Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.)

A.M. Finkers-Tomczak, E.H. Bakker, J.M. de Boer, E.A.G. van der Vossen, U. Achenbach, T.M. Golas, S. Suryaningrat, G. Smant, J. Bakker, A. Goverse

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.
Original languageEnglish
Pages (from-to)595-608
JournalTheoretical and Applied Genetics
Volume122
Issue number3
DOIs
Publication statusPublished - 2011

Fingerprint

cyst nematodes
Solanum tuberosum
Haplotypes
Sequence Analysis
Cysts
haplotypes
sequence analysis
potatoes
loci
physical chromosome mapping
Diploidy
diploidy
genes
Genotype
extensin
Genes
vpr Genes
amino acid transporters
Viverridae
Amino Acid Transport Systems

Keywords

  • gene conferring resistance
  • quantitatively-inherited resistance
  • plant-parasitic nematodes
  • broad-spectrum resistance
  • late blight resistance
  • high-resolution map
  • globodera-rostochiensis
  • disease resistance
  • transposable elements
  • soybean roots

Cite this

Finkers-Tomczak, A.M. ; Bakker, E.H. ; de Boer, J.M. ; van der Vossen, E.A.G. ; Achenbach, U. ; Golas, T.M. ; Suryaningrat, S. ; Smant, G. ; Bakker, J. ; Goverse, A. / Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.). In: Theoretical and Applied Genetics. 2011 ; Vol. 122, No. 3. pp. 595-608.
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abstract = "The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.",
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author = "A.M. Finkers-Tomczak and E.H. Bakker and {de Boer}, J.M. and {van der Vossen}, E.A.G. and U. Achenbach and T.M. Golas and S. Suryaningrat and G. Smant and J. Bakker and A. Goverse",
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Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.). / Finkers-Tomczak, A.M.; Bakker, E.H.; de Boer, J.M.; van der Vossen, E.A.G.; Achenbach, U.; Golas, T.M.; Suryaningrat, S.; Smant, G.; Bakker, J.; Goverse, A.

In: Theoretical and Applied Genetics, Vol. 122, No. 3, 2011, p. 595-608.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.)

AU - Finkers-Tomczak, A.M.

AU - Bakker, E.H.

AU - de Boer, J.M.

AU - van der Vossen, E.A.G.

AU - Achenbach, U.

AU - Golas, T.M.

AU - Suryaningrat, S.

AU - Smant, G.

AU - Bakker, J.

AU - Goverse, A.

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AB - The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.

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KW - quantitatively-inherited resistance

KW - plant-parasitic nematodes

KW - broad-spectrum resistance

KW - late blight resistance

KW - high-resolution map

KW - globodera-rostochiensis

KW - disease resistance

KW - transposable elements

KW - soybean roots

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DO - 10.1007/s00122-010-1472-9

M3 - Article

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SN - 0040-5752

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