Network Analysis of Nitrogen and Phosphorus Utilization Efficiency Genes in Wheat (Triticum Aestivum L.)

Abstract

Wheat (Triticum aestivum L.) holds the second spot among essential global food crops in terms of cultivation. It has the highest nitrogen requirement among major cereals for growth, yet its Nitrogen Use Efficiency (NUE) remains relatively low at 40-50%. This inefficiency causes nitrogen to escape into the environment, causing pollution and raising the costs of farming. Consequently, improving NUE in crops like wheat becomes immensely important. NUE hinges on two critical factors: nitrogen uptake and nitrogen utilization, with the latter affected by nitrogen assimilation and remobilization. Inadequate access to phosphorus can lead to a decrease in plant yield by about 10–15% compared to what they could achieve at their peak potential. Wheat greatly depends on phosphate (P) because of its vital contribution to the growth, maturity, and sprouting of wheat seeds. Phosphorus Use Efficiency (PUE) defines the connection between the production of biomass and the absorption of phosphorus within the plant. In the domain of phosphorus use efficiency, there are two primary categories: phosphorus uptake efficiency (PUpE) and phosphorus utilization efficiency (PUtE). In the present study, network was constructed for differentially expressed genes for nitrogen and phosphorus stress, respectively through Cytoscape software and their further analysis to retrieve hub genes for both stresses. For nitrogen and phosphorus, network of 1900 genes and 1193 genes, respectively were constructed in Cytoscape. Disconnected nodes were hidden from the network. In nitrogen stress network, it consists of total 208 nodes (genes) connected with 543 edges. In phosphorus stress network, it has 277 nodes connected with 473 edges. MCODE Cluster (plug in application in cytoscape) was performed on network of both nitrogen and phosphorus, separately. Total 8 clusters were opted in case of nitrogen and 11 clusters for phosphorus to find out hub genes with maximum edges connectivity. 29 hub genes and 26 hub genes for nitrogen use efficiency and phosphorus use efficiency respectively were retrieved from their respective clusters. On advanced analysis of hub genes, 15 hub genes were highly associated and function in nitrogen utilization efficiency and for phosphorus only 10 hub genes were associated with phosphorus utilization efficiency in wheat crop. KEGG pathway analysis reveals that 3 KEGG pathways were recognised with which nitrogen utilization efficiency hub genes were associated. In case of phosphorus, a maximum number of hub genes were involved in total 8 KEGG pathways. On expression analysis of hub genes, outcome was 4 hub genes each for nitrogen and phosphorus utilization efficiency have high expression levels in Wheat expression browser.