When a germinating seed is laid on its side, some roots promptly bend earthward, while others turn more slowly. Directed growth of plant roots toward gravity is critical to ensure the availability of water and nutrients. Understanding these directional mechanisms could improve agriculture and ensure food security with changes in global climate.
A new study used machine vision to measure the changes in the direction of growth in response to gravity (gravitropism) in thousands of corn seedling roots and mapped the genomic regions in corn that influence the process. Comparing earlier results from similar experiments conducted on the distantly related Arabidopsis plant with their data from corn, led the investigators to zero in on four genes that control root gravitropism.
The collaborative study led by scientists from the University of Wisconsin, the University of Illinois, Purdue University, Donald Danforth Plant Science Center and Max Planck Institute for Biology, that clarifies how gravity directs the growth of roots was published in the journal Proceedings of the National Academy of Sciences on September 26, 2022 “Leveraging orthology within maize and Arabidopsis QTL to identify genes affecting natural variation in gravitropism.”
An interesting phenotype
“Gravitropism is a fascinating response to a change in a plant’s external circumstances. Many responses plants mount to a change in their environment occur over days or weeks, but gravitropism is observable over minutes to hours. It has captured the attention of biologists for a long time,” said senior author of the study, Edgar Spalding, PhD, professor of botany at the University of Wisconsin. “This investigation was designed to be a step toward identifying genes that register the direction of the gravity vector and adjust growth to follow it.”
Mathew Hudson, PhD, a professor of crop sciences at the University of Illinois and a co-author of the paper said that the study grew out of discussions at conferences among researchers from the different collaborating organizations about using evolutionary orthology [divergence from a common ancestral gene] to extend the phenotype to genotype. Hudson added, “The researchers at Wisconsin pioneered the use of machine vision to investigate the growth of Arabidopsis, and then extended this to corn.”
Besides satisfying a plant biologist’s basic curiosity about how plants orient themselves with respect to gravity, the findings of the study would also be of interest to plant breeders and biotechnologists.
“The significance of this work lies partly in the design of the experiment and partly in the results,” said Spalding “Knowing the details of gravitropism may help the process of modifying crop species to produce steeper roots, which may help them access deeper water reserves. Above ground, shoots with steeper branch angles may tolerate denser planting in fields.”
Exactly how the genes identified in the study affect gravitropism is not clear yet, but the study opens doors for these investigations.
Hudson said, the study not only identifies genes that could improve water and fertilizer utilization in maize crops, but also describes a broadly applicable method that could improve climate-challenged phenotypes. He added, “NASA is interested in growing crops on other planets or in space and they need to know what you’d have to breed for to do that. Plants are pretty discombobulated without gravity.”
New methods
To identify the genes regulating gravitropism, the researchers first used an approach that coarsely maps broad areas of the genome that control gravitropism. They conducted these coarse mapping studies in two distantly related species—corn and Arabidopsis thaliana. They then compared these broad maps to obtain a finer, gene-level mapping for gravitropism.
“Only a handful of genes were in the Arabidopsis and the maize gene sets. The haystack was efficiently swept away and we were left to puzzle over just a few remaining needles. Ultimately, we obtained evidence that four of the needles, or causal genes, truly modified gravitropism,” said Spalding.
The researchers measured gravitropism in the two plant species in a common and highly controlled environment. “These seeds were grown on a petri plate, and the assay lasted just hours, as opposed to traits you might measure in the real world that are open to all sorts of variabilities,” Spalding added.
Hudson said, machine vision phenotyping of root gravity responses and quantitative trait analysis via gene orthology are new methods used in this study.
Spalding said, the search for genes involved in gravitropism is amenable to the new approach because that trait was key to the original specialization of shoots and roots after plants successfully colonized land. Not all traits however, make good candidates for this method. Only traits fundamental to plant function mediated by ancient genes present in unrelated species, can be investigated using this approach.
Next steps
In future studies the investigators intend to use the new gene mapping approach that compares distantly related species to identify other phenotype-genotype relations. In addition, they would like to further probe into mechanisms the four new genes use to accomplish gravitropism.
The research was funded by the National Science Foundation.
