Transcriptome Analysis Revealed Dose Dependent Variation of Nickel Induced Gene Expression in Red Maple (Acer rubrum).

The main objective of the present study was to assess the effects of different nickel dosages on toxicity and gene expression in red maple (Acer rubrum) To assess nickel toxicity A. rubrum plants were treated under controlled conditions in growth chambers. Commercial Ni(NO₃)₂ salts were used for Ni and Cu treatments, respectively. The experimental design was a completely randomized block with 15 replications per treatment. Plants were treated with a control (0 mg/kg) and three doses of Ni(NO₃)₂ equivalent to 150 mg/kg (150 mg of Ni per 1 kg of dry soil), 800 mg/kg (800 mg of Ni per 1 kg of dry soil), and 1, 600 mg/kg (1,600 mg of Ni per 1 kg of dry soil). Water and potassium nitrate salts were used as controls. To determine gene expression, total RNA was extracted using the Plant/Fungi Total RNA Purification kit from Norgen Biotek Corporation (Thorold, Canada). RNA-seq libraries and De Novo Transcripts Assembly were performed as per previously described protocols. The raw reads were mapped to Trinity assembled transcripts using bowtie and RSEM was used to quantify transcript and gene expression levels. Gene expression was calculated and expressed as Reads Per Kilobase per Million reads mapped (RPKM). Baseline filtering of genes that are likely the effect of nitrate was conducted to assess only genes response to nickel and not nitrate. A pairwise comparison among different dosages and the controls for all the differentially expressed genes was performed. All the red maple genotypes were resistant to all levels of nickel treatments as no damage or symptom of nickel toxicity was observed. The level of gene expression increased significantly with the increase of nickel dosage treatment. Detailed characterization of key differentially expressed genes will be discussed.