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Genome-wide mapping with biallelic markers in Arabidopsis thaliana

Nature Genetics volume 23, pages 203–207 (1999)Cite this article

Abstract

Single-nucleotide polymorphisms, as well as small insertions and deletions (here referred to collectively as simple nucleotide polymorphisms, or SNPs), comprise the largest set of sequence variants in most organisms1,2. Positional cloning based on SNPs may accelerate the identification of human disease traits and a range of biologically informative mutations3,4,5,6. The recent application of high-density oligonucleotide arrays to allele identification has made it feasible to genotype thousands of biallelic SNPs in a single experiment3,7. It has yet to be established, however, whether SNP detection using oligonucleotide arrays can be used to accelerate the mapping of traits in diploid genomes. The cruciferous weed Arabidopsis thaliana is an attractive model system for the construction and use of biallelic SNP maps. Although important biological processes ranging from fertilization and cell fate determination8,9,10,11 to disease resistance12,13 have been modelled in A. thaliana, identifying mutations in this organism has been impeded by the lack of a high-density genetic map consisting of easily genotyped DNA markers14. We report here the construction of a biallelic genetic map in A. thaliana with a resolution of 3.5 cM and its use in mapping Eds16, a gene involved in the defence response to the fungal pathogen Erysiphe orontii. Mapping of this trait involved the high-throughput generation of meiotic maps of F2 individuals using high-density oligonucleotide probe array-based genotyping. We developed a software package called InterMap and used it to automatically delimit Eds16 to a 7-cM interval on chromosome 1. These results are the first demonstration of biallelic mapping in diploid genomes and establish means for generalizing SNP-based maps to virtually any genetic organism.

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Figure 1: Genetic positions of the 237 SNP markers used to define a biallelic SNP map for A.thaliana.
Figure 2: Calculated probability of random segregation in the A.thaliana genome using 28 F2 plants from the Eds16-1×Landsberg erecta cross that display a susceptibility phenotype to the fungal pathogen pathogen Erysiphe orontii.

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References

  1. Kruglyak, L. The use of a genetic map of biallelic markers in linkage studies. Nature Genet. 17, 21–24 (1997).

    Article  CAS  Google Scholar 

  2. Kwok, P.Y., Deng, Q., Zakeri, H., Taylor, S.L. & Nickerson, D.A. Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics 31, 123–126 (1996).

    Article  CAS  Google Scholar 

  3. Wang, D.G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077–1082 (1998).

    Article  CAS  Google Scholar 

  4. Winzeler, E.A. et al. Direct allelic variation scanning of the yeast genome. Science 281, 1194–1197 ( 1998).

    Article  CAS  Google Scholar 

  5. Hacia, J.G., Brody, L.C., Chee, M.S., Fodor, S.P. & Collins, F.S. Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis. Nature Genet. 14, 441– 447 (1996).

    Article  CAS  Google Scholar 

  6. Buetow, K.H., Edmonson, M.N. & Cassidy, A.B. Reliable identification of large numbers of candidate SNPs from public EST data. Nature Genet. 21, 323–325 (1999).

    Article  CAS  Google Scholar 

  7. Winzeler, E.A. & Davis, R.W. Functional analysis of the yeast genome. Curr. Opin. Genet. Dev. 7, 771– 776 (1997).

    Article  CAS  Google Scholar 

  8. Sawa, S., Ito, T., Shimura, Y. & Okada, K. FILAMENTOUS FLOWER controls the formation and development of Arabidopsis inflorescences and floral meristems. Plant Cell 11, 69– 86 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Preuss, D., Lemieux, B., Yen, G. & Davis, R.W. A conditional sterile mutation eliminates surface components from Arabidopsis pollen and disrupts cell signaling during fertilization. Genes Dev. 7, 974–985 (1993).

    Article  CAS  Google Scholar 

  10. Meyerowitz, E.M. Pattern formation in plant development: four vignettes. Curr. Opin. Genet. Dev. 4, 602–608 ( 1994).

    Article  CAS  Google Scholar 

  11. Lloyd, A.M., Schena, M., Walbot, V. & Davis, R.W. Epidermal cell fate determination in Arabidopsis: patterns defined by a steroid-inducible regulator. Science 266, 436– 439 (1994).

    Article  CAS  Google Scholar 

  12. Mindrinos, M., Katagiri, F., Yu, G.L. & Ausubel, F.M. The A. thaliana disease resistance gene RPS2 encodes a protein containing a nucleotide-binding site and leucine-rich repeats. Cell 78, 1089–1099 (1994).

