Nitrogen (N) is an important macronutrient that supports wheat growth and development, and its deficiency is one of the main factors causing abiotic stress. N-deficiency caused by extremely low- or high-water availability, is regarded as an agro-climatic stress that critically affects wheat productivity. Nitrate (NO3-) and ammonium (NH4+) are the primary N sources in agriculture; their uptake and assimilation are tightly controlled. In this study, we evaluated the response to severe N-deficiency (0.37 µM NO3- and NH4+) for 26 days, in the N deficiency tolerant introgression line (IL99) that carries a GPC QTL (QGpc.huj.uh-5B.2) derived from wild emmer wheat (WEW), as compared with its susceptible recipient bread wheat cultivar Ruta.

We identified in IL99 significant changes in 16 root system architecture (RSA) traits, as compared with Ruta (e.g., increased steep angle frequency, reduced shallow angle frequency, increased total root length, number of root tips in the lower part of root area, average root orientation, maximum number of roots, and root tips/root length ratio), along with five vegetative traits. The changes of RSA traits shifted root growth towards longer, deeper, and steeper root orientation, enabling nutrient acquisition from deeper soil layers and a larger soil volume. This mode of adaptability by RSA traits modifications to irregular distribution of N in the soil is a key determinant of IL99 performance.

Comparative transcriptome analyses at the whole plant level showed that IL99 also has distinct gene expression reactions to NS, including more upregulated genes in the leaves and the roots (3.14 and 4.45 times more) than in Ruta. GO and KEGGs pathway enrichment analyses identified unique pathways in IL99, such as phenylpropanoid biosynthesis, glutathione metabolism, and plant hormone signal transduction and metabolism. Specific genes in these pathways can be regarded as candidate genes for NS tolerance, including protein kinases, signaling and metabolism of plant hormones (JA, IAA, GA, ABA, and Ethylene), nitrogen recycling, carbohydrate metabolism, transcription factors, and amino acid metabolism.

The unique transcriptome reprogramming and whole plant-level morphological modifications identified in IL99 provided valuable insights into the mechanisms for improved N-use efficiency and N stress tolerance.

These sophisticated molecular adaptations conferred by the introgression of a QTL from WEW, recalibrated gene networks, enzymatic nodes, hormonal crosstalk, and resource allocation under stress mitigation. As a result, IL99 exhibits better vigor than the cultivar, which struggles under N limitations.

These insights hold great promise for enhancing crop productivity and resilience in nitrogen-limited environments.