Investigating the heritability of resistance fueling copy number variation in glyphosate resistant Amaranthus palmeri

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Authors
Han, Lisa
Keyword
Evolutionary ecology , Copy number variation , Herbicide Resistance , Agricultural weeds , Evolutionary Genetics , Quantitative Genetics
Abstract
Gene copy number variation (CNV) can arise as a response to selection pressure from the environment. Herbicide is one selective agent targeting and promoting the evolution of resistance in agricultural weed populations. In Amaranthus palmeri, CNV of the EPSPS gene, the target of glyphosate herbicide, ranges from 1 to over 160 copies, and is the primary genetic determinant of glyphosate resistance. The amplified copies of EPSPS are found as extrachromosomal circular DNA, which raises questions about the heritability of resistance gene copies. I used 799 F1 progeny from 30 crosses to examine the following: (i) Is there a relationship between EPSPS copy number (CN) of offspring and mean of the parental pair copy number? (ii) Is there variability in the directionality of EPSPS inheritance with increasing mean CN? EPSPS gene CN estimates were obtained by probe-based droplet digital PCR and the copy number estimates were used to perform controlled crosses to create the F1 generation. The results illustrate an overall increase in mean copy number in response to increasing mean EPSPS copies in the parents. I report a significant heritability estimate of EPSPS gene copies between parental pairs and their offspring mean EPSPS copy number, with a threshold point of 48.8 EPSPS copies. The heritability is significantly higher (h2=0.69) for low to moderate mean copy number plants below this 48.8 copy number threshold, but declines (h2=0.14) for high mean copy number plants. F1 data revealed progeny means decreasing as parental pair means increase, and minimal relation between the standard deviation of the progeny EPSPS copy number and the difference in parental pair copy number. Positive and negative transgressive segregants were observed, and the tendency to accumulate or lose amplified copies shifted with parental pair mean CN value. These results are discussed in the context of ecological, evolutionary, and genetic factors that may influence EPSPS CN inheritance in A. palmeri. This thesis investigates the properties the extent to which progeny CN is determined by parental CN in a system exhibiting extrachromosomal CNV, contributing to the ongoing effort to understand the evolutionary trajectory of gene copy number inheritance and resistance.
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