    Article  CAS  Google Scholar 

  13. Bent, A.F. et al. RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science 265, 1856–1860 (1994).

    Article  CAS  Google Scholar 

  14. Alonso-Blanco, C. et al. Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J. 14, 259 –271 (1998).

    Article  CAS  Google Scholar 

  15. Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D. & Koornneef, M. Arabidopsis thaliana: a model plant for genome analysis. Science 282, 662, 679– 682 (1998).

    Article  Google Scholar 

  16. Hoogendoorn, B. et al. Genotyping single nucleotide polymorphisms by primer extension and high performance liquid chromatography. Hum. Genet. 104, 89–93 (1999).

    Article  CAS  Google Scholar 

  17. O'Donovan, M.C. et al. Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 52, 44–49 (1998).

    Article  CAS  Google Scholar 

  18. Cronin, M.T. et al. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum. Mutat. 7, 244– 255 (1996).

    Article  CAS  Google Scholar 

  19. Liu, Y.G., Mitsukawa, N., Lister, C., Dean, C. & Whittier, R.F. Isolation and mapping of a new set of 129 RFLP markers in Arabidopsis thaliana using recombinant inbred lines. Plant J. 10, 733–736 (1996).

    Article  CAS  Google Scholar 

  20. Lander, E.S. et al. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1, 174–181 ( 1987).

    Article  CAS  Google Scholar 

  21. Konieczny, A. & Ausubel, F.M. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J. 4, 403–410 ( 1993).

    Article  CAS  Google Scholar 

  22. Li, J. & Chory, J. Preparation of DNA from Arabidopsis. Methods Mol. Biol. 82, 55– 60 (1998).

    CAS  PubMed  Google Scholar 

  23. Lockhart, D.J. et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol. 14, 1675– 1680 (1996).

    Article  CAS  Google Scholar 

  24. Chee, M. et al. Accessing genetic information with high-density DNA arrays. Science 274, 610–614 ( 1996).

    Article  CAS  Google Scholar 

  25. Adam, L. & Somerville, S.C. Genetic characterization of five powdery mildew disease resistance loci in Arabidopsis thaliana. Plant J. 9, 341–356 ( 1996).

    Article  CAS  Google Scholar 

  26. Volko, S.M., Boller, T. & Ausubel, F.M. Isolation of new Arabidopsis mutants with enhanced disease susceptibility to Pseudomonas syringae by direct screening. Genetics 149, 537–548 ( 1998).

    CAS  PubMed  PubMed Central  Google Scholar 

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Author notes

  1. Raymond J. Cho and Michael Mindrinos: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, 94305, California, USA

    Raymond J. Cho, Daniel R. Richards & Ronald W. Davis

  2. Biochemistry, Stanford University School of Medicine, , Stanford, 94305, California, USA

    Michael Mindrinos, Wei-Hsien Yang, Ronald W. Davis & Peter J. Oefner

  3. Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA

    Michael Mindrinos, Eliana Drenkard, Julia Dewdney, T. Lynne Reuber & Frederick M. Ausubel

  4. Genencor,, 925 Page Mill Road, Palo Alto, 94304, California, USA

    Ronald J. Sapolsky

  5. Division of Plant Science (University Park), Nottingham Arabidopsis Stock Centre, University of Nottingham, Nottingham , NG7 2RD, UK

    Mary Anderson

  6. Department of Molecular Genetics, John Innes Centre, Colney Lane, NR4 7UH, Norwich, UK

    Melanie Stammers & Caroline Dean

  7. Stanford DNA Sequencing and Technology Center,, Palo Alto, 94304, California, USA

    Nancy Federspiel, Melinda Au & Edward Y. Chung

  8. Plant Gene Expression Center Genome Sequencing Lab, , Albany, 94710, California, USA

    Athanasios Theologis

  9. Affymetrix, Inc.,, Santa Clara, 95051, California, USA

    Earl Hubbell & Robert J. Lipshutz

  10. Incyte Pharmaceuticals,, Fremont, 94555, California, USA

    Deval Lashkari

  11. Department of Biology, York University, North York, Ontario, Canada

    Bertrand Lemieux

Authors
  1. Raymond J. Cho
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  2. Michael Mindrinos
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  12. Wei-Hsien Yang
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  13. Earl Hubbell
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  14. Melinda Au
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  15. Edward Y. Chung
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  16. Deval Lashkari
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  17. Bertrand Lemieux
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  18. Caroline Dean
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  19. Robert J. Lipshutz
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  20. Frederick M. Ausubel
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  21. Ronald W. Davis
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  22. Peter J. Oefner
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Corresponding author

Correspondence to Peter J. Oefner.

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Cho, R., Mindrinos, M., Richards, D. et al. Genome-wide mapping with biallelic markers in Arabidopsis thaliana . Nat Genet 23, 203–207 (1999). https://doi.org/10.1038/13833

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