Pistachio (Pistacia vera L.) is an economically important tree nut that commonly thrives in semi-arid and arid environments. P. vera is highly adaptable to various abiotic stresses, including drought and salinity, making it suitable for reforesting arid and salinized zones. This study aimed to investigate the physiological and molecular mechanisms underlying stress tolerance in the UCB-1 cultivar. Five one-year-old pistachio rootstocks were subjected to four saline water regimes for 100 days. The rootstocks adopted the Na+ exclusion strategy to resist the salinity stress. Total proteins were isolated from the pistachio roots exposed to different NaCl concentrations. These proteins were characterized using high-throughput LC-MS/MS spectrometry, with the results searched against the Citrus database. Over 1600 protein IDs were detected, with comparative analysis identifying 245 proteins that were more abundant and 190 that were less abundant across three stress levels.

Proteins associated with amino acid metabolism, cell wall organization, protein homeostasis, response to stress, signal transduction, TCA cycle, and vesicular trafficking were constantly overexpressed at all stress levels. At low and moderate stress levels, proteins involved in chromatin and cytoskeleton organization and lipid metabolism were overexpressed, while these proteins remained unaffected at higher salt concentrations. Transcription and translation processes were down-regulated across all stress levels. The protein interaction network, mapped to Arabidopsis thaliana orthologs, revealed clusters associated with these proteins. Under control conditions, the highest number of proteins were involved in chloroplast and cytosolic pathways. Under low salinity stress, there was a slight shift, with the most interconnected node activity assigned to mitochondrial and cytosolic pathways. As salinity increased, the pathways shifted focus, emphasizing carbohydrate metabolism under moderate salinity stress and amino acid metabolism under severe salinity stress.