theor Appl Genet (2000) 100:439–446
L.S. Boiteux, J.G. Belter, P.A. Roberts, P.W. Simon
RAPD linkage map of the genomic region encompassing the root-knot nematode (Meloidogyne javanica) resistance locus in carrot

Population Description

The segregating population employed in the present study was derived from a cross between the M. javanica resistant inbred line ‘Brasilia-1252’ as female parent and the susceptible inbred line ‘B6274’ as male parent. A single F₁ plant was self-pollinated to produce 442 F₂ individuals that were evaluated for a M. javanica reaction under greenhouse conditions at University of California, Riverside, California. Resistance screening was carried out using individual carrot seedlings cultivated in pots containing sterilized sand. Each plant was infected with a suspension of 30,000 eggs, which were pipetted onto soil depressions around the rosette of the plants 30 days after germination. Sixty days after inoculation, taproots were harvested, the root system was carefully washed free of soil and a root gall rating was assigned where: 0 = no galls; 1 = 1–25%; 2 = 26–50%; 3 = 51–75%; 4 = 76–100% of fibrous roots galled. A strong positive correlation was observed between nematode multiplication levels on root tissues and root galling. Plants were considered as resistant in the 0–1 range and as susceptible in the range 2–4. After evaluation, all F₂ taproots were vernalized (4°C for 40 days) and were then planted in a greenhouse at Madison-Wisconsin. All DNA samples were extracted from lyophilized leaves collected from the F₂ plants originated from vernalized roots. In general, the high nematode infection observed in some F₂ roots did not preclude sample collection. Therefore, 412 leaf samples out 442 F₂ plants were collected and used for the construction of the linkage map.

A file listing the members of the population, as best as I can reconstruct it (Leonardo did not leave an original list) is in population.xls

Raw Data

the data used in making this map is (UNKNOWN)

Phenotypic markers

RAPD STS markers from the thesis and the TAG publication

RAPD STS markers listed only in the thesis

RAPD markers from Thesis

AFLP markers

Markers from the AFLP linkage map of the Mj-1 (Meloidogyne javanica resistance) locus in carrot. The map population was composed by 188 F₂ individuals from the cross ‘Brasilia-1252’ (resistant parent) × ‘6274B’ (susceptible parent).
Conversion from code to primer combination (information is from p.247, combined with table 6.1, pages 259-261):

Code	EcoRI primer	MseI primer	# scorable bands	# R vs. S bulks	‘Brasilia-1252’	‘6274B’	Fragment size (bp)
P3	ACT	CAG	30	1	1	-	300
P4	ACT	CAA	68	2	1	1	180//250
P5	AAG	CTC	29	2	-	2	60/50
P6	AAG	CTA	45	1	-	1	125
P7	ACA	CTT	49	1	1	-	500
P8	AAC	CAA	40	-	-	-	-

• P7B9Z was converted to SCAR: fragment 2a
• P5B6Z
• P4B5Z was converted to SCAR: fragment 22b
• P6B6U
• P3B3Z
• P8B8U
• P4B2U
• P8B3Z
• P6B11U
• P5B11U

Sequence Information

Table 6.2, pages 262-270. List of 15 nucleotide sequences of AFLP fragments found in putative linkage to the Mj-1 resistance locus in carrot. Bold letters represent the AFLP adapter sequences.

Note: The above does not seem to be true, not sure what bold letters represent, the AFLP adapter sequences, with first selective nucleotides in italics, are:

ctcgtagactgcgtaccaattca     gttactcaggactcat
   catctgacgcatggttaagt     caatgagtcctgagtagcag

1. AFLP fragment 1c primer combination [E-AAC/M-CAG]
   

   TGNATNCCTTTACTATAGGGCGAATNGGGCCCGACGTCGCATGCTCCCGGCCGCCATGGCCGCGGGATTGATGAGTCCTGAGTAACAGAAACAATCAACTCCCTGGAAAACCATACTCCATTTCCATATATCAACCCAAAACATCAACAATCTGAATCAAGGAGCTAGCTCATAACAAAAGAGGCCTATCAAACTAAGAGAAATCAATACAATAAGATCATTCTAGTTGAATTGGTACGCAGTCAATCACTAGTGCGGCCGCCTGCAGGTCGACCATATGGGAGAGCTCCCAACGCGTTGGATGCATAGCTTGAGTATTCTATAGTGTCACCTAAATAGCTTGGCGTAATCT

