Fig. 3. Transcriptome-wide association study (TWAS) for SPP and enrichment analysis of TWAS significant genes.

a Manhattan plot of TWAS for SPP. TWAS Z-scores (y-axis) are plotted against gene positions (x-axis) on each of the chromosomes. The gray dashed lines indicate the Z-scores at the FDR of 0.05, and genes exceeding this threshold are defined as TWAS significant genes in the following analysis. Known genes related to panicle development are labeled and marked as orange dots. b Gene Set Enrichment Analysis for TWAS significant genes of SPP. All genes were sorted in descending order (x-axis) by the TWAS Z-scores. The y-axis of the bottom panel indicates the TWAS Z-scores. Genes from different gene sets are shown in different colors. In the middle panel, a gene belonging to a certain gene set is indicated by a colored vertical line. In the top panel, the enrichment scores³⁶ (y-axis) for each gene set are plotted against the rank of TWAS Z-scores (x-axis). High exp in YP: genes preferentially expressed in young panicles. Decrease exp in YP: genes progressively down-regulated in panicle development. Increase exp in YP: genes progressively up-regulated in panicle development. c–e Transcription factor families (c), TF binding motifs (d), and gene ontology terms (e) enriched in TWAS significant genes for panicle traits (FDR <0.05). NAGs and PAGs: negatively and positively associated genes, respectively. The bubble size indicates the number of overlapping genes and the bubble color indicates the −log₁₀ FDR of the enrichment.