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Norway spruce is an ecologically and commercially important species, which currently suffers from climate change and is expected to decline because of heat and drought stress. A manipulative experiment with drought-stressed and well-watered (control) seedlings was established, comprising five populations of Norway spruce coming from a small territory but distributed along a steep elevational transect from 550 to 1280 m.a.s.l. Plants were phenotyped at physiological traits (content of phytohormones and monoterpenes, chlorophyll a fluorescence, gas exchange and hyperspectral indices) and genotyped using ddRAD sequencing. After filtering, 34 127 polymorphisms (SNPs) were retained and used for analysis. Association tests revealed 42 SNP-variable pairs located across 29 scaffolds exhibiting significant associations, among them 20 were found for drought-stressed seedlings and 22 for control …