Integrated Transcriptome and Phytohormone Analysis Reveal the Central Role of Auxin in Early Salt Stress Response of Pomegranate Roots

Soil salinization is one of the most severe abiotic stresses that restricts agricultural productivity worldwide. Pomegranate exhibits relative tolerance to salinity, yet the early response mechanisms in roots remain unclear. In this study, the physiological and transcriptional responses of pomegranate roots to salinity stress were systematically investigated. Salinity stress significantly induced the accumulation of total soluble sugar and proline by up to 8% and 67%, and enhanced the activities of superoxide dismutase (68%) and peroxidase (31%), indicating the activation of osmotic adjustment and antioxidant defense systems. A total of 7548 and 7462 genes were differentially expressed under 100 mM and 200 mM NaCl treatments, respectively. Functional annotation highlighted the critical roles of pathways involved in stress response and plant hormone signal transduction. Comprehensive transcriptional reprogramming was observed in the auxin pathway, involving biosynthesis (YUCCA), transport (PIN and AUX1), and signaling components (TIR1, AUX/IAA, ARF, and GH3). Hormone quantification and RT-qPCR validation confirmed the regulatory functions of auxin through sophisticated hormonal crosstalk. These findings revealed the pivotal role of auxin as a central hub in coordinating the early salinity stress response in pomegranate roots and provided crucial insights and candidate gene resources for enhancing salt tolerance in woody fruit species.