Fig. 2

Identification and validation of tissue-specific marker genes using in situ hybridization. A UMAP representation of the twelve unsupervised clusters. B Cell identity correspondence between annotated cell types and unsupervised clusters. Y-axis indicated annotation of cell types in grain. X-axis indicated seruat clusters. Color: scaled (overlapped cell proportions). C Bubble plot showing transcript enrichment (average expression and percentage) of representative cell type-specific marker genes in the ten cell types. Spot colors correspond to the same tissues in the bubble plot. Genes highlighted in red were validated by in situ hybridization. D In situ hybridization of selected marker genes (i) TraesCS5B02G531100; (ii) TraesCS2B02G347200; (iii) TraesCS7 A02G183600; (iv) TraesCS7 A02G261100; (v) TraesCS7B02G160000 confirmed localization of tissue type-specific transcripts at dap 12. For each in situ hybridization, top panels show spatial visualization and bottom panels with the antisense probes. Scale bar = 100 μm. Aleurone layer (AL), sub-aleurone (Sub-AL), cavity fluid (CF)