Fig. 3

Procyanidin biosynthesis pathway was prominent during seed development. a Seed samples from 16 to 60 DAF (bar = 0.5 mm). b Manhattan plot of TWAS results (FDR < 0.05; [39]) for SOC. Genes with the expression positively or negatively correlated with SOC are plotted above or under the black bold line. Each point represents a single gene tested. The yellow points indicate overlapped genes between the co-expression network hub genes and TWAS-significant genes. c TWAS-significant genes (FDR < 0.05) involved in PAs and lignin biosynthesis pathway are marked in red, and the FDRs are shown in blue circles. d Co-expression network of TT5, BAN, TT19, and TT1. Circles in orange represent acyl-lipid genes, and circles in green represent transcription factor genes. Correlation between the expression (TPM) of BnaC08.TT5 with oil content (e) and seed coat content (h). Box plots for oil content (f) and seed coat content (i) for the two haplotypes (n = 267 versus 91). g Box plots for the expressions for the two haplotypes (n = 135 versus 62). Center line, median; box limits, upper and lower quartiles; whiskers, 1.5 × the interquartile range; dots, outliers (P < 2e − 16, Student’s t test)