   Primers that were made (shown above as underline):
   aflp.aaccag1C.for Esther 12/1/1998 CTC CCT GGA AAA CCA TAC TCC
   aflp.aaccag1C.rev Esther 12/1/1998 CGC CAA GCT ATT TAG GTC ACA C (not a perfect match)
   These would make a 248 b.p. product

   ---

2. AFLP fragment 2a primer combination [E-ACA/M-CTT]
   This is derived from marker P7B9Z
   

   GAATTCGCCCTTGATGAGTCCTGAGTAACTTTGCATACCAGGCTTGTGGTGCCTGACGAAGTCCATACAAGGCCTTTATTAGCTTGTACACTAGATGCTCCTTTCTTTGTTCGACAAATCCTTCTGGTTGCGTTACGTATTCATCTTCTTGACGATCACCATTCAAGCAAGCTGATTTCACATCAAGGTGATGAACCTCCCAGCTATATTTTGCTTCTAAAGCCAATAATAGTCTCACTGTTTCGATCCGTGTAACTGGTGCATCAAACTTTACTACACCCAATGATAATAAAAACATCTTATCGGTCGATAGTCTGGAACATGTCCAGTAAGGACAATCCTTTACAATAGTAGTTGGAGTCCATTTCTCAAGTGCATTCTTAGATAACATGTTATGAGGAACAATTAGGTCAATCCAAGAATCGGAACGAGACTCATAAACACTGGCAGAACTCAAATCAGCCGACATAACTACAACCTTGTAATTATCATTTGCAGCATCATAACCGAATCCCATACTATAACAAAAATTATAGTCACGACTTGGTGGAAGTGTGAATTGGTACGCAGTCAAGGGCGAATTC

   Primers that were made (shown above as underline):
   AFLP2a upper 5/11/2000 TAA CTT TGC ATA CCA GGC TTG TG
   AFLP2a lower 5/11/2000 GTA TGG GAT TCG GTT ATG ATG CT
   These would make a 494 b.p. product

   ---

3. AFLP fragment 2c primer combination [E-AAC/M-CAG]
   

   GTNTTATTCTNANTTTGAATTCCCTTTNGAATANGCCNAATTGGGNTNCGACGTCGCATGCNCCCGGCCGCCATGGCCGCGGATTGACTGNGTACCAATTCAACAGTNTACTTCTCAGGAGAATNTCGTAGAGATATATATGAGAGAGAGAGAGTNTGANATGGGGTGGGGGTTAGGTGTGGAGCCNNACCTTATATCTAAACAATATNAAAGGGAATTAACCGGAACTAAACGGTGGGCCANAGGTGGTACNGTTTCTTATTCATTNTATATAATCCAGAATAATCTGGATATTGTACCTTNTGANTNTCTGTATCTNANGACTCATTAATCACTATTGCNGNCGNCTGCATGTCAANCATATGGGANAGCTCCCAANNCGTTNGATGCATAGCTTNGAGTATNCNTATANNAN

   ---

4. AFLP fragment 5a primer combination [E-ACA/M-CTC]
   

   GAATTCGCCCTTGACTGCGTACCAATTCACACTATAATTTAGATTCAACTTATAATAATTACCATGTCTAACGTAACAGTGTCAGCTGCGCTTCCTCCTCTCAGCAGCACACCAGGTACATTTTCCATAACTCAGGTTTACCTTACTTTCTGATCCTTTTAGTTTATCTCTAACTAATCTGATTTACATTTCTCTCACAGGGTCAGGGTCTTCCACACCTCACAATTTTGGTAATGTAGCACTAATCTATTTTTTTTTTCCTGTTTTGCTAAATCGTTACGTATCTTTCTTTATATATATTATTCCAGAACTTATCTGTTACTTTGTGATCGTGTATAACTAGAGTTACTCAGGACTCATCAAGGGCGAATTC

