Transcriptomic changes induced by applications of a commercial extract of Ascophyllum nodosum on tomato plants

Abstract

Extracts of Ascophyllum nodosum are commonly used as commercial biostimulants in crop production. To further understand the seaweed extract-induced phenomena in plants, a transcriptomic study was conducted. RNA-seq differential gene expression analysis of tomato plants treated with a commercial A. nodosum extract formulation (Stimplex) revealed the up-regulation of 635 and down-regulation of 456 genes. Ontology enrichment analysis showed three gene categories were augmented, including biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed that the extract had a strong influence on the expression of genes involved in carbon fixation, secondary metabolism, MAPK-signalling, plant hormone signal transduction, glutathione metabolism, phenylpropanoid and stilbenoid metabolism, and plant-pathogen interactions. qRT-PCR validation analysis using 15 genes established a strong correlation with the RNA sequencing results. The activities of defence enzymes were also significantly enhanced by seaweed extract treatment. Furthermore, AN-SWE treated tomato plants had significantly higher chlorophyll and growth hormone content and showed improved plant growth parameters and nutrient profiles than the control. It is postulated that seaweed extract-induced gene regulation was responsible for favourable plant responses that enabled better growth and tolerance to stress conditions. This study provides evidence at the transcriptomic level for the positive effects of foliar application of the Ascophyllum nodosum extract (Stimplex) observed in treated tomato plants.

Figure 1

Volcano-plot showing significantly different differentially expressed genes in tomato plants treated with AN-SWE. Genes were considered significantly up-regulated or down-regulated if the corresponding transcript had a log FC of ≥ + 2 and ≤ − 2 respectively and a corrected p-value and FDR of < 0.05.

Figure 2

Gene ontologies for the top 10 enriched factors for Cellular Component (CC), Molecular Function (MF), and Biological Process (BP).

Figure 3

Significantly different enriched KEGG pathways in AN-SWE treated tomato plants compared to control tomato plants. The enriched ratio refers to the ratio of observed differentially expressed genes vs. the total number of genes in this KEGG pathway category for the tomato—Solanum lycopersicum reference genome where all genes had a corrected p-value of < 0.05. The picture was created using KOBAS 2.0.

Figure 4

Visual representation of the key impacts of AN-SWE on the tomato transcriptome. The picture was created with BioRender.com.

Figure 5

Interactive plot showing the relationship between enriched pathways. Two pathways (nodes) are connected if they share 20% or more genes. Darker nodes are more significantly enriched gene sets. Bigger nodes represent larger gene sets. Thicker edges represent more overlapped genes.

Figure 6

Correlation analysis of selected DEGs compared to the FC values from the qPCR independent assay with the representative R² value.

Figure 7

Effect of treatment with AN-SWE on plant defence enzyme activities in tomato plants. β-1,3 glucanase (GLU), peroxidase (POD), phenylalanine ammonia lyase (PAL), chitinase (CHI) and polyphenol oxidase (PPO). The data represents the mean of three plants per treatment that were analysed for significance by the Student’s t-test. Horizontal bars signify one standard deviation and “*” represents significantly different (p < 0.05) values of AN-SWE treated plants, compared to control plants.

Figure 8

Effect of AN-SWE in tomato plants on phytohormone (auxin, cytokinin and gibberellin) levels in leaf tissue (DW). The data represents the mean of duplicate plants per treatment ± SD and was analysed for significance using the Student’s t-test where p < 0.05.