| Summary: | Aluminum (Al) toxicity is an important barrier to soybean (<i>Glycine max</i> (L.) Merr.) production in acid soils. However, little is known about the genes underlying Al tolerance in soybean. We aim to find the key candidate genes and investigate their roles in soybean tolerance to Al toxicity in this study. Comparative transcriptome analyses of the Al-tolerant (KF) and Al-sensitive (GF) soybean varieties under control and Al stress at 6, 12, and 24 h were investigated. A total of 1411 genes showed specific up-regulation in KF or more up-regulation in KF than in GF by Al stress, which were significantly enriched in the GO terms of peroxidase (POD) activity, transporter activity (including the known Al tolerance-related ABC transporter, ALMT, and MATE), and four families of transcription factors (AP2, C3H4, MYB, WRKY). The expression levels of seven <i>POD</i> genes were up-regulated by Al stress for at least one time point in KF. The H<sub>2</sub>O<sub>2</sub> pretreatment significantly improved Al tolerance of KF, which is likely due to increased POD activity induced by H<sub>2</sub>O<sub>2</sub>. Our results suggest that PODs play important roles in soybean tolerance to Al toxicity. We also propose a list of candidate genes for Al tolerance in KF, which would provide valuable insights into the Al tolerance mechanisms in soybean.
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