Differentially expressed gene profiles of soybean seeds with contrasting seed coat colour

Soybeans are a vital source of plant-based protein and are widely utilised for various agricultural and industrial purposes. One notable characteristic of soybeans is the diversity in their seed coat colour, which ranges from yellow, black, brown and green to bicoloured variants. This study aimed to identify key genes associated with seed quality by analysing transcriptome profiles of differentially expressed genes in seeds, naked seeds and seed coats of black and white soybean genotypes. The analysis revealed that several upregulated genes are involved in hormone signalling pathways and metabolic processes, such as lysine, starch, sucrose, protein and galactose metabolism. These genes also participate in biosynthetic pathways for ethylene, lipids, brassinosteroids, lignin and sulfur-containing amino acids. Such molecular activities are likely linked to the enhanced seed quality observed in black-coated cultivars, which exhibit greater longevity, improved resistance to ageing, moisture and physical stress. Furthermore, the identification of key transcription factors provided deeper insight into the regulatory mechanisms underlying these traits. This research offers a comprehensive understanding of the genomic and metabolic pathways that influence seed quality in soybeans and lays a foundation for future gene-silencing studies to further explore the biological significance of black seed coat characteristics.