Plant Molecular Biology

, Volume 16, Issue 4, pp 647–661

Acid phosphatase-11, a tightly linked molecular marker for root-knot nematode resistance in tomato: from protein to gene, using PCR and degenerate primers containing deoxyinosine


  • Jac M. M. J. G. Aarts
    • Department of Molecular BiologyAgricultural University
  • Jan G. J. Hontelez
    • Department of Molecular BiologyAgricultural University
  • Peter Fischer
    • Zentrum für Molekulare BiologieUniversität Heidelberg
  • Ruud Verkerk
    • Department of Molecular BiologyAgricultural University
  • Albert van Kammen
    • Department of Molecular BiologyAgricultural University
  • Pim Zabel
    • Department of Molecular BiologyAgricultural University

DOI: 10.1007/BF00023429

Cite this article as:
Aarts, J.M.M.J.G., Hontelez, J.G.J., Fischer, P. et al. Plant Mol Biol (1991) 16: 647. doi:10.1007/BF00023429


With a view to cloning the root-knot nematode resistance gene Mi in tomato by chromosome walking, we have developed a molecular probe for the tightly linked acid phosphatase-1 (Aps-1) locus. The acid phosphatase-1 allozyme (APS-11), encoded by the Aps-1 1 allele originating from Lycopersicon peruvianum, was purified to apparent homogeneity from tomato roots and suspension cells. Microsequencing of CNBr and tryptic peptides generated from APS-11 provided a partial amino acid sequence, which accounted for approximately 23% of the protein and revealed two stretches of homology with soybean proteins KSH3 and VSP27, comprising 22 matches within 26 amino acid residues. The partial amino acid sequence information enabled us to isolate a 2.4 kb genomic Aps-1 1 sequence by means of the polymerase chain reaction (PCR), primed by degenerate pools of oligodeoxyribonucleotides, synthesized on the basis of the amino acid sequences. Synthesis of the 2.4 kb PCR product was specific for genomic templates carrying the L. peruvianum Aps-1 1 allele. Crucial to the priming specificity and the synthesis of the 2.4 kb genomic sequence was the use of degenerate primer pools in which the number of different primer species was limited by incorporating deoxyinosine phosphate residues at three and four base ambiguities. In using cDNA as a template, a 490 bp sequence was obtained, indicating a high proportion of intron sequences in the 2.4 kb genomic Aps-1 1 sequence. The Aps-1 1 origin of the PCR product was confirmed by RFLP (restriction fragment length polymorphism) analysis, using both a chromosome 6 substitution line and a pair of nearly isogenic lines, differing for a small chromosomal region around the Aps-1/Mi loci.

Key words

acid phosphatase deoxyinosine-containing primers polymerase chain reaction restriction fragment length polymorphism analysis root-knot nematode resistance tomato

Copyright information

© Kluwer Academic Publishers 1991