Identification of long non-coding RNAs under nitrogen stress in maize (Zea mays L.)

Abstract

Nitrogen (N) is an essential nutrient for plant growth; however, a substantial proportion of the nitrogen applied to crops such as maize (Zea mays L.) remains unused, contributing to environmental pollution and inefficient resource use. Consequently, improving nitrogen use efficiency is a major objective of sustainable agriculture. Although the genetic and molecular mechanisms underlying nitrogen uptake and assimilation are relatively well characterized, the role of long noncoding RNAs (lncRNAs) in regulating nitrogen responses in maize remains largely unexplored. In this study, we investigated the involvement of lncRNAs in maize responses to low-nitrogen stress. Two inbred maize lines with contrasting nitrogen stress tolerance—DMI 56 (tolerant) and DMI 81 (susceptible)—were grown hydroponically under nitrogen-sufficient and nitrogendeficient conditions. Root and leaf tissues were analyzed for lncRNA expression, revealing a large number of differentially expressed lncRNAs, ranging from 226 to more than 1,025 across six experimental comparisons. The Gene Ontology (GO) classification and enrichment analysis helped to annotate the function of 155 lncRNAs in total. Notably, a greater number of lncRNAs were upregulated than downregulated in response to nitrogen stress, and several lncRNAs exhibited consistent expression patterns in root tissues of both genotypes. These observations suggest that certain lncRNAs may constitute a core regulatory network involved in plant adaptation to nitrogen-limited environments. Overall, this study provides new insights into the molecular responses of maize to nitrogen stress and highlights the potential of lncRNAs as targets for improving nitrogen utilization. Further functional characterization of these lncRNAs may facilitate the development of maize genotypes with enhanced performance under low-nitrogen conditions, contributing to more sustainable and efficient agricultural systems.