Herbicide Resistance in Erigeron bonariensis: Research and Analysis

This report investigates herbicide resistance in Erigeron bonariensis, focusing on its resistance to glyphosate. The study aims to determine the mechanisms behind this resistance, specifically examining the role of genes like EPSPS and ABC transporters through quantitative PCR and RNA-Seq analysis. Samples will be collected from multiple sites and analyzed to identify differential gene expression and provide insights into the weed's resistance. The findings from this research will inform future studies on glyphosate resistance in E. bonariensis and contribute to developing effective field control strategies for this weed species. The study uses RNA-Seq to create cDNA libraries, sequence reads, assemble de novo, and test for differential expression, followed by functional annotation using the NCBI database. The goal is to identify the genes responsible for glyphosate resistance and suggest methods for controlling the weed.

Running Head: HERBICIDE RESISTANT WEEDS
HERBICIDE RESISTANT WEEDS
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HERBICIDE RESISTANT WEEDS 2
ABSTRACT
Herbicide resistance is the heritable ability of weeds to survive and reproduce in the presence of
herbicide doses that are lethal to the wild type of the species. Erigeron Canadensis is a good
example of weed species which is known to resist herbicide such as glyphosate. The weed
species is known to adapt to different climate or soil conditions of a place. Resistance of
Erigeron canadensis to glyphosate is thought to involve this mechanism and it is believed that
upregulation of the target gene EPSPS in combination with the ABC transporter genes M10 and
M11 may be responsible for this resistance. One mechanism of such resistance is non-target site
reduced translocation of the herbicide, in which vacuolar sequestration prevents the chemical
from spreading around the plant. This study aims to determining through quantitative PCR and
RNA-Seq if these genes provide the mechanism for glyphosate resistance in Erigeron
bonariensis, a close relative of Erigeron canadensis, or if there are other genes responsible for
the observed glyphosate resistance. Sample leaves of the weed will be collected from the field in
10 different site in both Central Valley and two control populations of Erigeron bonariensis, for
quantitative real time PCR and RNA-Seq analysis. RNA will be extracted from the leaves of
glyphosate-treated and untreated individuals. Total RNA for RNA-Seq analysis will be used in
cDNA library synthesis and sequenced via Illumina HiSeq. Sequenced reads will be assembled
de novo using the software Trinity, assigned to respective genes with the pipeline HTSeq, tested
for differential expression by DESeq and functionally annotated using the NCBI nonredundant
protein (Nr) database. Expression data and transcriptomic resources obtained from RNA-Seq
will inform future more in-depth investigations of glyphosate resistance in E. bonariensis, and
help suggest mechanisms for field control of this weed.

HERBICIDE RESISTANT WEEDS 3
References
Moretti, M. L. (2016). Resistance to glyphosate and paraquat in Conyza bonariensis and
Conyza canadensis from California orchards: Management, distribution, and mechanism of
resistance.
In Wezel, A. (2017). Agroecological practices for sustainable agriculture: Principles,
applications, and making the transition.