Increasing nitrogen use efficiency in agronomically important plants: An insight into gene characteristics on a genome-wide scale in barley

Authors: PALUCH-LUBAWA, EWELINA - Adam Mickiewicz University; TANWAR, UMESH KUMAR - Adam Mickiewicz University; STOLARSKA, EWELINA - Adam Mickiewicz University; ARASIMOWICZ-JELONEK, MAGDALENA - Adam Mickiewicz University; Mattoo, Autar; SOBIESZCZUK-NOWICKA, EWA - Adam Mickiewicz University

Submitted to: Computers in Biology and Medicine
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/14/2024
Publication Date: 10/24/2024
Citation: Paluch-Lubawa, E., Tanwar, U., Stolarska, E., Arasimowicz-Jelonek, M., Mattoo, A.K., Sobieszczuk-Nowicka, E. 2024. Increasing nitrogen use efficiency in agronomically important plants: An insight into gene characteristics on a genome-wide scale in barley. Computers in Biology and Medicine. 183. Article e109277. https://doi.org/10.1016/j.compbiomed.2024.109277.
DOI: https://doi.org/10.1016/j.compbiomed.2024.109277

Interpretive Summary: Nitrogen (N) is a critical element for plant growth and development. Hence, improving crop nitrogen use efficiency (NUE) is vital for farmers’ input costs and to the environmental impacts. Understanding the genetic control of N metabolism is crucial to improve NUE. ARS scientists in collaboration with an international team of researchers have deciphered genes involved in NUE responses. The genetics coupled with bioinformatics analysis identified key nitrogen metabolism-related genes along with their possible functional roles. Findings from this study will provide new knowledge on NUE and will help scientists and farmers with new information useful for future breeding and generating genetically modified new germplasm.

Technical Abstract: Nitrogen (N) is a critical element for plant growth and development. Hence, improving nitrogen use efficiency (NUE) is vital for reducing costs and the environmental impact of agricultural practices. Understanding the genetic control of N metabolism is crucial to improve NUE, especially in agronomically important plants, such as barley (Hordeum vulgare). Using bioinformatics and functional genomics tools, we identified and characterized sixteen barley nitrogen metabolism-related gene families (HvNMGs) on a genome-wide scale, analysing gene features and evolution. These genes, located on six of seven barley chromosomes, are highly conserved in plants (including barley, rice, and Arabidopsis), as shown by phylogenetic analysis. We further explored the evolutionary relationships of NMGs through a genome-to-genome synteny analysis, which indicated higher conservation of NMGs between barley and other monocots, suggesting that these orthologous pairs predate species divergence. Protein-protein interaction analyses revealed that all of the HvNMGs show interactions, mainly with each other. The H. vulgare miRNAs target sites (hvu-miR) prediction identified six hvu-miR in 4 HvNMGs (HvGABA-T2, HvALDH10-1, HvALDH10-2 and HvARGAH), indicating their potential involvement in stress responses. The expression patterns analysis of publicly available RNA-seq data revealed that HvNMGs are expressed in all developmental stages of barley, and they respond to different stress conditions, indicating their essential role in plant growth, development and stress response. The organ-specific expression analysis, conducted using qPCR, of HvNMGs revealed higher expression of HvNiR and HvNRs in the leaf and significantly higher expression of HvARGAH and HvALDH10 in the spike than in other tissues, showing that some of the genes may be particularly important in some tissues than others. This data provides a foundation for understanding HvNMG function and could be used to improve barley yield by enhancing NUE — an important goal for both crop productivity and environmental sustainability.