According to a new study led by New York University, researchers have uncovered evolutionary differences between these important cereal crops after comparing individual cells of corn, sorghum and millet.
The findings, published in Nature, bring scientists closer to determining which genes control important agricultural traits such as drought tolerance, which will help scientists facing a changing climate adapt crops to drier environments.
Maize, sorghum and millet provide food for people and animals around the world. Maize and sorghum are ancient relatives that evolved into two different species about 12 million years ago, and millet is a more distant relative.
Despite their common ancestry, the crops have significant differences in key traits—for example, sorghum is much more drought-tolerant than corn, and the plants release unique gummy substances from their roots that shape how they interact with the surrounding soil. These differences can be traced back to maize, which underwent a whole genome duplication after its separation from sorghum.
“The importance of these crops, their evolutionary proximity, and their functional differences present an exciting opportunity to compare gene expression patterns at the cellular level,” said Bruno Guillotin, a postdoctoral fellow in NYU’s Department of Biology and first author of the study. “Although the three crops are similar, it’s important how they differ from each other because they have traits that we might want to transfer from one to the other, such as drought tolerance.”
The researchers performed single-cell mRNA profiling of maize, sorghum and millet roots, dissecting the roots to look at individual cells and track exactly where genes are expressed in a particular cell. They then compared the same specialized cells across the three crops.
“Roots are the first line of defense against drought and heat. You can think of a root as a machine with many working parts—in this case, cell types—so knowing how the machine works to collect water and deal with drought and heat is really important,” said Kenneth Birnbaum, a professor at New York University. Institute of Biology and Center for Genomics and Systems Biology and lead author of the study. “Comparing different species helps us distinguish which genes lead to key agricultural traits.”
Examining how cells evolved and diverged in different species, the researchers identified several trends that point to the “shuffling” — or rearranging of existing elements — of cells over time. First, they observed that cells frequently exchange modules of gene expression, or groups of 10 or 50 genes with coordinated functions, between cell types during evolution.
“This swapping of gene modules has been shown in animal systems, but the data we have generated is the first time it has been illustrated on a large scale in plants,” Birnbaum added.
This swapping of modules was demonstrated in the discovery of root mucilage – a gooey substance filled with nutrients that roots release into the soil. The slime is useful for lubricating the soil so the roots can pass through and can attract beneficial bacteria that protect the plant or provide hard-to-reach nutrients.
The researchers found that genes that help produce root mucilage were located in different parts of corn, sorghum and millet roots. In sorghum, the mucilage genes were found in the outer tissue of the root, while in corn they were swapped for a new type of cell in the root cap, an evolutionary change that may allow corn to attract bacteria that help the plant obtain nitrogen. They also identified other gene regulators that were swapped out in different cell types depending on the crop, giving researchers prime candidates to test for genes that convey specific traits.
In addition, the researchers found that the duplication of the whole genome in maize, after it split from sorghum 12 million years ago, affected specific cell types, allowing maize cells to specialize rapidly. They also observed that certain types of cells acted as donors of new genes, while others appeared to accumulate new gene duplicates, which may indicate that gene duplication accelerated the evolution of certain cells.
Recent advances in single-cell sequencing techniques have enabled this research and opened up new methods for investigating the link between genes and cell traits in crops.
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