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Genome-wide association study of leaf architecture in the maize nested association mapping population

Nature Genetics volume 43, pages 159–162 (2011)Cite this article

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Abstract

US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at the liguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.

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Figure 1: Low genetic overlap between leaf traits.
Figure 2
Figure 3: Associations around lg1 and lg2 explained the two most significant QTLs for upper leaf angle.
Figure 4: Comparison of allele frequency distributions of QTLs, associated SNPs and random SNPs.

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Acknowledgements

We thank L. Rigamer Lirette and S. Myles for editing the manuscript. This work was supported by US National Science Foundation grants (DBI-0820619, 0321467, 0703908 and 0638566) and USDA-ARS.

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Author notes

  1. Feng Tian and Peter J Bradbury: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA

    Feng Tian, Patrick J Brown & Edward S Buckler

  2. US Department of Agriculture–Agricultural Research Service (USDA-ARS), Ithaca, New York, USA

    Peter J Bradbury & Edward S Buckler

  3. Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA

    Patrick J Brown & Torbert R Rocheford

  4. Department of Crop Science, North Carolina State University, Raleigh, North Carolina, USA

    Hsiaoyi Hung & James B Holland

  5. Computational Biology Service Unit, Cornell University, Ithaca, New York, USA

    Qi Sun

  6. USDA-ARS, Columbia, Missouri, USA

    Sherry Flint-Garcia & Michael D McMullen

  7. Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA

    Sherry Flint-Garcia & Michael D McMullen

  8. Department of Agronomy, Purdue University, Urbana, Illinois, USA

    Torbert R Rocheford

  9. USDA-ARS, Raleigh, North Carolina, USA

    James B Holland

  10. Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA

    Edward S Buckler

Authors
  1. Feng Tian
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Contributions

F.T. and P.J. Bradbury contributed equally to this work. M.D.M., J.B.H. and E.S.B. contributed to the study design. S.F.-G., T.R.R., M.D.M., J.B.H. and E.S.B. collected phenotypes. F.T., P.J. Bradbury, P.J. Brown, H.H., Q.S. and E.S.B. carried out analysis. F.T., P.J. Bradbury and E.S.B. wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Edward S Buckler.

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The authors declare no competing financial interests.

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Supplementary Note, Supplementary Figures 1–7 and Supplementary Tables 1–14 (PDF 2033 kb)

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Tian, F., Bradbury, P., Brown, P. et al. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43, 159–162 (2011). https://doi.org/10.1038/ng.746

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