Transcriptome and Metabolome Analysis of the Mechanism of Environmental Adaptability in Populus Roots

Poplar (<i>Populus</i> spp.) is a keystone commercial tree species in Northeast China, valued for its high economic returns. The genotype-by-environment (G × E) interaction critically governs its growth performance and ecological adaptability, which are pivotal for ensuring the long-term sustainability and economic viability of poplar plantations. In this study, the fibrous roots of the (<i>P. simonii</i> × <i>P. nigra</i>) × <i>P. deltoides</i> clone planted at three distinct sites, including Lishu (named SR1), Xinmin (named SR2), and Cuohai (named SR3), were used to perform transcriptome and metabolome. Comparative analysis revealed 6246, 3455, and 3854 differentially expressed genes (DEGs) in the SR1 vs. SR2, SR1 vs. SR3, and SR2 vs. SR3 comparisons, respectively. These DEGs were functionally enriched in pathways associated with antioxidant enzyme activity, stimulus response, plant hormone signal transduction pathways, and α-linolenic acid metabolism. Metabolomic analysis identified 106, 147, and 189 significantly differentially accumulated metabolites (DAMs) across the same comparisons, primarily linked to glutathione metabolism, butanoate metabolism, and pentose-glucuronate interconversions. Notably, we identified a core regulatory module comprising 57 genes and four key metabolites within the α-linolenic acid metabolic pathway, which exhibited strong correlations with phenotypic adaptability. These findings provide mechanistic insights into poplar's plasticity under environmental heterogeneity, offering a molecular roadmap for future breeding strategies and the sustainable expansion of poplar cultivation.