Zinc oxide nanoparticle exposure triggers different gene expression patterns in maize shoots and roots

•The gene expression patterns of maize exposed to ZnO nanoparticles (nZnO) varied in the shoots and roots.•A majority of the differentially expressed genes induced by nZnO exposure were exclusive to either the shoots or roots.•A similar number of up- and down-regulated genes was observed in the exposed shoots.•More up-regulated than down-regulated genes were found in the exposed roots.•A greater number of GO processes were observed in the nZnO exposed maize roots than in the exposed shoots.•GO terms in the “nitrogen compound metabolic process” category were exclusively and highly expressed in the exposed roots.•GO terms in the “nutrient reservoir” category were exclusively and highly expressed in the exposed roots.•Term “small molecule metabolic process” was also exclusively up-regulated in the exposed roots.•Processes in “cellular metabolic”, “primary metabolic” and “secondary metabolic” were down-regulated in the exposed roots.

The potential impacts of environmentally accumulated zinc oxide nanoparticles (nZnOs) on plant growth have not been well studied. A transcriptome profile analysis of maize exposed to nZnOs showed that the genes in the shoots and roots responded differently. Although the number of differentially expressed genes (DEGs) in the roots was greater than that in the shoots, the number of up- or down-regulated genes in both the shoots and roots was similar. The enrichment of gene ontology (GO) terms was also significantly different in the shoots and roots. The “nitrogen compound metabolism” and “cellular component” terms were specifically and highly up-regulated in the nZnO-exposed roots, whereas the categories “cellular metabolic process”, “primary metabolic process” and “secondary metabolic process” were down-regulated in the exposed roots only. Our results revealed the DEG response patterns in maize shoots and roots after nZnO exposure.