Transcriptomic and Metabolic Insight into Flavonoid Biosynthesis Underlying Seed Coat Color Variation in Soybean (Glycine max)
Seed coat color in soybean (Glycine max) is determined by the accumulation of flavonoid-derived pigments. However, to date the molecular mechanisms driving natural variation remain poorly defined. This study integrated data from RNA sequencing (RNA-seq) with metabolite profiling via high-performance liquid chromatography (HPLC) to investigate genetic and metabolic differences between black and yellow seed coat soybean lines that share an identical genetic background. Transcriptomic analysis revealed that key anthocyanin biosynthesis genes, including flavanone 3-hydroxylase (F3H-3), anthocyanidin synthase (ANS), UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT), UDP-glycosyltransferase (UGT79B6), and glutathione S-transferase (GSTF11), were more highly expressed in black seed coats, where we also observed increased anthocyanin and proanthocyanidin (PA) accumulation and antioxidant activity. In contrast, leucoanthocyanidin reductase (LAR) was strongly expressed in yellow seed coats but did not correspond to PA levels, likely due to the specific expression of laccase (LAC5) in black seeds, which facilitates PA polymerization. Elevated expression of cytochrome P450 enzymes (i.e., CYP73A5, cinnamate 4-hydroxylase; CYP82C4) in yellow seed coats suggested activation of the isoflavone biosynthesis pathway. Further transcriptional profiling also indicated that black-seed-specific MYB transcription factors (i.e., MYB111, MYB113, and MYB17) promoted anthocyanin production. This study is the first to provide evidence that small heat shock proteins (sHSPs) are implicated in the regulation of seed coat pigmentation and stress adaptation. Together, these findings elucidate the genetic and metabolic regulation of seed coat color in soybean and identify candidate genes relevant to functional breeding and genomics research. Overall design: Identification of differentially expressed genes in black and yellow seed obtained in F9 from the cross of yellow (mother) and black ( father) soybeans