Developmental modules for SPM determinacy. (A) Expression signatures across wild-type libraries were used to cluster genes with dynamic expression during ear and/or tassel development. Twenty k-means clusters fell into four distinct clades of expression: enriched in SM/FM; tassel; 1- and 2-mm ear; IM/SPM (from top to bottom). Each cluster is assigned a number identifier (left) and the number of genes associated with each cluster is indicated (right). The heatmap represents cluster centers; (white-to-dark) low-to-high expression. Clusters 8 and 11 were highly enriched for DE genes in 1-mm ra mutants (blue arrows). (B) Genes in cluster 11 and (C) DE in all three mutants at 1 mm were either coordinately up- or down-regulated and (D) genes in cluster 8 and (E) DE in all mutants were almost entirely down-regulated. (F) DE genes in cluster 8 tended to be most strongly down-regulated in ra1 mutants consistent with a more severe phenotype. (G) Co-expressed genes in cluster 8 were also co-expressed across ra mutant backgrounds. Expression profiles are shown for examples of known genes implicated in determinacy and a gene of unknown function with grass-specific lineage. (H) Among these, an ortholog of ROXY (GRMZM2G442791) and (I) a CUC-like NAC TF (GRMZM2G393433) were temporally co-expressed in largely adjacent domains. (J) Of 31 cis-regulatory motifs significantly enriched within proximal promoters of genes co-expressed in cluster 8 and DE in 1-mm ra1 mutants, the 20 with the highest enrichment in this group of genes relative to genome-wide occurrences are shown.
