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Background  Forest species ranges are confined by environmental limitations such as cold stress. The natural range shifts of pine forests due to climate change and proactive-assisted population migration may each be constrained by the ability of pine species to tolerate low temperatures, especially in northern latitudes or in high altitudes. The aim of this study is to characterize the response of cold-tolerant versus cold-sensitive  Pinus halepensis  ( P. halepensis ) seedlings at the physiological and the molecular level under controlled cold conditions to identify distinctive features which allow us to explain the phenotypic difference. With this objective gas-exchange and water potential was determined and the photosynthetic pigments, soluble sugars, glutathione and free amino acids content were measured in seedlings of different provenances under control and cold stress conditions.    Results  Glucose and fructose content can be highlighted as a potential distinctive trait for cold-tolerant  P. halepensis  seedlings. At the amino acid level, there was a significant increase and accumulation of glutathione, proline, glutamic acid, histidine, arginine and tryptophan along with a significant decrease of glycine.    Conclusion  Our results established that the main difference between cold-tolerant and cold-sensitive seedlings of  P. halepensis  is the ability to accumulate the antioxidant glutathione and osmolytes such as glucose and fructose, proline and arginine.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1464-5) contains supplementary material, which is available to authorized users.

Distinctive physiological and molecular responses to cold stress among cold-tolerant and cold-sensitive Pinus halepensis seed sources