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Self-Custom-Made SFP Arrays for Nonmodel Organisms

  • Ron OphirEmail author
  • Amir Sherman
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 815)

Abstract

Successful genetic mapping is dependent upon a high-density set of markers. Therefore, tools for high-throughput discovery of genetic variation are essential. The most abundant genetic marker is the single-nucleotide polymorphism (SNP). However, except for model organisms, genomic information is still limited. Although high-throughput genomic sequencing technologies are becoming relatively inexpensive, only low-throughput genetic markers are accessible (e.g., simple sequence repeats). The use of sequencing for the discovery and screening of high-density genetic variation in whole populations is still expensive. Alternatively, hybridization of genomic DNA (gDNA) on a reference (either genome or transcriptome) is an efficient approach for genetic screening without knowing the alleles in advance (Borevitz et al. Proc Natl Acad Sci USA 104:12057–12062). We describe a protocol for the design of probes for a high-throughput genetic-marker discovery microarray, termed single feature polymorphism (SFP) array. Starting with consensus cDNA sequences (UniGenes), we use OligoWiz to design T m-optimized 50-bp long oligonucleotide probes (Ophir et al. BMC Genomics 11:269, 2010). This design is similar to expression arrays and we point out the differences.

Key words

Single-feature polymorphism Microarray Probe design Crop 

References

  1. 1.
    Borevitz, J. O., Hazen, S. P., Michael, T. P., Morris, G. P., Baxter, I. R., Hu, T. T., Chen, H., Werner, J. D., Nordborg, M., Salt, D. E., Kay, S. A., Chory, J., Weigel, D., Jones, J. D., and Ecker, J. R. (2007) Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana, Proc Natl Acad Sci USA 104, 12057–12062.PubMedCrossRefGoogle Scholar
  2. 2.
    Nordborg, M., Hu, T. T., Ishino, Y., Jhaveri, J., Toomajian, C., Zheng, H., Bakker, E., Calabrese, P., Gladstone, J., and Goyal, R. (2005) The pattern of polymorphism in Arabidopsis thaliana, PLoS Biology 3, e196.PubMedCrossRefGoogle Scholar
  3. 3.
    Aranzana, M. J., Kim, S., Zhao, K., Bakker, E., Horton, M., Jakob, K., Lister, C., Molitor, J., Shindo, C., Tang, C., Toomajian, C., Traw, B., Zheng, H., Bergelson, J., Dean, C., Marjoram, P., and Nordborg, M. (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes, PLoS Genet 1, e60.PubMedCrossRefGoogle Scholar
  4. 4.
    Singer, T., Fan, Y., Chang, H. S., Zhu, T., Hazen, S. P., and Briggs, S. P. (2006) A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization, PLoS Genet 2, e144.PubMedCrossRefGoogle Scholar
  5. 5.
    Zhu, T., and Salmeron, J. (2007) High-definition genome profiling for genetic marker discovery, Trends Plant Sci 12, 196–202.PubMedCrossRefGoogle Scholar
  6. 6.
    Borevitz, J. O., Liang, D., Plouffe, D., Chang, H. S., Zhu, T., Weigel, D., Berry, C. C., Winzeler, E., and Chory, J. (2003) Large-scale identification of single-feature polymorphisms in complex genomes, Genome Res 13, 513–523.PubMedCrossRefGoogle Scholar
  7. 7.
    Lai, C. Q., Leips, J., Zou, W., Roberts, J. F., Wollenberg, K. R., Parnell, L. D., Zeng, Z. B., Ordovas, J. M., and Mackay, T. F. (2007) Speed-mapping quantitative trait loci using microarrays, Nat Methods 4, 839–841.PubMedCrossRefGoogle Scholar
  8. 8.
    Edwards, J. D., Janda, J., Sweeney, M. T., Gaikwad, A. B., Liu, B., Leung, H., and Galbraith, D. W. (2008) Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice, Plant Methods 4, 13.PubMedCrossRefGoogle Scholar
  9. 9.
    Kaczorowski, K. A., Ki-Seung Kim, K. S., Diers, B. W., and Hudson, M. E. (2008) Microarray-Based Genetic Mapping Using Soybean Near-Isogenic Lines and Generation of SNP Markers in the Rag1 Aphid-Resistance Interval, THE PLANT GENOME 1, 89–98.CrossRefGoogle Scholar
