Low stringency tests revealed differential gene expression in red maple (Acer rubrum) treated with low doses of nickel

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Recent field studies have revealed that Acer rubrum is a nickel (Ni) avoider and it does not store Ni in its tissues. Analysis of nickel toxicity at low and high doses in this species is limited. The main objectives of this study were to 1) determine the effect of low and high Ni doses on A. rubrum seedlings, 2) to assess the effects of low doses of nickel on gene expression using a less stringent test based on P-values, and 3) to identify differential gene expression in resistant and susceptible genotypes. All the Ni toxicity tests were conducted in growth chambers. No morphological damage or change in plant growth were observed when A. rubrum where treated with a low dose (150 mg/kg) and high doses (800 mg/kg, and 1600 mg/kg) of Ni. Differential gene expression from the transcriptome analysis using P-values revealed that 464 genes were downregulated and 609 upregulated in samples treated with 150 mg/kg Ni compared to water. These numbers were 994 down regulated and 1569 upregulated genes when the 800 mg/kg dose was compared to water and 3760 down regulated and 7098 when 1600 mg/kg was compared to the same water control. There were more upregulated genes (1482) than downregulated (623) when Ni-resistant and Ni-susceptible genotypes were compared based on low stringency test (P-values). Among the top 50 most upregulated, Serine/threonine-protein kinase, O-methyltransferase, sugar transporter, glutathione-s-transferase and s-adenosylmethioninie-dependent methyltransferase were the only ones that could be relevant for Ni toxicity based on their role in plants. On the other hand, the top 50 most downregulated genes that could be associated with environmental stress include Peroxisomal ascorbate peroxidase, Glycine-rich protein DC7.1, Aquaporin NIP6.1 family protein, Putative membrane protein (Fragment), and Serine/threonine protein kinase. Overall, the study shows that a less stringent test such as P-Values could be a good tool to study gene expression when the effects of Ni or other metals on global gene transcription are low.