Molecular analysis of Betula papyrifera populations from a mining reclaimed region: genetic and transcriptome characterization of metal resistant and susceptible genotypes

Abstract

The objectives of the present study were to; 1) determine if there’s an association between plant population diversity and genetic variation in white birch (Betula papyrifera) populations with soil metal contamination in the Greater Sudbury region (GSR), 2) assess if metal contamination and soil liming has an effect on global DNA methylation, 3) develop and characterize the transcriptome of B. papyrifera under nickel stress and, 4) assess gene expression dynamics in white birch in response to nickel stress. No association between plant population diversity and genetic variation with metal contamination was found. Liming increases plant population diversity but has no effect on genetic variation in the studied white birch populations. There was a decrease in root cytosine methylation in metal-contaminated sites compared to references. Treatment with the dose corresponding to total level of Ni or Cu (1,600 mg/kg Ni, 1,312 mg/kg Cu or combined) in sites of the GSR generated different responses within segregating populations analyzed. The main Ni resistance mechanism of white birch was associated with the prevention of translocation of Ni from root to shoot. We also observed lower ZAT11 and glutathione reductase expression in resistant genotypes compared to susceptible. The transcriptome of B. papyrifera was developed for the first time using Next Generation Sequencing. RNA from Ni resistant, moderately-susceptible, susceptible and water controls treatment was sequenced. A total of 209,802 trinity genes were identified and were assembled to 278,264 total trinity transcripts. In total, 215,700 transcripts were annotated and compared to the published B. nana genome. Overall, a genomic match for 61% transcripts with the reference genome was found. Expression profiles were generated and 62,587 genes were found to be significantly differentially expressed among the nickel resistant, susceptible, and untreated libraries. The main nickel resistance mechanism in B. papyrifera is a downregulation of genes associated with translation and cell growth, and upregulation in genes involved in the plasma membrane. Seven candidate genes associated to nickel resistance were identified. They include Glutathione S-transferase, Thioredoxin, Putative transmembrane protein, Nramp transporter, TonB-like family protein and TonB-like dependent receptor. This TonB receptor was found to be exclusive to the Betula genus.