Spatially resolved transcriptomic analysis of the germinating barley grain

Abstract

Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.

Advancing Sustainable Malting Practices: Aquaporins as Potential Breeding Targets for Improved Water Uptake during Controlled Germination of Barley (Hordeum vulgare L.)

“…We found TIP1;1 abundance to be greater in Flinders than in IGB1467. TIP1;1 is known to be a housekeeping APQ involved in the establishment of basal tonoplast hydraulic conductance. , Therefore, TIP1;1 abundance may contribute to the initially increased water uptake seen in Flinders, although we saw a greater increase in the level of TIP1;1 in IGB1467 from 0 to 24 HAI (Figure D) suggesting an additonal role discussed further below. These findings are also supported by our discovery and quantitative proteomics results presented in our previous study, where TIP1;1, TIP3;1, and TIP3;2 are in the raw grain of IGB1467 and Flinders, with greater abundance in Flinders.…”

“…Previous studies have found that the protein storage vacuole-specific TIP1;1, TIP3;1, and TIP3;2 isoforms are coexpressed and colocalized to the same tonoplast in the germinating grain after imbibition . However, TIP3;1 and TIP3;2 are the only embryo- and endosperm-specific TIP isoforms found in Arabidopsis in the late stages of seed maturation and early-stage germination (phases I and II). − During the early-stage of barley germination, Peirats-Llobet et al (2023) found the TIP1;1 isoform was the most abundantly expressed member of the TIP family . We found TIP1;1 abundance to be greater in Flinders than in IGB1467.…”

“…Functional GO annotation of DAPs found that the increased water uptake seen in Flinders may be attributed to the significantly increased abundance of transmembrane proteins, specifically AQPs (Figure ). Based on previous spatial expression studies in barley, members of the AQP gene family are known to allow transmembrane solute passage and are essential in water flux and cell expansion, enabling sufficient pressure for radicle protrusion. , Therefore, we focused our proteomic exploration on the seven quantified AQP proteins, specifically PIPs and TIPs, demonstrating significant differentially abundant protein profiles between IGB1467 and Flinders in the early stages of malting, indicating their possible major role in water uptake during controlled germination (Figures and ).…”

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] .…”

Plant Transcriptomic Responses in a Diverse Organ and Stress Conditions

“…Recently, a spatial transcriptomic profiling of germinating barley (Hordeum vulgare) seeds was exhaustively studied by Peirats-Llobet et al [74]. Such methodology (Visium Gene Expression slides, 10x Genomics) allowed for a complete study of gene expression profiles across individual cell types within the plant seeds.…”