QQS-Responsive Soybean Genes Increase Protein and Reduce Starch

Improving protein accumulation without undesirable effects on plant growth remains an important goal in plant physiology and crop improvement. The orphan gene Qua-Quine Starch (QQS) from Arabidopsis thaliana increases protein and reduces starch across several plant species, but the downstream genes associated with these effects remain poorly defined. This study aimed to identify QQS-responsive genes in soybean (Glycine max) and determine whether they can reproduce the characteristic protein and starch phenotypes of QQS when expressed in A. thaliana. Previously published RNA-sequencing datasets from QQS-overexpressing (QQS-OE) Arabidopsis leaves and QQS-expressing (QQS-E) soybean leaves were compared to identify conserved differentially expressed genes. Nine soybean genes showing consistent QQS-responsiveness, including eight upregulated genes and one downregulated gene, were expressed individually in A. thaliana. Total protein was quantified in leaves and seeds, whereas starch was measured in leaves. Candidate promoters were analyzed for transcription factor motif enrichment, and the reporter activation capacity of DNA-tethered QQS was examined in yeast. The eight upregulated soybean genes significantly increased total protein and reduced starch in A. thaliana, whereas the downregulated gene produced the opposite phenotype, decreasing protein and increasing starch. Plant growth and morphology were largely unaffected. Candidate promoters shared motifs associated with nitrogen metabolism, sugar signaling, and plastidial functions. DNA-tethered QQS activated reporter expression in yeast, although this assay does not establish transcriptional activation with these soybean genes. These results identify a conserved QQS-responsive gene module that coordinately influences protein and starch accumulation and provides candidate genes for improving crop protein content.