Whole genome expression analysis of trembling aspen (Populus tremuloides) genotypes exposed to increasing concentrations of nickel

Excess metals in the soil are a known type of abiotic stress and many plant species have evolved specific metal resistance mechanisms to cope and avoid or reduce toxicity symptoms. Studies on P. tremuloides genetic response to nickel are limited. This present study aims to 1) Assess gene expression dynamics in P. tremuloides seedlings treated with varying concentrations of nickel salts and, 2) Compare gene expression profiles among the different treatment groups. Trembling aspen (Populus tremuloides) seedlings were treated with varying concentrations of nickel nitrates (150 mg Ni / 1 kg of dry soil, 800 mg / kg, and 1, 600 mg / kg). The whole genome expression was analyzed using Illumina sequencing. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. In general, there was an increase in number of differentially expressed genes as the nickel concentration increased when compared to water. The number of downregulated (439–600) and upregulated (123–560) genes increases with the nickel concentration increase. A detailed analysis suggested that the 800 mg / kg nickel concentration is the threshold at which an early abiotic stress response may be triggered as seen by the highly upregulated LEA protein and two calcium binding proteins when compared to water. For the highest nickel concentration, 7-deoxyloganetin glucosyltransferase was highly upregulated while an auxin response factor, Flavonol 3-sulfotransferase, and a predicted ABC transporter family protein were downregulated. The heatmap showed that the genes were grouped into six clusters based on the changes in expression as nickel concentration increased. The cluster of genes that had increased gene expression with increasing nickel concentration also had multiple enriched Gene ontology (GO) terms related to heavy metal and abiotic stress including metal ion transport, antioxidant activity, photosynthesis, and ribosomal activity. GO terms that decreased in expression with increasing nickel concentrations include ATP and ADP binding, protein kinase activity, integral component of membrane, protein phosphorylation and transmembrane transport.