Transcriptional, metabolic and DNA methylation changes underpinning the response of Arundo donax ecotypes to NaCl excess

Main conclusion Arundo donax ecotypes react differently to salinity, partly due to differences in constitutive defences and methylome plasticity. Arundo donax L. is a C3 fast-growing grass that yields high biomass under stress. To elucidate its ability to produce biomass under high salinity, we investigated short/long-term NaCl responses of three ecotypes through transcriptional, metabolic and DNA methylation profiling of leaves and roots. Prolonged salt treatment discriminated the sensitive ecotype ‘Cercola’ from the tolerant ‘Domitiana’ and ‘Canneto’ in terms of biomass. Transcriptional and metabolic responses to NaCl differed between the ecotypes. In roots, constitutive expression of ion transporter and stress-related transcription factors’ genes was higher in ‘Canneto’ and ‘Domitiana’ than ‘Cercola’ and 21-day NaCl drove strong up-regulation in all ecotypes. In leaves, unstressed ‘Domitiana’ confirmed higher expression of the above genes, whose transcription was repressed in ‘Domitiana’ but induced in ‘Cercola’ following NaCl treatment. In all ecotypes, salinity increased proline, ABA and leaf antioxidants, paralleled by up-regulation of antioxidant genes in ‘Canneto’ and ‘Cercola’ but not in ‘Domitiana’, which tolerated a higher level of oxidative damage. Changes in DNA methylation patterns highlighted a marked capacity of the tolerant ‘Domitiana’ ecotype to adjust DNA methylation to salt stress. The reduced salt sensitivity of ‘Domitiana’ and, to a lesser extent, ‘Canneto’ appears to rely on a complex set of constitutively activated defences, possibly due to the environmental conditions of the site of origin, and on higher plasticity of the methylome. Our findings provide insights into the mechanisms of adaptability of A. donax ecotypes to salinity, offering new perspectives for the improvement of this species for cultivation in limiting environments.