Single-Cell RNA Sequencing of Developing Ears Facilitates Functional Analysis and Trait Candidate Gene Discovery in Maize

Crop productivity depends on activity of meristems that produce optimized plant architectures, including that of the maize ear. A comprehensive understanding of development requires insight into the full diversity of cell types and developmental domains, and the gene networks required to specify them. Until now, these were identified primarily by morphology and insights from classical genetics, and insights are limited by genetic redundancy and pleiotropy. Here, we investigated the transcriptional profiles of 12,525 single cells from developing maize ear inflorescence primordia. The resulting developmental atlas provides the first comprehensive single-cell RNA sequencing (scRNA-seq) map of an inflorescence. We validated our results by mRNA in situ hybridization and by Fluorescence-Activated Cell Sorting (FACS) RNA-seq, and show how these data may facilitate genetic studies by predicting genetic redundancy, integrating transcriptional networks, and identifying candidate genes associated with crop yield traits.