Figure 5.

Genes affected by germination and seed size show a similar expression profile.

(A and B) Gene expression signature values (mean normalized expression) of two main co-expressed gene groups overlaid on the PCA plot. Gene expression correlation among seeds was calculated (scran R package), and gene pairs with correlation >0.5 were used for clustering (RBGL R package). Identified groups were used to calculate signatures (Seurat AddModuleScore). The spread of signature values for each condition is shown as a violin plot.

(C) Plot of group 1 and group 2 gene expression signature values for each seed.

(D) Germination competence signature overlaid on PCA plot. Composite signature values were calculated using the Vision R package on the basis of the expression of cluster 1 and cluster 2 genes.

(E) Seed size signature overlaid on PCA plot. Composite signature values were calculated using the Vision R package on the basis of differentially expressed genes between small and large seeds (mean normalized expression of genes with upregulated and downregulated expression had negative and positive input, respectively). The spread of signature values for each condition is shown as a violin plot.

(F) Size and germination signatures are correlated across the seeds.