Xu, Xiaosa, Passalacqua, Michael, Rice, Brian, Demesa-Arevalo, Edgar, Kojima, Mikiko, Takebayashi, Yumiko, Yu, Xingyao, Harris, Benjamin, Liu, Yuchen, Gallavotti, Andrea, Sakakibara, Hitoshi, Gillis, Jesse, Jackson, David (August 2025) Large-scale single-cell profiling of stem cells identifies redundant regulators of shoot development and yield trait variation. Developmental Cell. S1534-5807(25)00500. ISSN 1534-5807
Abstract
Plant shoot stem cells generate organs essential for food, feed, and biofuels. However, plant single-cell analyses struggled to capture these rare cells or to detect stem cell regulators like CLAVATA3 and WUSCHEL. Here, we dissected stem cell-enriched shoot tissues from maize and Arabidopsis for single-cell RNA sequencing (scRNA-seq), and we optimized protocols to recover thousands of CLAVATA3- and WUSCHEL-expressing cells. A cross-species comparison identified deeply conserved stem cell regulators. We also profiled maize stem cell mutants, validated candidate regulators with spatial transcriptomics, and confirmed their roles in shoot development. These include a family of RNA-binding protein genes and two families of sugar kinase genes. Finally, we show how coupling large-scale single-cell profiling with allelic variation analysis in diverse maize germplasm serves as a valuable resource for identifying stem cell regulators significantly associated with grain yield components. Our discoveries advance the study of shoot stem cells and open avenues for rational crop engineering.
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