Durum Wheat Responses to Organic and Conventional Management Systems: Agronomic Traits and Tissue-Specific Expression of Nitrogen Transport and Assimilation Genes

Efficient nitrogen acquisition and utilization are essential for sustainable wheat production in contrasting management systems. However, little is known about how genotype × management interactions are associated with tissue-specific expression of nitrogen (N)-related genes in durum wheat under organic and conventional field conditions. This study evaluated the agronomic, physiological, and molecular responses of 12 durum wheat genotypes (Triticum turgidum L. subsp. durum) grown under organic and conventional management during the 2022–2023 and 2023–2024 growing seasons. Six genotypes, comprising four higher-performing and two lower-performing genotypes, were selected for molecular analysis. The expression of ten genes involved in nitrate and ammonium transport and N assimilation was analyzed using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in leaf, stem, and root tissues. The mean grain yield was 4078.29 kg ha−1 under organic management and 3997.35 kg ha−1 under conventional management. Thus, mean grain yield was approximately 2.0% higher under organic management. Genotypic responses differed between the two systems: AYM-6 had the highest grain yield under conventional management (5201.92 kg ha−1), whereas AYM-3 had the highest grain yield under organic management (5059.72 kg ha−1). Among the ten genes, NRT2.1 and GS1 had higher transcript abundance under conventional management, whereas the other eight had higher transcript abundance under organic management. GS1 generally had the highest transcript abundance, while NRT1 had the lowest. Gene expression was strongly tissue-dependent, with leaves generally showing the highest transcript levels. Gene–trait analysis further revealed a positive relationship between leaf NRT2.1 expression and grain yield under conventional management (R2 = 0.78, p = 0.020) and a negative relationship between root NRT1.1 expression and grain yield under organic management (R2 = 0.68, p = 0.043). The results showed management- and genotype-specific agronomic responses, while selected N-related gene-expression patterns were associated with grain yield in a tissue- and management-dependent manner. These findings support the evaluation and selection of durum wheat genotypes directly within the target management system.