Screening Key Genes Related to Nitrogen Use Efficiency in Cucumber Through Weighted Gene Co-Expression Network Analysis

Cucumber (<i>Cucumis sativus</i> L.) is a crucial vegetable crop, requiring significant nitrogen fertilizer inputs. However, excessive nitrogen application not only impairs growth but also poses severe environmental risks. Thus, enhancing nitrogen use efficiency (NUE) in cucumber is imperative. For the identification of genes associated with NUE in cucumber, roots of high NUE and low NUE lines were analyzed under high nitrogen conditions. Using transcriptome sequencing through WGCNA, a total of 15,180 genes were categorized into 35 co-expression modules, with 5 modules being highly correlated with NUE. Based on differential expression within the five modules and the results of GO and KEGG enrichment analyses, 25 genes were identified as potentially related to NUE. Among these, <i>CsaV4_1G002492</i> (GLR22), <i>CsaV4_2G003460</i> (GLR35), <i>CsaV4_3G000307</i> (NRT1.1), and <i>CsaV4_7G001709</i> (UPS2) were homologous to genes in <i>Arabidopsis</i> known to directly participate in NUE related process. These four genes were chosen as key genes for further analysis. qRT-PCR analysis revealed that <i>CsaV4_3G000307</i> and <i>CsaV4_7G001709</i> were more active during the early stages of the high nitrogen treatment in the high NUE line. Conversely, <i>CsaV4_1G002492</i> and <i>CsaV4_2G003460</i> were more active in the low NUE line. Using transcriptomic analysis, a frameshift INDEL mutation was observed in <i>CsaV4_3G000307</i> in the low NUE line, which impacted the compactness of the protein structure, potentially altering its function. Analysis of protein interactions of these four key genes predicted some potential interaction networks. This research offers critical insights into the genetic factors influencing NUE in cucumber, presenting potential targets for genetic modification or breeding programs.