Annotation and gene ontology analysis
To identify the potential role of significant SNPs in coding regions of genes, genomic annotation was run using the blastn function (Altschul et al., 1997) from BLAST (https://blast.ncbi.nlm.nih.gov/). The 75 bp sequences associated with each SNP were annotated against theEucalyptus grandis genome (Myburg et al., 2014) and considered if their significance valuesmet two related thresholds: an E ‐value < 1 × 10−8 and a blast-score of at least 60.0. Chromosome number and location of significant SNPs were recorded, as well as specific gene functions. The annotated SNPs were used to predict broader biological functions using GO enrichment analysis through the web interface PlantRegMap (Tian et al., 2020). GO terms are organized within three categories: molecular function, cellular component and biological process. We explored the biological process aspect from the GO analysis, which refers to broad category of tasks that the genes or gene products are programmed to achieve. Each of the output GO terms delivered a set of genes that is associated with a specific biological process. We use this output to explore how functionally related SNPs, associated with the GO genes, might be additively correlated with environmental factors (e.g., abiotic stress response). For each climate variable, Fisher’s exact test was used to test for significantly over-represented GO terms, with a threshold ofp-value <0.01. GO terms with the highest number of SNPs and/or with pertinent biological processes associated with environmental response (e.g., response to heat, cold and drought) were recorded and considered for further landscape genomic analysis.