Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat

The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture. Despite its importance, the way in which epigenetic modifications regulate cultivar-specific responses to low nitrogen (LN) constraints is not yet well understood. Here, we analyzed the chromatin landscapes in the roots, leaves, and seeds of two wheat cultivars (KN9204 and J411) that differ radically in NUE under varied nitrogen conditions. The chromatin regions responsible for regulating gene transcription exhibited clear cultivar-specificity between the two cultivars, and the regulation of nitrogen metabolism genes (NMGs) was closely linked to variation in histone modification levels instead of differences in DNA sequence. We also found that cultivar-specific histone modification regions contribute to the genetic regulation of NUE-related traits, such as the QTL locus of maximum root length of qMRL-7B. Additionally, LN-induced H3K27ac and H3K27me3 dynamics enhanced root growth more significantly in KN9204, while strengthened the nitrogen uptake system remarkably in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of the H3K27me3 methyltransferase further showed that changes in epigenetic modifications can alter the strategy for root development and nitrogen uptake in response to LN constraint. Taken together, our data highlight the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.