Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

U. Achenbach, M.J. Caldas Paulo, E. Ilarionova, J. Lübeck, J. Strahwald, E. Tacke, H.R. Hofferbert

Research output: Contribution to journalArticleAcademicpeer-review

22 Citations (Scopus)

Abstract

The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family
Original languageEnglish
Pages (from-to)619-629
Number of pages11
JournalTheoretical and Applied Genetics
Volume118
Issue number3
DOIs
Publication statusPublished - 2009

Fingerprint

Globodera pallida
cyst nematodes
Quantitative Trait Loci
Linkage Disequilibrium
Solanum tuberosum
linkage disequilibrium
single nucleotide polymorphism
Single Nucleotide Polymorphism
Cysts
quantitative trait loci
Chromosomes
potatoes
chromosomes
loci
Breeding
Tetraploidy
Nematoda
tetraploidy
breeding
Solanum vernei

Keywords

  • high-resolution map
  • pathogen resistance
  • solanum-spegazzinii
  • disease resistance
  • dna variation
  • late blight
  • genome
  • rostochiensis
  • tomato
  • segments

Cite this

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title = "Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V",
abstract = "The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family",
keywords = "high-resolution map, pathogen resistance, solanum-spegazzinii, disease resistance, dna variation, late blight, genome, rostochiensis, tomato, segments",
author = "U. Achenbach and {Caldas Paulo}, M.J. and E. Ilarionova and J. L{\"u}beck and J. Strahwald and E. Tacke and H.R. Hofferbert",
year = "2009",
doi = "10.1007/s00122-008-0925-x",
language = "English",
volume = "118",
pages = "619--629",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
publisher = "Springer Verlag",
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}

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V. / Achenbach, U.; Caldas Paulo, M.J.; Ilarionova, E.; Lübeck, J.; Strahwald, J.; Tacke, E.; Hofferbert, H.R.

In: Theoretical and Applied Genetics, Vol. 118, No. 3, 2009, p. 619-629.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V

AU - Achenbach, U.

AU - Caldas Paulo, M.J.

AU - Ilarionova, E.

AU - Lübeck, J.

AU - Strahwald, J.

AU - Tacke, E.

AU - Hofferbert, H.R.

PY - 2009

Y1 - 2009

N2 - The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family

AB - The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family

KW - high-resolution map

KW - pathogen resistance

KW - solanum-spegazzinii

KW - disease resistance

KW - dna variation

KW - late blight

KW - genome

KW - rostochiensis

KW - tomato

KW - segments

U2 - 10.1007/s00122-008-0925-x

DO - 10.1007/s00122-008-0925-x

M3 - Article

VL - 118

SP - 619

EP - 629

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 3

ER -