image: Field of modern maize with upright architecture allows for dense planting and enhanced yield potential.
Credit: Donald Danforth Plant Science Center
ST. LOUIS, MO, March 5, 2025 — A research team led by Andrea Eveland, PhD, associate member at the Donald Danforth Plant Science Center, has uncovered key genetic regulatory factors that control pleiotropy—a phenomenon where a single gene influences multiple traits. Their study, “Regulatory variation controlling architectural pleiotropy” recently published in the journal, Nature Communications, sheds new light on how genes governing leaf angle and tassel branching in maize can be modulated to optimize crop productivity.
Pleiotropy poses a challenge for crop improvement because selecting for one beneficial trait can negatively impact another. In addition to Eveland’s research team, scientists from the University of Illinois Urbana-Champaign, the University of California, Berkeley, and North Carolina State University demonstrated that common gene networks that function early in maize organ development contribute to pleiotropy in leaf angle and tassel branching. By integrating developmental biology, statistical genetics, and graph theory, they identified regulatory variation in these networks that could potentially decouple these traits, offering a new approach to fine-tuning crop architecture.
When a plant organ develops, a boundary layer of cells forms between the differentiating organ and the pool of stem cells it came from. This process is true regardless of organ type, so you can imagine that common sets of genes are deployed to function in organ boundaries during both leaf organogenesis and tassel branching, contributing to pleiotropy. Eveland and her team leveraged this genetic system to examine differences in how such genes are modulated in specific developmental contexts.
“There are certain maize genes that when perturbed, dramatically affect both leaf and tassel morphology,” said Eveland. “By teasing apart how these genes are specifically regulated in early developmental programs that pattern different plant organs, we can gain flexibility in crop improvement and optimize key traits independently.”
Advancing Precision Breeding for Higher Yields
Over the past century, hybrid-based breeding has improved maize yields by selecting for compact plants with upright leaves and fewer tassel branches, enabling higher planting densities and greater light penetration. Future yield gains, however, will require more precise engineering of genomes and regulatory pathways. Eveland’s research targets gene regulatory events that occur early in plant development—critical stages that determine final plant architecture and productivity.
Another major outcome of the study showed that biological data derived from specific developmental contexts tailored to the trait(s) of interest could inform relevant subsets of genetic markers for use in genome-wide association studies (GWAS) and genomic prediction models. GWAS are statistical analyses that link genetic markers in the genome to certain phenotypic traits, i.e., genotype to phenotype. Using many markers ensures that the genomic space is covered but is computationally intensive and tends to favor marker associations at genetic loci with large effects at the expense of those with small effect sizes, which are typically more agronomically relevant. Using this biologically informed marker reduction approach, new genes were identified at the nexus between regulation of leaf angle and tassel branching.
A related study leveraged the same biologically informed network graphs to demonstrate increased prediction accuracy for these traits in genomic prediction models. This related work led by Edoardo Bertolini, PhD., research scientist at the Danforth Center and Alexander E. Lipka, PhD., associate professor, University of Illinois, Urbana-Champaign, was published on December 4, 2024 in the journal Genetics, “Genomic prediction of cereal crop architectural traits using models informed by gene regulatory circuitries in maize”. This approach, especially when combined with high-throughput, high-resolution field phenotyping, is potentially game-changing for breeders.
“One of the most exciting findings from this study was evidence that similar classes of transcription factors can accurately predict leaf angle in both maize and sorghum,” said Lipka.
From Research to Real-World Impact
Eveland’s work was supported by a National Science Foundation (NSF) award (IOS-1733606), which has contributed to 24 scientific publications to date. The Nature Communications study marks a key milestone in the collaborative research between developmental geneticists, computational biologists, and statisticians.
“This was the culmination of years of interdisciplinary work,” said Eveland. “By integrating diverse expertise, we’ve gained invaluable insights into gene networks that regulate important agronomic traits. The ultimate goal is to translate these findings into improved breeding strategies that enhance food security.”
The NSF grant also funded the Genotype-to-Phenotype Authentic Research Experience (ARE), offered through the Danforth Center’s Education Research and Outreach Lab. The ARE program provides high school and community college students across the St. Louis region (and beyond) from urban to rural schools with hands-on experience in core areas of plant science, equipping them with skills essential to a workforce that can fuel modern agriculture.
About the Donald Danforth Plant Science Center
Founded in 1998, the Donald Danforth Plant Science Center is a nonprofit research institute with a mission to improve the human condition through plant science. The Center’s research, education, and outreach efforts focus on food security and environmental sustainability, positioning the St. Louis region as a global leader in plant science. The Center is supported by funding from organizations such as the National Science Foundation, National Institutes of Health, U.S. Department of Energy, U.S. Department of Agriculture, The Gates Foundation and generous individual and corporate donors. For more information, visit danforthcenter.org.
Media Contact:
Karla Roeber, Vice President of Public and Government Affairs, kroeber@danforthcenter.org
Journal
Nature Communications