Genome-wide mapping with biallelic markers in Arabidopsis thaliana (original) (raw)

• Letter
• Published: October 1999
• Michael Mindrinos2,3 na1,
• Daniel R. Richards1,
• Ronald J. Sapolsky4,
• Mary Anderson5,
• Eliana Drenkard3,
• Julia Dewdney3,
• T. Lynne Reuber3,
• Melanie Stammers6,
• Nancy Federspiel7,
• Athanasios Theologis8,
• Wei-Hsien Yang2,
• Earl Hubbell9,
• Melinda Au7,
• Edward Y. Chung7,
• Deval Lashkari10,
• Bertrand Lemieux11,
• Caroline Dean6,
• Robert J. Lipshutz9,
• Frederick M. Ausubel3,
• Ronald W. Davis1,2 &
• …
• Peter J. Oefner2

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

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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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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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3. Daniel R. Richards
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4. Ronald J. Sapolsky
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5. Mary Anderson
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6. Eliana Drenkard
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7. Julia Dewdney
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8. T. Lynne Reuber
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9. Melanie Stammers
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10. Nancy Federspiel
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11. Athanasios Theologis
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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 toPeter 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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• Received: 12 April 1999
• Accepted: 20 August 1999
• Issue Date: October 1999
• DOI: https://doi.org/10.1038/13833