LC-MS/MS-based Phenolic Profiling and IRAP-PCR Analysis Reveal Biochemical and Genomic Responses of Flax (Linum Usitatissimum L.) to Salt Stress

Abstract

Background: Salinity is a major abiotic stress factor that affects plant growth, secondary metabolism, and genomic stability. Phenolic compounds and antioxidant capacity are key biochemical indicators of plant stress responses, while retrotransposon activity reflects molecular-level genomic plasticity. This study investigated the physiological and molecular responses of Linum usitatissimum L. (flax) to different salt concentrations, aiming to better understand the mechanisms underlying salinity tolerance. Methods and results: Flax plantlets were grown in vitro on Murashige and Skoog (MS) medium supplemented with 15, 30, or 60 mM NaCl for 15 days. Total phenolic content (TPC) was quantified using the Folin–Ciocalteu method, while antioxidant activity was assessed via DPPH and ABTS radical scavenging assays. LC-MS/MS was employed to identify and quantify individual phenolic compounds, and IRAP-PCR was used to evaluate retrotransposon mobility. Salinity resulted in a significant reduction in biochemical parameters. TPC decreased from 1.13 µg GAE/100 µg extract in the control to 0.85, 1.06, and 0.69 µg GAE under 15, 30, and 60 mM NaCl, respectively. Antioxidant activity showed a similar decline: DPPH inhibition dropped from 25% (control) to approximately 12% under 60 mM stress, while ABTS inhibition decreased from over 90% to approximately 72% at 0.03 mg/mL. LC-MS/MS profiling revealed salt-sensitive reductions in chlorogenic acid, caffeic acid, trans-ferulic acid, and naringenin, with chlorogenic acid particularly diminished at 60 mM NaCl. At the molecular level, IRAP-PCR yielded high polymorphism rates, ranging from 50% to 100% (primer 1845), 60% to 100% (1846), 54% to 100% (1875), and 36% to 100% (1899), indicating enhanced retrotransposon activity under increasing salinity. Conclusion: Overall, rising salt concentrations reduced phenolic accumulation and antioxidant potential while increasing retrotransposon-mediated genomic variability in flax. These results suggest that both biochemical markers (phenolics, antioxidant activity) and molecular indicators (IRAP polymorphism) are valuable tools for assessing salinity stress responses and can support the development of salt-tolerant cultivars in flax breeding programs. © The Author(s), under exclusive licence to Springer Nature B.V. 2025.