Deciphering transcriptional programming during lupin (Lupinus angustifolius) seed development using RNA-seq

Lupin (Lupinus spp.) seeds are valued for their high protein content (35-40%) for both human and animal consumption. Seed development in crop plants is a critical factor influencing both seed fate and yield, hence, understanding the molecular mechanisms of seed development is essential. This study conducted a transcriptome analysis of Narrow Leaf Lupin (NLL) during seed development stages (3, 6, 9, 12, 15, 18, and 21 days after flowering) to investigate transcriptional dynamics and identify key candidate genes that control seed development. Approximately 357 million sequencing reads were generated from nine samples from leave, flower and seed tissues, enabling the identification of 34,769 expressed genes. The analysis revealed dynamic gene expression, with early stages marked by high metabolic activity and later stages focusing on storage protein synthesis and nutrient reservoir formation. The differential expression patterns of seed storage protein genes, including cupin groups (, {beta}, {gamma}, and {delta} conglutins), were notable. The expression of and {beta} conglutins increased at later stages (15-21 days after flowering), supporting their role in grain filling and nutrient storage. Genes related to quinolizidine alkaloid biosynthesis, such as lysine/ornithine decarboxylase and purine permease transporter 1, showed late expression patterns suggesting alkaloid synthesis and transport during later stages. Many of the well-established transcription factors (TFs) known for their roles in seed development (bHLH, AP2, MYB, ERF, C2H2, NAC, WRKY, and C3H zinc finger families) showed differential expression, thus reinforcing the validity of our findings. These findings lay the groundwork for understanding the genetic and molecular mechanisms of seed development in lupin, contributing to enhanced crop management and breeding programs.