Insights into nitrogen metabolism in the wild and cultivated lettuce as revealed by transcriptome and weighted gene co-expression network analysis

Authors: Kumar, Pawan; Eriksen, Renee; Simko, Ivan; SHI, AINONG - University Of Arkansas; Mou, Beiquan

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/31/2022
Publication Date: 6/14/2022
Citation: Kumar, P., Eriksen, R.L., Simko, I., Shi, A., Mou, B. 2022. Insights into nitrogen metabolism in the wild and cultivated lettuce as revealed by transcriptome and weighted gene co-expression network analysis. Scientific Reports. 12. Article 9852. https://doi.org/10.1038/s41598-022-13954-z.
DOI: https://doi.org/10.1038/s41598-022-13954-z

Interpretive Summary: Lettuce, Lactuca sativa L., cultivation is resource intensive; it is reliant on high amounts of nitrogen fertilizer application for its productivity and quality. Large amounts of nitrogen fertilizers applied during production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed gene expression analysis of the cultivated and wild lettuce under control and nitrogen stress conditions. Our results show that the wild lettuce has better NUE and identified several genes with altered expression in response to nitrogen starvation. Many of these genes are involved in nitrogen uptake, nitrogen transportation, and assimilation. We propose that targeting wild genes for introgression into the elite germplasm can significantly improve NUE of the cultivated lettuce.

Technical Abstract: Lettuce, Lactuca sativa L., is a shallow rooted crop, and therefore requires frequent irrigation which often leads to leaching of nitrate into groundwater. Improving nitrogen use efficiency (NUE) of the cultivated lettuce germplasm can potentially lessen environmental pollution and also reduce the cost of lettuce production. Over 300 million clean reads were generated for comparative transcriptomic analysis of the cultivated lettuce (Lactuca sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. We identified a total of 2,704 differentially expressing genes (DEG) of which 1,999 were identified in the cultivated lettuce and 1,235 DEG in the wild lettuce. The DEG included genes that control important physiological processes such as photosynthesis, carbon assimilation, cell wall formation, and nitrogen uptake and assimilation. The transcription factors (TFs) belonging to ethylene responsive factor (ERF) family and basic helix-loop-helix (bHLH) family were top differentially expressing TFs. The weighted gene co-expression network analysis (WGCNA) identified 8 co-expression modules of which two were significantly associated with total nitrogen content and photosynthetic efficiency of photosystem II (PSII). We identified three highly correlated clusters which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific transcription factors TFs. The expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species and thereby provides the opportunity of introgression of wild alleles into the cultivated germplasm for developing high NUE lettuce cultivars.