A spatial transcriptome map of developing maize ear

Abstract

Abstract A comprehensive understanding of inflorescence development is crucial for crop genetic improvement, as inflorescence meristems give rise to reproductive organs and determine grain yield. However, dissecting inflorescence development at the cellular level has been challenging due to the lack of distinct marker genes to distinguish each cell types, particularly the various types of meristems that are vital for organ formation. In this study, we used spatial enhanced resolution omics-sequencing (Stereo-seq) to construct a precise spatial transcriptome map of developing maize ear primordia, identifying twelve cell types, including the four newly cell types that mainly distributed on inflorescence merisetm. Through integrating single-cell RNA transcriptomes, we identified a series of spatially-specific networks and hub genes, which may provide new insights on understanding the formation of different tissues. Furthermore, by extracting the meristem components for detailed clustering, we identified three subtypes of meristem, and validated two MADS-box genes specifically expressed at the apex of determinate meristems, involved in stem cell determinacy. In summary, this study provides a valuable resource for cereal inflorescence development studies, offering new clues for yield improvement.