Integrative transcriptomic and functional analyses reveal candidate transcription factors associated with sorghum grain quality

Sorghum grains are rich in protein and starch but exhibit low protein digestibility, limiting their value for food and feed. However, the molecular mechanisms underlying these traits remain largely unknown, particularly the roles of structural genes and transcription factors (TFs), hindering efforts to improve grain quality. To address this, we constructed a gene co-expression network using transcriptome data from grain development in two different field seasons. In parallel, we quantified starch and protein content and measured protein digestibility. Two major gene co-expression modules were identified. The first was linked to the loss of protein digestibility, involving genes related to disulfide bond formation and modulation. The second contained most kafirin and starch metabolism genes, as well as orthologs of TFs known to regulate protein and starch accumulation in other species. Functional assays in protoplasts for six TFs suggest a central role for SbPBF1a, SbPBF1b, and SbNF-YC13 in modulating the expression of genes involved in protein and starch biosynthesis. This study provides new insights into the transcriptional regulation of protein and starch accumulation in sorghum. It identifies candidate regulatory and structural genes that offer promising targets for future validation and for improving grain quality in breeding programs.