Co-Transcriptomic Analysis of the Maize-Western Corn Rootworm Interaction

Abstract

The Western corn rootworm (WCR; Diabrotica virgifera virgifera) is an economically important belowground pest of maize. Belowground feeding by WCR is damaging because it weakens the roots system, diminishes nutrient uptake, and creates entry points for fungal and bacterial pathogens and increases lodging, all of which can significantly suppress maize yields. Previously, it was demonstrated that belowground herbivory can trigger plant defense responses in the roots and the shoots, thereby impacting intraplant communication. Although several aspects of maize-WCR interactions have been reported, co-transcriptomic remodeling in the plant and insect are yet to be explored. We used a maize genotype, Mp708, that is resistant to a large guild of herbivore pests to study the underlying plant defense signaling network between below and aboveground tissues. We also evaluated WCR compensatory transcriptome responses. Using RNA-seq, we profiled the transcriptome of roots and leaves that interacted with WCR infestation up to 5 days post infestation (dpi). Our results suggest that Mp708 shoots and roots had elevated constitutive and WCR-feeding induced expression of genes related to jasmonic acid and ethylene pathways, respectively, before and after WCR feeding for 1 and 5 days. Similarly, extended feeding by WCR for 5 days in Mp708 roots suppressed many genes involved in the benzoxazinoid pathway, which is a major group of indole-derived secondary metabolites that provides resistance to several insect pests in maize. Furthermore, extended feeding by WCR on Mp708 roots revealed several genes that were downregulated in WCR, which include genes related to proteolysis, neuropeptide signaling pathway, defense response, drug catabolic process, and hormone metabolic process. These findings indicate a dynamic transcriptomic dialog between WCR and WCR-infested maize plants.

Keywords: Mp708; RNA-seq; Transcriptome; Western Corn Rootworm; maize.

Figure 1

Principal component analysis (PCA) of the 35,032 genes expressed in at least one of the conditions. Conditions are represented with colors (Mp708 leaves: red, Mp708 roots: blue) and shapes (circle: 0 dpi, triangle: 1 dpi and square: 5 dpi). Each shape indicates a replicate.

Figure 2

Barplot of the upregulated and downregulated differentially expressed genes (DEGs) for each tissue. (A) Leaves, (B) roots, and (C) roots vs. leaves for each time point.

Figure 3

Venn diagrams of differentially expressed genes (DEGs) in Mp708 plants. The number of DEGs are indicated in parenthesis. DEGs in each tissue. (A) Leaves and (B) roots or at each time point: (C) 1 dpi and (D) 5 dpi. Up: upregulated; Down: downregulated.

Figure 4

Weighted gene co-expression network analysis (WGCNA) of the 17,383 differentially expressed genes (DEGs). Barplots represent the expression pattern of the genes assigned into 10 co-expression modules (M1–10). n indicates the number of DEGs in each WGCNA module.

Figure 5

Heatmap of genes encoding plant hormonal pathways related to ethylene (ET), jasmonic acid (JA), and salicylic acid (SA). Each column corresponds to a condition for each tissue (L: leaves or R: roots). Each cell contains the corresponding log₂ (fold-change (FC Infested/Uninfested); genes upregulated are indicated in orange and downregulated in blue) and adjusted p value (*** < 0.001, 0.001 < ** < 0.01, 0.01 < * < 0.05).

Figure 6

Heatmap of differentially expressed genes (DEGs) associated with DIMBOA biosynthesis pathway in maize. Each column corresponds to a condition for each tissue (L: leaves or R: roots). Each cell contains the corresponding log₂ (fold-change (FC Infested/Uninfested); genes upregulated are indicated in orange and downregulated in blue) and adjusted p value (*** < 0.001, 0.001 < ** < 0.01, 0.01 < * < 0.05). Maize gene IDs for the DIMBOA pathway were obtained from the maizeGDB database [62].

Figure 7

Principal component analysis (PCA) of the 19,358 genes expressed in WCR. Conditions are represented with colors (replicate 1: red, replicate 2: green and replicate 3: blue) and shapes (circle: 0 dpi, triangle: 1 dpi and square: 5 dpi).

Figure 8

Organization of the 4609 WCR differentially expressed genes (DEGs). (A) Barplot of the number of upregulated (orange) and downregulated (blue) DEGs. (B) UpSet intersection plot of DEGs. Intersections are represented by a line connected to one or more dots. The number of common DEGs are indicated at the top of each bar, and conditions are organized according to the number of DEGs. D, downregulated in cond2; U, upregulated in cond2 when cond1/cond2.