Using Natural Allelic Diversity to Evaluate Gene Function

  • Sherry R. Whitt
  • Edward S. BucklerIV
Part of the Methods in Molecular Biology™ book series (MIMB, volume 236)


Genomics has developed a wide range of tools to identify genes that play roles in specific pathways. However, relating individual genes and alleles to agronomic traits is still quite challenging. We describe how association analysis can be used to relate natural variation at candidate genes with agronomic phenotypes. Association approaches in plants can provide very high resolution and can evaluate a wide range of alleles rapidly. We discuss issues related to experimental design, germplasm sample, molecular assay, population structure, and statistical analysis necessary for association analysis in plants.

Key Words

association analysis candidate gene linkage disequilibrium LD maize phenotypic variation population structure mapping QTL quantitative trait loci selection diverse germplasm 


  1. 1.
    Thornsberry, J. M., Goodman, M. M., Doebley, J., Kresovich, S., Nielsen, D., and Buckler, E. S., IV. (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28, 286–289.PubMedCrossRefGoogle Scholar
  2. 2.
    Remington, D. L., Thornsberry, J. M., Matsuoka, Y., et al. (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc. Natl. Acad. Sci. USA 98, 11479–11484.PubMedCrossRefGoogle Scholar
  3. 3.
    Nordborg, M., Borevitz, J. O., Bergelson, J., et al. (2002) The extent of linkage disequilibrium in Arabidopsis thaliana. Nat. Genet. 30, 190–193.PubMedCrossRefGoogle Scholar
  4. 4.
    Sharbel, T. F., Haubold, B., and Mitchell-Olds, T. (2000) Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe. Mol. Ecol. 9, 2109–2118.PubMedCrossRefGoogle Scholar
  5. 5.
    Pritchard, J. K. and Rosenberg, N. A. (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am. J. Hum. Genet. 65, 220–228.PubMedCrossRefGoogle Scholar
  6. 6.
    Reich, D. E. and Goldstein, D. B. (2001) Detecting association in a case-control study while correcting for population stratification. Genet. Epidemiol. 20, 4–16.PubMedCrossRefGoogle Scholar
  7. 7.
    Pritchard, J. K., Stephens, M., and Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945–959.PubMedGoogle Scholar
  8. 8.
    Pritchard, J. K., Stephens, M., Rosenberg, N. A., and Donnelly, P. (2000) Association mapping in structured populations. Am. J. Hum. Genet. 67, 170–181.PubMedCrossRefGoogle Scholar
  9. 9.
    Hudson, R. R., Kreitman, M., and Aguade, M. (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159.PubMedGoogle Scholar
  10. 10.
    Ewing, B., Hillier, L., Wendl, M. C., and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175–185.PubMedGoogle Scholar
  11. 11.
    Rozas, J. and Rozas, R. (1999) DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174–175.PubMedCrossRefGoogle Scholar
  12. 12.
    Hey, J. and Wakeley, J. (1997) A coalescent estimator of the population recombination rate. Genetics 145, 833–846.PubMedGoogle Scholar
  13. 13.
    Schneider, S., Roessli, D., and Excoffier, L. (2000) Arlequin ver. 2.000: A Software for Population Genetics Data Analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.Google Scholar
  14. 14.
    Rafalski, A. (2002) Applications of single nucleotide polymorphisms in crop genetics and breeding. Curr. Opin. Plant Biol. 5, 94–100.PubMedCrossRefGoogle Scholar
  15. 15.
    Hill, W. G. and Robertson, A. (1968) Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38, 226–231.CrossRefGoogle Scholar
  16. 16.
    Tenaillon, M. I., Sawkins, M. C., Long, A. D., Gaut, R. L., Doebley, J. F., and Gaut, B. S. (2001) Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98, 9161–9166.PubMedCrossRefGoogle Scholar
  17. 17.
    Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595.PubMedGoogle Scholar
  18. 18.
    Churchill, G. A. and Doerge, R. W. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138, 963–971.PubMedGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2003

Authors and Affiliations

  • Sherry R. Whitt
    • 1
  • Edward S. BucklerIV
    • 1
    • 2
  1. 1.USDA-ARSRaleigh
  2. 2.Department of GeneticsNorth Carolina State UniversityRaleigh

Personalised recommendations