Whole transcriptome response of wheat seedlings to nitrogen starvation in wheat introgressions of GPC-QTL from wild emmer wheat

Wheat productivity and grain protein concentration (GPC) depends on the amount and timing of nitrogen (N) application, which must be reduced for environmental sustainability. Whole transcriptome response to reduced N was compared between introgression lines of a GPC-QTL from wild emmer wheat (IL99; at BC3F5), two recombinant lines with partial QTL introgressions (RC26 and RC46, at BC4F3) and their recurrent cultivar Ruta. At 14 days of N-stress, IL99 and RC46 were 13.4% taller on average than Ruta and RC26, and the development of the third leaf was faster. A total of 11,456 differentially expressed genes (DEGs) were identified between leaves of Ruta vs. IL99, and 6,480 DEGs between RC26 vs. RC46. Hierarchical clustering analysis identified two clusters of 67 and 141 DEGs sharing similar patterns of up-regulation in IL99 and RC46, and down-regulation in Ruta and RC26. These clusters were enriched in genes involved in the efficient N-transport and activation of N-metabolism, and adaptation to the environment, including genes: encoding nitrate transporter-family proteins (NRT), ureide permease (UPS); auxin-response factors (ARf), heavy metal-associated proteins, encoding antioxidant enzyme catalase (CATs), and a subset of transcription factors (ERF, bHLH, NLP, and MADS-box). Our study shows that introgressions from WEW (IL99 and RC46), were better adapted to N-stress at the seedling stage than the cultivar Ruta and RC26. The introgression affected the whole genome response to N-stress associated with N-use efficiency in wheat, and enable better understanding of the mechanisms of wheat adaptation to N-stress.