Fig. 1: Transcriptional analyses across maize mutants with defects in leaf angle and tassel branching.

a Panel of maize mutants used in this study depicts tassel branching phenotypes compared to B73 controls. Heatmap color scale indicates the severity of tassel branch number (TBN), tassel branch angle (TBA), and leaf angle (LA) phenotype deviations from B73. b Enrichment of GO terms associated with DE gene sets during shifts from stage (stg)1 to stg2 tassels and from shoot apex 1 to shoot apex 2. c A two-dimensional section of first and second PCs from the B73 tassel developmental gradient (n = 20). The blue line represents the b-spline fit with three degrees of freedom modeled within the dataset and classifies samples relative to developmental progression coded as expression time (ET). Colored squares represent the 20 tassel samples in ET. The dot plot below represents stg1 and 2 tassel primordia from mutants with data points color-coded relative to B73 ET. Stages of meristem development along normal tassel developmental time are indicated: inflorescence meristem (IM), branch meristem (BM), spikelet pair meristem (SPM), and spikelet meristem (SM). d Venn diagram shows genes DE in tassels during the shift from stg1 to 2 and DE in bri1-RNAi and bin2-RNAi mutants compared to B73 controls. Those with stronger deviations at stg1 are in parentheses. The ternary plot below shows the relative expression of genes commonly mis-expressed between the two mutants compared to B73 (stg1). Each dot represents a gene, and its coordinates indicate relative expression among genotypes. Some classical maize genes are noted. e The top heatmap shows GO terms enriched among DE genes commonly expressed (higher or lower) in BR mutants compared to B73 in stg1 tassels (from the ternary plot in d); the bottom heatmap shows overrepresented TF classes among genes expressed higher in both BR mutants at stg1 and those expressed higher in bin2 only compared to B73. f Relative gene expression trends for ZHD and SBP family members expressed higher in bin2 and/or bri1 mutants compared to B73 at stg1. Arrows indicate the direction of expression change between stg1 and 2 tassels. Source data are provided as a Source Data file.