Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.)

Species that repeatedly evolve phenotypic clines across environmental
gradients have been highlighted as ideal systems for characterizing the
genomic basis of local environmental adaptation. However, few studies have
assessed the importance of observed phenotypic clines for local
adaptation: conspicuous traits that vary clinally may not necessarily be
the most critical in determining local fitness. The present study was
designed to fill this gap, using a plant species characterized by
repeatedly-evolved adaptive phenotypic clines. White clover is naturally
polymorphic for its chemical defense cyanogenesis (HCN release with tissue
damage); climate-associated cyanogenesis clines have evolved throughout
its native and introduced range worldwide. We performed landscape genomic
analyses on 415 wild genotypes from 43 locations spanning much of the
North American species range to assess the relative importance of
cyanogenesis loci vs. other genomic factors in local climatic adaptation.
We find clear evidence of local adaptation, with temperature-related
climatic variables best describing genome-wide differentiation between
sampling locations. The same climatic variables are also strongly
correlated with cyanogenesis frequencies and gene copy number variations
(CNVs) at cyanogenesis loci. However, landscape genomic analyses indicate
no significant contribution of cyanogenesis loci to local adaptation.
Instead, several genomic regions containing promising candidate genes for
plant response to seasonal cues are identified — some of which are shared
with previously-identified QTLs for locally-adaptive fitness traits in
North American white clover. Our findings suggest that local adaptation in
white clover is likely determined primarily by genes controlling the
timing of growth and flowering in response to local seasonal cues. More
generally, this work suggests that caution is warranted when considering
the importance of conspicuous phenotypic clines as primary determinants of
local adaptation.