Molecular insights into Solanum sisymbriifolium's resistance against Globodera pallida via RNA-seq

Abstract

Background: The presence of potato cyst nematodes (PCN) causes a significant risk to potato crops globally, leading to reduced yields and economic losses. While the plant Solanum sisymbriifolium is known for its resistance to PCN and can be used as a trap crop, the molecular mechanisms behind this resistance remain poorly understood. In this study, genes differentially expressed were identified in control and infected plants during the early stages of the S. sisymbriifolium - G. pallida interaction.

Results: Gene expression profiles were characterized for two S. sisymbriifolium cultivars, Melody and Sis6001, uninfected and infected by G. pallida. The comparative transcriptome analysis revealed a total of 4,087 and 2,043 differentially expressed genes (DEGs) in response to nematode infection in the cultivars Melody and Sis6001, respectively. Gene ontology (GO) enrichment analysis provided insights into the response of the plant to nematode infection, indicating an activation of the plant metabolism, oxidative stress leading to defence mechanism activation, and modification of the plant cell wall. Genes associated with the jasmonic and salicylic acid pathways were also found to be differentially expressed, suggesting their involvement in the plant's defence response. In addition, the analysis of NBS-LRR domain-containing transcripts that play an important role in hypersensitive response and programmed cell death led to the identification of ten transcripts that had no annotations from the databases, with emphasis on TRINITY_DN52667_C1_G1, found to be upregulated in both cultivars.

Conclusions: These findings represent an important step towards understanding the molecular basis underlying plant resistance to nematodes and facilitating the development of more effective control strategies against PCN.

Keywords: Globodera pallida; Solanum sisymbriifolium; Gene expression; NBS-LRR; RNA-seq.

Fig. 1

Differentially expressed genes (DEGs) in infected Solanum sisymbriifolium cultivars Melody and Sis6001 compared to uninfected plants. A. Number of DEG (Fold change ≥ 2 or ≤ -2 and p-value ≤ 0.05). Bars represent the total number of up (red) and downregulated (blue) genes compared to the respective control. B. Venn diagram representing exclusive and shared DEG between the two cultivars of S. sisymbriifolium after infection by Globodera pallida. C-D. Volcano plot highlighting genes expressed differentially between control and inoculated plants, S. sisymbriifolium cv. Melody (C) and cv. Sis6001 (D). Genes are colored if their p-value ≤ 0.05) and have a log fold change |FC| ≥ 2, red if they are upregulated, and blue if they are downregulated

Fig. 2

Heatmap of the top 1000 significantly DEG in control (Ct) and infected (Gp) S. sisymbriifolium cv. Melody (A) and cv. Sis6001 (B) plants. The expression profile of the three replicas is presented. Expression level is color patterned, the brightest red indicates the most upregulated genes and the brightest green the most downregulated genes in the inoculated samples relative to their respective controls

Fig. 3

Enriched Gene Ontology (GO) terms of S. sisymbriifolium cvs. Melody and Sis6001 transcriptome during the infection with G. pallida, analysed through Gene set enrichment (GSEA). BP – Biological Processes, CC – Cellular Components, MF – Molecular Function

Fig. 4

Top 10 terms under the Gene Ontology categories of biological processes (BP), cellular components (CC) and molecular function (MF) enriched among the upregulated genes in S. sisymbriifolium cv. Melody transcriptome during the infection with G. pallida, resulting from the over-representation analysis (ORA)

Fig. 5

Enriched terms under the Gene Ontology categories of biological processes (BP) and cellular components (CC) among the downregulated genes in S. sisymbriifolium cv. Melody transcriptome during the infection with G. pallida, resulting from the over-representation analysis (ORA)

Fig. 6

Enriched terms under the Gene Ontology categories of biological processes (BP), cellular components (CC) and molecular function (MF) among the upregulated genes in S. sisymbriifolium cv. Sis6001 transcriptome during the infection with G. pallida

Fig. 7

RT-qPCR validation of S. sisymbriifolium cv. Melody (A) and cv. Sis6001 (B), Ct – Control plants, Gp – Plants infected with G. pallida. The Y-axis indicates the normalized expression patterns based on RT-qPCR, transformed by the mean relative quantities (RQ). Y-axis break between RQ value of 2.5-5 (A) and 5–15 (B). Error bars indicate SD. The calculation of RQ was controlled with non-infected plants