Genetic Module Swapping between Cells Leads to Evolution of Crops, Finds Study

A team of researchers from New York University has conducted a study shedding light on the evolutionary variances among three vital cereal crops: corn, sorghum, and millet. By examining individual cells in these crops, scientists have come closer to identifying the genes responsible for crucial agricultural traits, particularly drought tolerance. Such knowledge will assist scientists in adapting crops to drier climates, a pressing concern in the face of global climate change.

Corn, sorghum, and millet are staple food sources for both humans and animals worldwide. While corn and sorghum diverged from a common ancestor around 12 million years ago, millet is more distantly related. Despite their shared ancestry, these crops exhibit significant differences in key characteristics. For instance, sorghum displays greater tolerance to drought compared to corn, and the plants release distinct sticky substances from their roots, influencing their interactions with the surrounding soil. These dissimilarities may be traced back to a whole genome duplication that occurred in corn after its split from sorghum.

The study's first author, Bruno Guillotin, a postdoctoral associate in NYU's Department of Biology, emphasized the importance of comparing gene expression patterns at the cellular level among these crops due to their significance, evolutionary proximity, and functional disparities. The researchers performed single-cell mRNA profiling of the roots of corn, sorghum, and millet, meticulously examining gene expression in individual cells to identify specialized cells across all three crops.

Roots play a crucial role in defending against drought and heat, functioning as a complex machine with various components, represented by different cell types. Understanding how this "machine" collects water and copes with adverse conditions is of paramount importance. Professor Kenneth Birnbaum, the senior author of the study and a professor in NYU's Department of Biology and Center for Genomics and Systems Biology, highlighted the significance of comparing different species to discern the genes responsible for essential agricultural traits.

Through their investigation into how cells have evolved and diverged across the three species, the researchers identified a notable trend known as "tinkering." This refers to the rearrangement of existing elements within cells over time. One observation was the swapping of gene expression modules, consisting of groups of genes with coordinated functions, between different cell types during evolution. While this gene module swapping has been observed in animal systems, this study provides the first comprehensive illustration of this phenomenon in plants.

The researchers specifically found evidence of gene module swapping in relation to root slime—a nutrient-rich, viscous substance released by roots into the soil. The slime aids in lubricating the soil, allowing roots to navigate through it, while also attracting beneficial bacteria that protect plants or provide vital nutrients that are otherwise difficult to obtain. The study revealed that the genes responsible for producing root slime were located in different parts of the corn, sorghum, and millet roots. Sorghum, for instance, contained slime genes in the outer tissue of its roots, whereas corn exhibited a swapping of these genes into a new cell type in the root cap. This evolutionary change may enable corn to attract bacteria that facilitate nitrogen absorption. The researchers also identified other gene regulators that had been switched among different cell types in each crop, presenting promising candidates for further testing of genes associated with specific traits.

Furthermore, the study highlighted the impact of the whole genome duplication event that occurred in corn 12 million years ago after its divergence from sorghum. This duplication affected specific cell types within corn, allowing them to specialize rapidly. The researchers also observed that certain types of cells acted as donors of new genes, while others seemed to accumulate duplicated genes. This suggests that gene duplication expedited the evolution of particular cells.

The study was made possible by recent advancements in single-cell sequencing techniques, which enabled the analysis of tens of thousands of cells in routine experiments.