Aluminum (Al) toxicity severely restricts crop growth and productivity in acidic soils. The rubber tree is one of the most economically important crops in tropical regions, which is tolerant to high concentrations of Al in sand or hydroponic culture conditions compared with other plants that have been reported. However, the mechanisms of Al tolerance in rubber trees remain unknown. In this study, we conducted a transcriptome and metabolome analysis for rubber tree sapling roots treated with 200 mM Al for 0 (CK), 2 or 5 days, respectively. Compared with the CK, a total of 9534 differentially expressed genes (DEGs) and 3821 differentially expressed metabolites (DEMs) were identified in 2 d of Al treatment. There were 10,373 DEGs and 4636 DEMs after 5 d of Al treatment, and 1626 DEGs and 1674 DEMs between 2 and 5 d of Al treatment. The DEGs mainly concentrated in transporters, transcription factors (TFs), cell wall biosynthesis and antioxidant systems, and the DEMs were mainly focused on lipids and lipid-like molecules, organic acids and derivatives, organic oxygen compounds, phenylpropanoids and polyketides. The combined transcriptome and metabolome analysis indicated DEGs and DEMs involved in ABC transporters, glutathione metabolism, flavonoid biosynthesis and phenylalanine metabolic pathways were identified to be closely associated with the Al tolerance of rubber trees. Our study elucidated the mechanism of rubber trees’ tolerance to Al at the transcriptional and metabolic levels, which provides a theoretical basis for the study of Al tolerance both for rubber trees and other woody plants.
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