Adaptation to temperature and precipitation
GDM analysis on all candidate SNPs found the highest deviance explained for a SNP associated with TSEAS (39.2%), closely followed by PWQ (36.9%), with overall results for all candidates showing low to moderate deviance across the 5 variables. Furthermore, PWQ was linked to GO:1901566, with the highest number of associated SNPs (21) and also showed the highest deviance explained by the GDM analysis (Figure 4e). Overall, both temperature and precipitation variables are linked to adaptive genetic variants through the multi-EAA and annotation approach; although, GO and GDM analysis highlighted the specific precipitation variable (PWQ) as a stronger adaptation driver.
The annotations of identified genes were made based on the reference genome of Eucalyptus grandis , a distant relative, so we provide a pertinent but cautious preliminary interpretation of functional results until a full jarrah (E. marginata ) reference genome becomes available. Gene functions associated with the temperature and precipitation variables show biological functions associated with response and adaptation to these abiotic factors. For example, the KCS gene family (JAR02659), that was associated with TSEAS, has been linked to cold and light responses (Joubès et al., 2008) inArabidopsis , being involved in the biosynthesis of waxes that cover the leaves surface. Two SNPs (JAR13256 and JAR08936) are linked to the ABC transporter gene families, which have been shown to be associated with heat response and abiotic stress tolerance during seed germination (Zhang et al., 2012; Hwang et al., 2016). Similarly, for TMAX, several SNPs were found to be linked to this same gene family (JAR07223, JAR03208, JAR09260, JAR00867, JAR09847, JAR03598 and JAR08936) as well as one for TMIN (JAR01172). The HSF gene family was linked to a SNP (JAR02134) associated with both TSEAS and TMAX, and this gene family is identified as a strong thermotolerance regulator (Scharf et al., 1990) and has been widely reported in various plant species (Duan et al., 2019; Zhang et al., 2020a). The SNP JAR07972 associated with TMIN was found in CBL genes that have been related to adaptation and tolerance to low temperatures, among other abiotic stresses (Ren et al., 2014; Su et al., 2020). The MYB transcription factors gene family has been extensively associated with abiotic tolerance, specifically cold and heat stress, but also dehydration (Mmadi et al., 2017; Liao et al., 2017). SNPs linked to this family were found across four climatic variables: TSEAS (JAR07671 and JAR04859), TMAX (JAR00038, JAR00207, JAR07671, JAR04859 and JAR07108), TMIN (JAR08943) and PWQ (JAR07671). In addition, the SNP associated with PWQ (JAR13490) was found in the chromatin-remodelling factor PKL gene that has been consistently linked to multiple plant development processes, particularly to the abscisic acid (ABA) pathway regulation (Perruc et al., 2007). ABA is a phytohormone that is well known for controlling stomatal closure (Rajab et al., 2019, Maheshwari et al., 2020), thus being crucial for efficient drought response (Yu et al., 2019, Zhang et al., 2020b). From PMA, one SNP (JAR01263) was found associated with the methionine gamma-lyase (MGL) gene. MGL is an enzyme which activity is upregulated by osmotic stress caused by drought (Joshi & Jander, 2009) and it is considered to act as an osmolyte, protecting the plant tissues from dehydration (Gagné-Bourque et al., 2016). These are just a sample of the many compelling gene functions associated to both temperature and precipitation found across the five tested climatic variables, identifying these as potential drivers of local adaptation.