Amaranthus palmeri EPSPS copy number and glyphosate resistance variation

Gene copy number variation (CNV) has been increasingly associated with
organismal responses to environmental stress, but we know little about the
quantitative relation between CNV and phenotypic variation. In this study
we quantify the relation between variation in EPSPS
(5-enolpyruvylshikimate-3-phosphate synthase) copy number using digital
drop PCR and variation in phenotypic glyphosate resistance in 22
populations of Amaranthus palmeri (Palmer Amaranth), a range-expanding
agricultural weed. Overall, we detected a significant positive relation
between population mean copy number and resistance. The majority of
populations exhibited high glyphosate resistance yet maintained
low-resistance individuals, resulting in bimodality in many populations.
We also investigated threshold models for the relation between copy number
and resistance, and found evidence for a threshold of ~15 EPSPS copies:
there was a steep increase in resistance below the threshold, followed by
a much shallower increase. Across 924 individuals, as copy number
increases the range of variation in resistance decreases, yielding an
increasing frequency of high phenotypic resistance individuals. Among
populations we detected a decline in variation (s.d.) as mean phenotypic
resistance increased from moderate to high, consistent with the prediction
that as phenotypic resistance increases in populations, stabilizing
selection decreases variation in the trait. Our study demonstrates that
populations of A. palmeri can harbour wide variation in EPSPS copy number
and phenotypic glyphosate resistance, reflecting the history of, and
template for future, resistance evolution.