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.