   Primers that were made (shown above as underline):
   AFLP5a upper 5/11/2000 TGT CAG CTG CGC TTC CTC CTC
   AFLP5a lower 5/11/2000 TCT AGT TAT ACA CGA TCA CAA AGT
   These would make a 265 b.p. product

   ---

5. AFLP fragment 5b primer combination [E-ACA/M-CTC]
   

   GAATTCGCCCTTGACTGCGTACCAATTCACAATTAGTTGATAGTTGAACAATAAGTAAGAATGAATAAATGAATCTATCCAAACTCATATGATAATATATCTCAGAGATTTTGTTAACAAACCCGTATGACATATTTATACATTGTCATACTGGTTACTTCATCTTCCCCATTCATCACATACACACATACACGCAACTTTTCCGATCGGTTTTCAAGTTTCaTCCATAAAACTTGTTGGTTACTCGATTACAAGCACGATTTTGCTTGCTGGTTACTAATTTATCGATTTCTAAGCCGTTACTCTGCCTGATTTTGCACCGATTTCACCGAGTTTGACTGAGTTACTCAGGACTCATCAAGGGCGAATTC

   ---

6. AFLP fragment 5c primer combination [E-ACA/M-CTC]
   

   GAATTCGCCCTTGACTGCGTACCAATTCACACTATAATTTAGATTCAACTCATAATAATTACCATGTCTAACGTAACAGTGTCAGCTGCGCTTCCTCCTCTCAGCAGCACACCTGGTACATTTTCCATAACTCAGGTTTACCTTACTTTCTGATCCTTTTAGTTTATCTCTAACTAATCTGATTTACATTTCTCTCACAGGGTCAGGGTTTTCCACACCTCACAATTTTGGTAATGTAGCACTAATCTATTTTTTTTTTTCCTGTTTTGCTAAATCGTTACGTATCTTTCTTTATATATATTATTCCAGAACTTATCTGTTACTTTGTGATCGTGTATAACTAGAGTTACTCAGGACTCATCAAGGGCGAATTC

   ---

7. AFLP fragment 6a primer combination [E-AAC/M-CAT]
   

   GAATTCGCCCTTGACTGCGTACCAATTCAACAGTACCGACACCAACGTAGCCTATAGAGGCTGCTGCTGCAACCGCTGCATCACCCATTGCTTTACGCAACTCGGCAGTTAAGGCCAATGTGCAGCCAGCACAAGCTTACAGAAGTGGTTATAATGAAAGTGGTGGATTTTTGGTGAAGAAAATTGGTGGGAGTGTCAACAGCATCGGCAAGTTTACTCAGTTGTGGAAGAGTTTTACAACTCAGAAGACTAGAATAAAAATCAAACGTGGGACTGTCTCCTCTGTTCTTACATCTGATGTTACTCAGGACTCATCAAGGGCGAATTC

   ---

8. AFLP fragment 6b primer combination [E-AAC/M-CAT]
   

   GAATTCGCCCTTGACTGCGTACCAATTCAACTAAAAGATCTTGATAGGCATTGGAAGATAAACATAAACAACATCCCGGAGTGAGTTTACAATTGGATAGGCCCAGCAGAGTGCTTTCACCGTTTGTATTTTTTTCGATCTCCAGTTGCACCTAATTATTTAGTGAAATTCAGACACAACACAATCATACAGTACAAAATTGTTAGAAGGAAAAAAAAGTGAACTGATACAAATACTAATATGCATGTAAATAAGTCAAGAAAGAACAAGAATGAAAGAAATGATCAGCAGAAAAATGTTACTCAGGACTCATCAAGGGCGAATTC

   ---

9. AFLP fragment 12a primer combination [E-AGG/M-CTT]
   

   GAATTCGCCCTTGATGAGTCCTGAGTAACTTCATTTTTCTCTTACATCTTATGAAAAATATAATAAAAATTAGGATGAATTATTTGTATTTCAAAGATTTTTTGAACAATAATGTGACATGGATTCTAGGTTGAATAAACCTGAATTGGTACGCAGTCAAGGGCGAATTC

