Crop plants must integrate signals from the environment and prioritize responses to stresses that may occur individually or simultaneously throughout the growing season. Stress responses can adversely affect plant growth and quality traits such as protein and starch. The ability to optimize protein productivity of plant-based foods has far-ranging impact on world health and sustainability. Plant diseases each year cause major losses to crop production. The Arabidopsis thaliana QQS (Qua Quine Starch) orphan gene modulates carbon allocation to protein and starch(1). Ectopic QQS expression increases protein content (2) in leaf and seed in soybean, in corn and rice (3,4). QQS transcript levels are altered in plants under stresses and in mutants of genes involved in all sorts of stress responses, indicating that QQS may integrate primary metabolism with environmental perturbations, thus adjusting the plant’s adaption to abiotic and biotic stresses (5). The QQS protein binds to a transcriptional regulator in Arabidopsis and its homologs in crops: Nuclear Factor Y subunit C4 (NF-YC4). NF-YC4 overexpression mimics QQS-overexpression phenotype (4). Mutants overexpressing QQS or NF-YC4 have significantly increased resistance to plant pathogens and pests (6,7). We are developing a non-transgenic strategy to create high-protein crops and enhance broad-spectrum disease resistance (6). Transcriptomics analyses enable new discovery to advance basic research and application in crops.