Transcriptomic and proteomic analyses reveal effects of nitrogen deficiency on photosynthesis and carbon metabolism in wheat

Key message Combined transcriptome–proteome profiling revealed coordinated RNA–protein regulation of key photosynthesis and carbon metabolism genes in wheat shoots and roots responding to nitrogen deficiency. Abstract Excessive nitrogen application poses a significant challenge to sustainable agriculture. Exploring potential genes involved in photosynthesis and carbon metabolism holds promise for enhancing the nitrogen use efficiency in wheat and advancing molecular breeding efforts. However, the coordination between transcriptomic and proteomic responses to nitrogen deficiency, particularly those associated with photosynthesis and carbon metabolism in wheat, remains poorly understood. In this study, we analyzed transcriptomes and proteomes of winter wheat ( Triticum aestivum L.) grown under normal (N1) and nitrogen-deficient (N0) conditions. We found that nitrogen deficiency reduced the fresh weight, nitrogen content of shoots and roots, as well as the net photosynthetic rate in shoots. Under the two conditions, we identified 3,949 differentially expressed genes (DEGs) and 164 differentially expressed proteins (DEPs) in shoots, and 3,911 DEGs and 129 DEPs in roots. Among them, 13 shoot and 26 root genes showed positive RNA-protein correlations (i.e., DEGs and DEPs were both up- or downregulated), while 1 shoot and 4 root genes had negative correlations (i.e., DEGs and DEPs were regulated in opposite directions). Pathway enrichment analysis highlighted key candidate genes, including 3 related to photosynthesis and 16 involved in carbon metabolism across shoots and roots. Furthermore, chromosomal and subcellular localizations of these genes were identified, providing preliminary candidate molecular targets into improving nitrogen use efficiency through molecular breeding.