   Primers that were made (shown above as underline):
   AFLP12a upper 5/11/2000 TAA CTT CAT TTT TCT CTT AC
   AFLP12a lower 5/11/2000 AAT TCA GGT TTA TTC AAC
   These would make a 122 b.p. product

   ---

10. AFLP fragment 13a primer combination [E-AGG/M-CTT]
    

    GAATTCGCCCTTGACTGCGTACCAATTCAGGGCTGCCACGAACTTCCTGATAGGATTCATGAAGTCTCGTTATTCAAACCAACAGGTAACAAGAATTATCAAATTAACACGTCCTAAAGCTGGAAACGGCACCCCACAAGTTACTCAGGACTCATCAAGGGCGAATTC

    ---

11. AFLP fragment 18a [E-ACT/M-CTG]
    

    GAATTCGCCCTTGATGAGTCCTGAGTAACTGGACAAATAGTGTTTATGGTTAGCTGATTTCATATCATTTTTTCTGTCTAAAAAATTAGGTTAGATATGTGGTTCTTGTTTCCATTCAAACATCCGTGATATGTGTCATTATGGCCAATAACTGCTAAATAACTGATTGCAACAGAGTATTCTCTTTTCTTGAGTTATTTCTTTGTCTTGTAGTGAATTGGTACGCAGTCAAGGGCGAATTC

    ---

12. AFLP fragment 18b primer combination [E-ACT/M-CTG]
    

    GAATTCGCCCTTGACTGCGTACCAATTCACTATATGTTGGACCAACTCGACTGAGCAGCTAATATTCTGTAGGTGCTAACAAGATATGCAATACCATCACCATAAAAAGAGCAATGTTTGGAATATTGATAAAGCAAAGCATATGCATATGATTCTTACAAGGCAGATAGTGCACTGTTCGTCATAGTTCTGATCTCCCGAACAGTAAGCTTTTTCAGTTACTCAGGACTCATCAAGGGCGAATTC

    ---

13. AFLP fragment 18c primer combination [E-ACT/M-CTG]
    

    GAATTCGCCCTTGATGAGTCCTGAGTAACTGGATTCCTGAGTAACGGATGAGTCCTGAGTAACTGAATATATGCCTGATTCCCCAAACCGCCAGTATAACTTGTCAACTTGCTCTGGTGTAGATAAAGGAATAGCCAGAATCCCCTCCTGATCCCTTTCATTGAAAACATCATGAACTACTTCCATATCCCACTCCATCTTGTTCATGCACATTAGTGAATTGGTACGCAGTCAAGGGCGAATTC

    ---

14. AFLP fragment 22a primer combination [E-ACT/M-CAA]
    

    GAATTCGCCCTTGATGAGTCCTGAGTAACAAATCATCAAATATCTAACACAAATAGCTAAGCTTCACATATATACACTAATATAAATGGATTCAGCCTAGAGAGAATCTAAGTAACTCCACGAACACTGGTATATCATGACTAAATTCTAACTAGATTCTAACCACATACCAATTACTGATACAAGTCACAAGTCTAGAAACAAATAAGTCATGCTTCAGATTTTATACCTATAAAAGTGAATTGGTACGCAGTCAAGGGCGAATTC

    ---

15. AFLP fragment 22b primer combination [E-ACT/M-CAA]
    This is derived from marker P4B5Z
    

    GAATTCGCCCTTGATGAGTCCTGAGTAACAAGAGAAAGAGCGGTGACCAACGAATAAAGAATCGAATACATATCAAATAATGCAACTGCTGCCAACTGTACTCACGGTCACTACTCACCTTTTGGATATTTATCCCCAAATCGGGTTTTTGAATTTTCAAAACCCTAACTATCTCCCCGCTCTCTCCTCTCTCTCCTCTGTCTCTCTCCCTCTCTCTCCCACACACAAACACTAGTGAATTGGTACGCAGTCAAGGGCGAATTC

    Primers that were made (shown above as underline) Note that despite name of AFLP22a, they match the AFLP22b sequence:
    AFLP22a upper 5/11/2000 AGA GCG GTG ACC AAC GAA
    AFLP22a lower 5/11/2000 GAA TTC ACT AGT GTT TGT GTG TG (not a perfect match)
    These would make a 206 b.p. product

    ---