Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox

Authors: Wright, Alice; SASIDHARAN, RAJKUMAR - Basf Corporation North America; KOSKI, LIISA - Basf Corporation North America; RODRIGUEZ, MARIANELA - Basf Corporation North America; PETERSON, DANIEL - Mississippi State University; Nandula, Vijay; Ray, Jeffery - Jeff; BOND, JASON - Mississippi State University; SHAW, DAVID - Mississippi State University

Submitted to: Planta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2017
Publication Date: 6/27/2018
Citation: Wright, A.A., Sasidharan, R., Koski, L., Rodriguez-Carres, M., Peterson, D.G., Nandula, V.K., Ray, J.D., Bond, J.A., Shaw, D.R. 2018. Transcriptomic changes in Echinochloa colona in response to treatment with the herbicide imazamox. Planta. 247:369-379.

Interpretive Summary: Herbicides are the most frequently used means of controlling weeds. For many herbicides how they function to damage or kill plants is known. However, it is considerably less clear how plant gene expression changes in response to herbicide exposure. Understanding which genes are activated in response to herbicides provides insight not only into basic plant stress reactions, but can illuminate means by which plants evolve resistance to herbicides. Scientists from the Crop Production Systems Research Unit (USDA-ARS), Stoneville, MS, BASF, Mississippi State University, and other USDA-ARS research units examined changes in gene expression in response to herbicide exposure in sensitive and resistant junglerice plants. Additionally, as no reference genome sequence is available for this weed, a reference leaf transcriptome was generated by sequencing messenger RNA transcripts from untreated susceptible and resistant plants. The transcriptome was assembled, annotated, and differential gene expression analysis was performed to identify transcripts that were upregulated or downregulated in response to herbicide exposure for both plant types. Many of the differentially expressed transcripts belong to families of genes whose members are known to participate in stress responses. A time course study examining a subset of transcripts showed that they were upregulated and then returned to untreated levels within 48 hr of exposure. This study showed that within 48 hr, junglerice mounts a stress response to herbicide exposure. The assembled transcriptome represents the first reference leaf transcriptome for this weed.

Technical Abstract: Herbicides are the most frequently used means of controlling weeds. For many herbicides the target site is known; however, it is considerably less clear how plant gene expression changes in response to herbicide exposure. Understanding which genes are activated in response to herbicides provides insight not only into basic plant stress reactions, but can illuminate means by which plants evolve resistance to herbicides. In this study, changes in gene expression in response to herbicide exposure in imazamox sensitive (S) and resistant (R) junglerice biotypes was examined. As no reference genome is available for this weed, a reference leaf transcriptome was generated. Messenger RNA was isolated from imazamox treated and untreated R and S plants and the resulting cDNA libraries were sequenced on an Illumina HiSeq2000. The transcriptome was assembled, annotated, and differential gene expression analysis was performed to identify transcripts that were upregulated or downregulated in response to herbicide exposure for both biotypes. Many of the differentially expressed transcripts belong to families of genes whose members are known to participate in stress responses. A time course study examining a subset of transcripts showed that they were upregulated and then returned to untreated levels within 48 hr of exposure. Expression for the upregulated transcripts peaked between 4 to 12 hr. Testing of plants from two additional biotypes showed a similar change in gene expression four hours after herbicide exposure compared to the resistant and sensitive populations. This study shows that within 48 hr, junglerice mounts a stress response to imazamox exposure.