Fig. 4: Transcriptome analysis of HX3 and ef1.

a Volcano plot showing differentially expressed genes in HX3 and ef1. Upregulated and downregulated genes in ef1 compared with HX3 are highlighted in red and blue, respectively. Differential expression analysis was performed using DESeq2 with its default Wald test (two-sided). P values were adjusted for multiple comparisons using the Benjamini–Hochberg method to control the false discovery rate (FDR). Genes with FDR < 0.05 were considered significantly differentially expressed. b and c Enriched Gene Ontology terms in the 440 genes upregulated or 372 genes downregulated in ef1, respectively. GO enrichment analysis was conducted using GOATOOLS with default parameters. Fisher’s exact test (two-sided) was used to assess enrichment significance, and P values were adjusted for multiple testing using the Benjamini–Hochberg correction. The outer circle indicates the classification of GO terms, and the middle circle represents gene number of each GO in the soybean genome background, and the inner circle represents the number of differentially expressed genes. P-values are presented in purple. d Heat map of expression profiles of known flowering control genes in HX3 and ef1. Source data are provided as a Source Data file.