Molecular and genetic determinism of sorghum grain quality

Abstract

Sorghum grains are rich in proteins and starch but exhibit low protein digestibility, limiting their use in food and feed. However, the genetic and molecular mechanisms underlying these traits remain poorly understood, particularly the genomic regions involved, as well as the structural genes and transcription factors (TFs) that regulate them, hindering efforts to improve sorghum grain quality. To address this, we adopted an integrated genomic and genetic approach. At the genomic level, we constructed a gene co-expression network using transcriptomic data collected during grain development (10 stages) over two years. 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 cereal species. Functional assays performed in protoplasts for six TFs revealed a central role for SbPBF1a, SbPBF1b, and SbNF-YC13 in modulating the expression of genes involved in protein and starch biosynthesis. In the genetic approach, we used a diversity panel of 300 sorghum genotypes representing global genetic diversity. This panel was cultivated at two sites in France over two growing seasons. Protein, starch contents and protein digestibility were measured. Whole-genome sequencing (WGS) was performed for all genotypes. These biochemical and genotypic data were analysed through genome-wide association studies (GWAS) using both single and multilocus models. Several significant SNPs were identified near genes previously associated with grain quality traits. Together, our work provides novel insights into the genetic basis and transcriptional regulation of protein and starch accumulation, as well as protein digestibility in sorghum grains. It also identifies regulatory and structural genes that could be targeted to enhance grain quality, thereby supporting the development of improved sorghum varieties with higher nutritional value