In a groundbreaking study, Cold Spring Harbor Laboratory (CSHL) plant biologists have mapped two key stem cell regulators across thousands of maize and Arabidopsis shoot cells. Their work, using advanced single-cell RNA sequencing, also uncovered previously unknown stem cell genes, some of which are directly tied to productivity and size variations in corn.

Plant stem cells are vital for growth, reproduction, and productivity in crops. They drive food, feed, and fuel production, yet much about their genetic regulation has remained elusive. This study provides an unprecedented atlas of gene expression in maize stem cells - a resource that could dramatically accelerate crop improvement and breeding programs.

The team focused on CLAVATA3 and WUSCHEL, two known regulators of plant stem cell activity. Led by Professor David Jackson, the research involved dissecting tiny maize and Arabidopsis shoots and using a microfluidics system to isolate individual cells. These cells were then tagged and analyzed to identify the specific genes they expressed.

The results were striking: the researchers recovered over 5,000 CLAVATA3 and 1,000 WUSCHEL-expressing cells, enabling them to trace the broader genetic network that governs stem cell behavior. Importantly, they identified hundreds of genes preferentially expressed in both species, suggesting these regulators are conserved across plant types and could be harnessed across the plant kingdom.

"This gives us the tools to understand and engineer plant diversity," said Jackson. "It's foundational knowledge that could guide research for the next decade - not just for developmental biology but for breeders and agronomists looking to improve crop resilience and yields."

By linking specific genes to size differences in maize, the study offers a direct genetic roadmap for selecting traits like ear size, plant height, or biomass production - all critical for addressing global food security and input efficiency.

This leap in plant genomics also opens doors for precision agriculture applications, allowing for more targeted interventions in crop development and trait selection. The availability of this gene expression atlas will enable other researchers to skip replicating the experiment and instead build upon the CSHL team's data.

As climate pressures and population demands grow, the need for crops that are both productive and resilient becomes more urgent. This research brings scientists closer to engineering plants from the cellular level, with implications that stretch across the entire agricultural value chain.

The use of single-cell sequencing in maize - a notoriously complex genome - sets a new bar for plant molecular biology. It also provides an essential toolkit for the development of next-generation corn hybrids, optimized for yield, climate tolerance, and sustainability goals.