Spatially Resolved Transcriptomic Analysis of the Germinating Barley Grain

Abstract

Seeds, which provide a major source of calories for humans, are a unique stage of a flowering plant's lifecycle. During seed germination the embryo reactivates rapidly and goes through major developmental transitions to become a seedling. This requires extensive and complex spatiotemporal coordination of cell and tissue activity. Existing gene expression profiling methods, such as laser capture microdissection followed by RNA-seq and single-cell RNA-seq, suffer from either low throughput or the loss of spatial information about the cells analysed. Spatial transcriptomics methods couple high throughput analysis of gene expression simultaneously with the ability to record the spatial location of each individual region analysed. We developed a spatial transcriptomics workflow for germinating barley grain to better understand the spatiotemporal control of gene expression within individual seed cell types. More than 14,000 genes were differentially regulated across 0, 1, 3, 6 and 24 hours after imbibition. This approach enabled us to observe that many functional categories displayed specific spatial expression patterns that could be resolved at a sub-tissue level. Individual aquaporin gene family members, important for water and ion transport, had specific spatial expression patterns over time, as well as genes related to cell wall modification, membrane transport and transcription factors. Using spatial autocorrelation algorithms, we were able to identify auxin transport genes that had increasingly focused expression within subdomains of the embryo over germination time, suggestive of a role in establishment of the embryo axis. Together, our data provides an unprecedented spatially resolved cellular map for barley grain germination and specific genes to target for functional genomics to define cellular restricted processes in tissues during germination. The data can be viewed at https://spatial.latrobe.edu.au/.

A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis

“…A deeper investigation of the shared markers of germinating seeds revealed that many of the identified genes with shared expression across cell types encode a diverse range of ribosomal protein subunits. The unified expression of ribosomal proteins across cell types in the germinating seed dataset coincides with global increases in ribosome biogenesis and translation during seed germination in both Arabidopsis 41,42 and Barley grains 43 . While the expression of many ribosomal protein genes is present across several cell types of germinating seeds, this was not observed for all of the other tissues assayed, where subsets of ribosomal proteins were expressed only in specific cell types among all tissue and organs assayed, supporting the hypothesis that the heterogeneous composition of ribosomes is developmentally regulated 44 , and may explain the higher levels of homogeneity within this tissue.…”

PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns

“…This allows for the examination of how a gene's expression level changes temporally along a continuous process [7][8][9][10][11][12][13] . ST, on the other hand, measures both the gene expression and spatial locations of single cells or small clusters of cells, enabling the direct interrogation of spatial gene expression patterns from the observed data [14][15][16][17][18][19] .…”

Temporal-spatial transcriptomics reveals key gene regulation for grain yield and quality in wheat

“…In orchids, the crucial roles of MADS-box genes and other potential downstream genes in organ initiation and morphogenesis have been elucidated through spatial transcriptomics (Liu et al, 2022a). By combine the temporal and spatial expression distribution of genes during maize kernels development constructed a comprehensive gene network regulating in grain filling process (Fu et al, 2023), By adding different germination time to barley germination spatial transcriptomics also help to reveal aquaporin gene families and auxin transport genes roles in zygote embryo activation and embryo polarity establishment processes (Peirats-Llobet et al, 2023). Meanwhile, integrating single-nucleus and spatial transcriptomics could enhance resolution of plant-microbe interactions in nodulating plants (Liu et al, 2023b).…”