Dwarf8 polymorphisms associate with variation in flowering time

Abstract

Historically, association tests have been used extensively in medical genetics1,2, but have had virtually no application in plant genetics. One obstacle to their application is the structured populations often found in crop plants3, which may lead to nonfunctional, spurious associations4. In this study, statistical methods to account for population structure5 were extended for use with quantitative variation and applied to our evaluation of maize flowering time. Mutagenesis and quantitative trait locus (QTL) studies suggested that the maize gene Dwarf8 might affect the quantitative variation of maize flowering time and plant height6,7,8. The wheat orthologs of this gene contributed to the increased yields seen in the 'Green Revolution' varieties6. We used association approaches to evaluate Dwarf8 sequence polymorphisms from 92 maize inbred lines. Population structure was estimated using a Bayesian analysis4 of 141 simple sequence repeat (SSR) loci. Our results indicate that a suite of polymorphisms associate with differences in flowering time, which include a deletion that may alter a key domain in the coding region. The distribution of nonsynonymous polymorphisms suggests that Dwarf8 has been a target of selection.

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Figure 1: Schematic diagram of Dwarf8 gene structure and plot of linkage disequilibrium.

References

  1. 1

    Lander, E.S. & Schork, N.J. Genetic dissection of complex traits. Science 265, 2037–2048 (1994).

  2. 2

    Templeton, A.R. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/control sampling designs: Alzheimer's disease and the apoprotein E locus. Genetics 140, 403–409 (1995).

  3. 3

    Risch, N. & Merikangas, K. The future of genetic studies of complex human diseases. Science 273, 1516–1517 (1996).

  4. 4

    Pritchard, J.K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).

  5. 5

    Pritchard, J.K., Stephens, M., Rosenberg, N.A. & Donnelly, P. Association mapping in structured populations. Am. J. Hum. Genet. 67, 170–181 (2000).

  6. 6

    Peng, J. et al. 'Green revolution' genes encode mutant gibberellin response modulators. Nature 400, 256–261 (1999).

  7. 7

    Koester, R., Sisco, P. & Stuber, C. Indentification of quantitative trait loci controlling days to flowering and plant height in two near-isogenic lines of maize. Crop Sci. 33, 1209–1216 (1993).

  8. 8

    Schon, C. et al. RFLP mapping in maize – quantitative trait loci affecting testcross performance of elite European flint lines. Crop Sci. 34, 378–389 (1994).

  9. 9

    Wang, R.-L. et al. The limits of selection during maize domestication. Nature 398, 236–239 (1999).

  10. 10

    White, S. & Doebley, J. The molecular evolution of terminal ear1, a regulatory gene in the genus Zea. Genetics 153, 1455–1462 (1999).

  11. 11

    Wessler, S.R., Bureau, T.E. & White, S.E. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5, 814–821 (1995).

  12. 12

    Koch, C.A., Anderson, D., Moran, M.F., Ellis, C. & Pawson, T. SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins. Science 252, 668–674 (1991).

  13. 13

    Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989).

  14. 14

    Kende, H. Hormone response mutants. A plethora of surprises. Plant Physiol. 125, 81–84 (2001).

  15. 15

    Peng, J. et al. The Arabidopsis GAI gene defines a signaling pathway that negatively regulates gibberellin responses. Genes Dev. 11, 3194–3205 (1997).

  16. 16

    Watterson, G. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7, 256–276 (1975).

  17. 17

    Nei, M. Molecular Evolutionary Genetics (Columbia University Press, New York, 1987).

  18. 18

    Rozas, J. & Rozas, R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174–175 (1999).

  19. 19

    Hey, J. & Wakeley, J. A coalescent estimator of the population recombination rate. Genetics 145, 833–846 (1997).

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Acknowledgements

We would like to thank T. Helentjaris for his input on this project, and N. Harberd and Plant Bioscience Ltd. for providing genomic sequence. D. Remington provided the tb1 sequence alignments and contributed helpful discussions. We would like to thank anonymous reviewers for their thoughtful comments regarding this manuscript. All sequencing was performed at the North Carolina State University Genome Research Laboratory. This work was supported by NSF (DBI-9872631) and USDA-ARS.

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Correspondence to Edward S. Buckler IV.

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