Integrated Transcriptome and Metabolome Analysis to Identify Sugarcane Gene Defense against Fall Armyworm (Spodoptera frugiperda) Herbivory

Abstract

Sugarcane is the most important sugar crop, contributing ≥80% to total sugar production around the world. Spodoptera frugiperda is one of the main pests of sugarcane, potentially causing severe yield and sugar loss. The identification of key defense factors against S. frugiperda herbivory can provide targets for improving sugarcane resistance to insect pests by molecular breeding. In this work, we used one of the main sugarcane pests, S. frugiperda, as the tested insect to attack sugarcane. Integrated transcriptome and metabolomic analyses were performed to explore the changes in gene expression and metabolic processes that occurred in sugarcane leaf after continuous herbivory by S. frugiperda larvae for 72 h. The transcriptome analysis demonstrated that sugarcane pest herbivory enhanced several herbivory-induced responses, including carbohydrate metabolism, secondary metabolites and amino acid metabolism, plant hormone signaling transduction, pathogen responses, and transcription factors. Further metabolome analysis verified the inducement of specific metabolites of amino acids and secondary metabolites by insect herbivory. Finally, association analysis of the transcriptome and metabolome by the Pearson correlation coefficient method brought into focus the target defense genes against insect herbivory in sugarcane. These genes include amidase and lipoxygenase in amino acid metabolism, peroxidase in phenylpropanoid biosynthesis, and pathogenesis-related protein 1 in plant hormone signal transduction. A putative regulatory model was proposed to illustrate the sugarcane defense mechanism against insect attack. This work will accelerate the dissection of the mechanism underlying insect herbivory in sugarcane and provide targets for improving sugarcane variety resistance to insect herbivory by molecular breeding.

Keywords: RNA sequencing; Spodoptera frugiperda; metabolism; plant defense; sugarcane.

Figure 1

Overview of the transcriptomic analysis. (A) BUSCO analysis of the assembled transcripts. Light blue represents complete (C) and single copy (S); deep blue represents complete (C) and duplicated (D); yellow represents fragment (F); red represents missing (M). Trinity.fasta is the sequence assembled by the software Trinity. Cluster.fasta and unigene.fasta were obtained from trinity.fasta by removing the redundant sequence. (B) A Venn diagram of the genes annotated in different databases.

Figure 2

Function enrichment analysis of DEGs. (A) KEGG pathway enrichment of DEGs. Color indicates the degree of enrichment. Red represents stronger enrichment, green represents strong enrichment, blue represents enrichment. Gene ratio means the ratio of differential abundant proteins in this pathway accounting for total enriched proteins. (B) GO terms of DEGs.

Figure 3

Gene expression levels from qPCR and RNA-seq. Orange columns represent the qPCR results, and blue columns represent the RNA-seq results. The y-axis represents the fold change in the relative expression level of the gene between the treated sample and control (HS vs. CS).

Figure 4

PLS-DA dispersion point diagrams and sorting verification diagrams: (A) PLS-DA dispersion point diagram (negative ion mode); (B) PLS-DA sorting verification diagram (negative ion mode); (C) PLS-DA dispersion point diagram (positive ion mode); (D) PLS-DA sorting verification diagram (positive ion mode).

Figure 5

KEGG enrichment of the differential metabolites. (A) Metabolites identified in negative mode. (B) Metabolites identified in positive mode. The size of the dots corresponds to the number of DEGs in each pathway. The color displays the significance of enrichment. Ratio means the number of metabolites in this pathway with regard to the total enriched metabolite number.

Figure 6

Putative model of sugarcane’s response to Spodoptera frugiperda herbivory. The names in light-type letters are metabolite compounds. The DEGs are exhibited in bold type with the arrows.