Seed function in space and time: how spatial transcriptomics completes the picture

Spatiotemporal gene expression is the underlying determinant of how living things grow and function, including the processes of seed development and germination. Understanding how these regulatory pathways work in space and time is critical to harnessing the functional diversity of the components of the seed and enhancing beneficial traits. The recent development of spatial transcriptomics technologies has greatly added to the knowledge of gene expression within plant and animal tissues but has only been applied in a handful of studies to seeds. Here we conduct a review of the literature on spatial omics research in developing and germinating seeds of wheat, barley, maize, rice, wild soybean and Arabidopsis, highlighting the major contributions to the field and the challenges faced. We outline how spatial transcriptomics has significantly improved the scale and resolution of gene expression analyses, revealing how the transcriptome explains the complete tissue architecture of the seed. This has resulted in the discovery of novel cell-subtypes, spatiotemporal gene expression gradients, and coordinated nutrient transport across tissues, completing the picture of seed composition in greater detail than could previously be achieved.