  10. 10.
    Cossins, A. R., and Crawford, D. L. (2005) Fish as models for environmental genomics, Nat Rev Genet 6, 324–333.PubMedCrossRefGoogle Scholar
  11. 11.
    Sotiriou, C., and Piccart, M. J. (2007) Taking gene-expression profiling to the clinic: when will molecular signatures become relevant to patient care?, Nat Rev Cancer 7, 545–553.PubMedCrossRefGoogle Scholar
  12. 12.
    Buckley, P. G., Mantripragada, K. K., Piotrowski, A., Diaz de Stוhl, T., and Dumanski, J. P. (2005) Copy-number polymorphisms: mining the tip of an iceberg, Trends in Genetics 21, 315–317.Google Scholar
  13. 13.
    Guo, Y., Tan, L. J., Lei, S. F., Yang, T. L., Chen, X. D., Zhang, F., Chen, Y., Pan, F., Yan, H., Liu, X., Tian, Q., Zhang, Z. X., Zhou, Q., Qiu, C., Dong, S. S., Xu, X. H., Guo, Y. F., Zhu, X. Z., Liu, S. L., Wang, X. L., Li, X., Luo, Y., Zhang, L. S., Li, M., Wang, J. T., Wen, T., Drees, B., Hamilton, J., Papasian, C. J., Recker, R. R., Song, X. P., Cheng, J., and Deng, H. W. (2010) Genome-wide association study identifies ALDH7A1 as a novel susceptibility gene for osteoporosis, PLoS Genet 6, e1000806.PubMedCrossRefGoogle Scholar
  14. 14.
    Royce, T. E., Rozowsky, J. S., Bertone, P., Samanta, M., Stolc, V., Weissman, S., Snyder, M., and Gerstein, M. (2005) Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping, Trends Genet 21, 466–475.PubMedCrossRefGoogle Scholar
  15. 15.
    Wu, J., Smith, L. T., Plass, C., and Huang, T. H. (2006) ChIP-chip comes of age for genome-wide functional analysis, Cancer Res 66, 6899–6902.PubMedCrossRefGoogle Scholar
  16. 16.
    Rouillard, J. M., Zuker, M., and Gulari, E. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, Nucleic Acids Res 31, 3057–3062.PubMedCrossRefGoogle Scholar
  17. 17.
    Royce, T. E., Rozowsky, J. S., and Gerstein, M. B. (2007) Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification, Nucleic Acids Res 35, e99.PubMedCrossRefGoogle Scholar
  18. 18.
    Wernersson, R., Juncker, A. S., and Nielsen, H. B. (2007) Probe selection for DNA microarrays using OligoWiz, Nat Protoc 2, 2677–2691.PubMedCrossRefGoogle Scholar
  19. 19.
    Wernersson, R., and Nielsen, H. B. (2005) OligoWiz 2.0 – integrating sequence feature annotation into the design of microarray probes, Nucleic Acids Res 33, W611–615.PubMedCrossRefGoogle Scholar
  20. 20.
    Mueckstein, U., Leparc, G. G., Posekany, A., Hofacker, I., and Kreil, D. P. Hybridization thermodynamics of NimbleGen microarrays, BMC Bioinformatics 11, 35.Google Scholar
  21. 21.
    Kane, M. D., Jatkoe, T. A., Stumpf, C. R., Lu, J., Thomas, J. D., and Madore, S. J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50 mer) microarrays, Nucleic Acids Res 28, 4552–4557.PubMedCrossRefGoogle Scholar
  22. 22.
    He, Z., Wu, L., Li, X., Fields, M. W., and Zhou, J. (2005) Empirical establishment of oligonucleotide probe design criteria, Appl Environ Microbiol 71, 3753–3760.PubMedCrossRefGoogle Scholar
  23. 23.
    Hughes, T. R., Mao, M., Jones, A. R., Burchard, J., Marton, M. J., Shannon, K. W., Lefkowitz, S. M., Ziman, M., Schelter, J. M., Meyer, M. R., Kobayashi, S., Davis, C., Dai, H., He, Y. D., Stephaniants, S. B., Cavet, G., Walker, W. L., West, A., Coffey, E., Shoemaker, D. D., Stoughton, R., Blanchard, A. P., Friend, S. H., and Linsley, P. S. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer, Nat Biotechnol 19, 342–347.PubMedCrossRefGoogle Scholar
  24. 24.
    Ophir, R., Eshed, R., Harel-Beja, R., Tzuri, G., Portnoy, V., Burger, Y., Uliel, S., Katzir, N., and Sherman, A. (2010) High-throughput marker discovery in melon using a self-designed oligo microarray., BMC Genomics 11, 269.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Institute of Plant Sciences, Agricultural Research Organization, Volcani Research CenterBet DaganIsrael

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