Genome-wide association analysis of stalk biomass and anatomical traits in maize

Mona Mazaheri, Marlies Heckwolf, Brieanne Vaillancourt, Joseph L. Gage, Brett Burdo, Sven Heckwolf, Kerrie Barry, Anna Lipzen, Camila Bastos Ribeiro, Thomas J.Y. Kono, Heidi F. Kaeppler, Edgar P. Spalding, Candice N. Hirsch, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler

Research output: Contribution to journalArticlepeer-review

37 Scopus citations


Background: Maize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area). Results: Using a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22. Conclusion: Substantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass.

Original languageEnglish (US)
Article number45
JournalBMC plant biology
Issue number1
StatePublished - Jan 31 2019

Bibliographical note

Funding Information:
This research was funded by the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-FC02-07ER64494) which supported all components of the research. Funding from the National Science Foundation (grant IOS-1546727) and the Minnesota Supercomputing Institute (MSI) at the University of Minnesota provided computation resources that contributed to the analysis and interpretation of data.

Publisher Copyright:
© 2019 The Author(s).


  • Genome-wide association
  • Maize
  • Plant height
  • Rind
  • Stalk
  • Stover
  • Vascular bundle
  • Zmm22


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