Co-Regulatory Networks Underlying Protein and Starch Biosynthesis and Digestibility in Developing Sorghum Grain

  • SorghumBase Team
  • 13 April 2026

Integrated transcriptomic–biochemical network analysis of developing sorghum grain identified interconnected regulatory modules for protein and starch biosynthesis, highlighting SbPBF1a, SbPBF1b, and SbNF-YC13 as candidate central transcriptional regulators and revealing structural genes potentially underlying low protein digestibility.

Keywords: Gene Co-expression Network, Grain Quality, Protein, Protein Digestibility, Protoplast Transient over-expressions, Sorghum, Starch, Transcription Factor

By integrating transcriptomic network analysis with biochemical measurements during grain development, we identified key regulatory hubs coordinating starch and protein accumulation in sorghum endosperm. We also uncovered a specific module associated with protein digestibility loss, enriched in genes involved in disulfide bond formation and modulation. Using protoplast transient transformation assays, transcription factors such as SbPBF1a, SbPBF1b, and SbNF-YC13 were validated as central regulators of starch and protein accumulations. Together, these findings provide new mechanistic insights into the coordination of carbon and nitrogen allocation during grain filling and highlight promising targets for improving sorghum grain nutritional quality through molecular breeding and genetic engineering. – Terrier

Improving sorghum grain nutritional quality requires disentangling the genetic networks that coordinate protein and starch accumulation and influence protein digestibility. Researchers from Université de Montpellier and collaborating institutions constructed a gene co-expression network from transcriptomic data across developing sorghum grains and integrated it with biochemical measurements of protein and starch accumulation rates and digestibility loss. This approach identified modules strongly associated with both protein and starch biosynthesis, capturing 87% of known α-kafirin genes and 41% of starch biosynthetic genes, along with multiple transcription factors (TFs) whose orthologs regulate grain filling in other cereals. The strong positive correlations between protein and starch accumulation rates, and the co-enrichment of their structural genes within shared modules, highlight the tight interconnection of these pathways in the endosperm. Comparative analysis with previous network studies revealed substantial overlap but also unique regulators in our integrative framework, underscoring the added value of combining transcriptomic and biochemical data to resolve coordinated biosynthetic processes.

Functional assays using transient overexpression in sorghum protoplasts provided initial validation of six candidate TFs. Among them, SbPBF1a, SbPBF1b, and SbNF-YC13 emerged as central regulators, inducing broad transcriptional changes in genes related to storage protein and starch biosynthesis. SbPBF1a and SbPBF1b uniquely activated kafirin genes and shared conserved targets with maize PBF1, including key starch biosynthetic enzymes, supporting dual regulatory roles in carbon and nitrogen partitioning. SbNF-YC13 showed high network connectivity and extensive effects on both protein and starch genes, consistent with roles reported for NF-YC orthologs in cereal endosperm development. In parallel, network analysis identified candidate genes linked to low protein digestibility, including those involved in disulfide bond formation, sulfur amino acid metabolism, and starch–protein interactions, notably SbGBSSIIa. These findings define candidate regulatory hubs and structural determinants for improving sorghum grain composition and digestibility through targeted functional validation and breeding.

SorghumBase Examples: 

Authors have suggested a central role for SbPBF1a, SbPBF1b and SbNF-YC13 transcription factors in modulating the expression of genes involved in protein and starch biosynthesis. 

We selected the SbPBF1b (SORBI_3008G001700) to explore SorghumBase

Figure 1: The location tab of the SorghumBase search interface of SbPBF1b (SORBI_3008G001700)(Sb08g000330, Sobic.008G001700, SbDOF25, similar to Dof zinc finger protein PBF) shows that this gene is located on chromosome 8:152342-157820.
Figure 2: The sequence tab of the SorghumBase search interface of SbPBF1b (SORBI_3008G001700)(Sb08g000330, Sobic.008G001700, SbDOF25, similar to Dof zinc finger protein PBF) provides the genomic, transcript and peptide sequence. 
Figure 3: The homology tab of the SorghumBase search interface of SbPBF1b (SORBI_3008G001700)(Sb08g000330, Sobic.008G001700, SbDOF25, similar to Dof zinc finger protein PBF) displays the evolutionary relationships of SbPBF1b gene with sorghum paralogs and orthologs from other grasses (Oryza sativa, Andropogoneae, Poaceae) and more distant lineages (rosids, Magnoliophyta). Clade sizes and numbers of paralogs are indicated. The alignment overview (right) depicts conserved protein domains identified by InterPro, color-coded by domain family. Blue blocks indicate strongly conserved domains present across grasses, while gray regions mark less conserved or lineage-specific sequences. There are a total 66 orthologs and 11 paralogs of this gene. Zm00001eb094330 is the closest annotated homolog in maize by 69% identity. 
Figure 4: The All Studies tab of the Expression Tab of the SorghumBase search interface of SbPBF1b (SORBI_3008G001700)(Sb08g000330, Sobic.008G001700, SbDOF25, similar to Dof zinc finger protein PBF) displays the transcription profiling of this gene across 9 studies in different tissue types. This tab provides detailed insights into the gene’s expression notably in the different parts of the seeds. The datasets are curated and processed by EMBL-EBI expression atlas in collaboration with the SorghumBase team.
Figure 5: The Paralog view of the Expression Tab of the SorghumBase search interface of SbPBF1b (SORBI_3008G001700)(Sb08g000330, Sobic.008G001700, SbDOF25, similar to Dof zinc finger protein PBF) displays the transcription profiling of the paralogs of this gene in the selected baseline study “RNA-seq of various Sorghum bicolor (BTx623) tissues: flowers, vegetative and floral meristems, embryos, roots and shoots”. Similar to the SbPBF1b gene, another paralog SORBI_3005G001500 shows the expression only in plant embryos whereas the other paralogs of this gene show the expression profiles in various other tissues.  
Figure 6: eFP expression view under the Expression tab of the SorghumBase search interface allows user to select the expression of SbPBF1b (SORBI_3008G001700)(Sb08g000330, Sobic.008G001700, SbDOF25, similar to Dof zinc finger protein PBF) under different conditions or studies. Here the gene expression visualization is studied under “Atlas W BS cells” and it clearly shows the strong expression of this gene in the seed.
Reference:

Séne M, Calatayud C, Berger A, Soriano A, Richaud F, De Bellis F, Sotillo A, Rios M, Bonicel J, Mameri H, Pot D, Terrier N. Integrative transcriptomic and functional analyses reveal candidate transcription factors associated with sorghum grain quality. J Exp Bot. 2026 Jan 15:erag015. PMID: 41539970. doi: 10.1093/jxb/erag015. Read more

Related Project Websites: 

Sampling of sorghum grains (Macia variety) from 7 to 40 days after anthesis (Field trials in 2017 and 2018). Photo credit : David Pot / Nancy Terrier
All the plants were followed individually, their anthesis date were noted (pink label). For each experiment / sampling date / replicate, 3 plants with the same anthesis date were harvested and their grains were pooled. Photo credit : David Pot / Nancy Terrier
Mamadou Séne, David Pot