Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions

Authors: Horvath, David; DOHERTY, COLLEEN - North Carolina State University; DESAI, JIGAR - Wave Life Sciences Boston; CLARK, NATALIE - Broad Institute Of Mit/harvard; Anderson, James; Chao, Wun

Submitted to: AoB Plants
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/27/2023
Publication Date: 4/6/2023
Citation: Horvath, D.P., Doherty, C.J., Desai, J., Clark, N.M., Anderson, J.V., Chao, W.S. 2023. Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions. AoB Plants. https://doi.org/10.1093/aobpla/plad013.
DOI: https://doi.org/10.1093/aobpla/plad013

Interpretive Summary: Weeds reduce corn yield by changing how corn grows rather than by directly competing with the corn for light, water, and nutrients. Thus, it should be possible to prevent yield losses by blocking the ability of corn to detect the nearby weeds. We identified the corn genes that were turned on and off when they were exposed to weeds over a short period of time and then used computer programs to identify key proteins that may allow corn to detect nearby weeds. This information will be used to design new experiments to prevent these key proteins form working and see if blocking these proteins allows corn to have greater yield even if weeds are present. This could allow growers to use less herbicides and may even allow growers to grow different crops at the same time.

Technical Abstract: There is growing evidence that weeds primarily reduce crop yield by altering crop developmental and physiological processes long before the weeds reduce resources through competition. Multiple studies have implicated stress response pathways are activated when crops such as maize are grown in contact with weeds during the first 4 to 8 weeks of growth in which weeds have their greatest impact on subsequent crop yields. However, to date, these studies have mostly focused on the response of above-ground plant parts and have not examined the early signal transduction processes associated with maize response to weeds. We developed a system designed to allow the identification of very early changes in the maize transcriptome when it is exposed to just below-ground signals from a competitor during the time when the maize plants are most vulnerable to weed pressure. Gene set enrichment analyses identified over-represented ontologies associated with oxidative stress signaling throughout the time of weed exposure, with additional ontologies associated with nitrogen use and transport and abscisic acid (ABA) signaling, and defense responses being enriched at later time points. Enrichment of promoter motifs indicated over-representation of sequences known to bind FAR1, several AP2/ERF transcription factors and others. Likewise, co-expression networks were identified using WGCNA and SC-ION algorithms. WGCNA highlighted the potential roles of several transcription factors including a MYB 3r-4, TB1, WRKY65, CONSTANS-like5, ABF3, HOMEOBOX 12, among others. These studies also highlighted the role of several specific proteins involved in ABA signaling as being important for the initiation of the early response of maize to weeds. SC-ION highlighted potential roles for NAC28, LOB37, NAC58, and GATA2 transcription factors, among many others.