Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development

Area of Science:

• Plant Biology
• Molecular Biology
• Genomics

Background:

• Wheat is crucial for global food security.
• Understanding molecular mechanisms of wheat spike and spikelet development is key to improving crop yields.

Purpose of the Study:

• To create a comprehensive atlas of cell clusters and gene expression domains during early wheat spike development.
• To identify and characterize genes involved in regulating wheat spike and spikelet development.

Main Methods:

• Integration of single-molecule fluorescence in situ hybridization (smFISH) and single-cell RNA sequencing (scRNA-seq).
• Spatiotemporal expression analysis of 99 genes across 48,225 cells at key developmental stages (W1.5, W2.5, W3.5).
• scRNA-seq profiling of 26,009 cells, imputation of gene expression, and co-expression analyses.

Main Results:

• Identification of 21 distinct expression domains and 23 cell clusters during wheat spike development.
• Characterization of spatiotemporal gene expression patterns, including LFY, SPL14, and FZP, with revealed functional roles.
• Generation of a public website for visualizing imputed gene expression in spatially anchored cells.

Conclusions:

• smFISH and scRNA-seq offer powerful complementary approaches for dissecting gene networks in wheat spike development.
• The study provides a valuable resource for identifying novel co-expressed genes for future functional studies and crop improvement.