UW-Madison inventors have performed extensive multi-omic and gene network analyses to predict key autophagy regulators for autophagy, since upregulated autophagy has been shown to be beneficial for plant resilience and nutrient utilization in some plants grown under controlled conditions. The inventors have performed a multi-omic analysis of autophagy and wild type maize plants grown under either control or stressful conditions to identify expression patterns and gene networks that control nutrient recycling through autophagy and other pathways. Their analyses predict that three maize autophagy genes (ATG1, ATG9, ATG12) that mediate various steps in autophagy and one novel transcription factor regulator (bZIP87) should upregulate autophagy. In addition, based on single cell type multi-omic analyses the inventors found that autophagy in bundle sheath cells around vascular bundles is important for nutrient export from leaves (unpublished results).