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. 2022 Apr 7;11(8):1008.
doi: 10.3390/plants11081008.

RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars

Saranya Chandrasekar  1 , Purushothaman Natarajan  2   3 , Priyank Hanuman Mhatre  4 , Mahesh Mahajan  5 , Sundararaj Nivitha  6 , Venkatasalam E Palanisamy  4 , Umesh K Reddy  2   7 , Palanisamy Sundararaj  1
Affiliations

RNA-Seq of Cyst Nematode Infestation of Potato (Solanum tuberosum L.): A Comparative Transcriptome Analysis of Resistant and Susceptible Cultivars

Saranya Chandrasekar et al. Plants (Basel). .

Abstract

Potato (Solanum tuberosum L.) is an important food crop worldwide, and potato cyst nematodes (PCNs) are among the most serious pests. The identification of disease resistance genes and molecular markers for PCN infestation can aid in crop improvement research programs against PCN infestation. In the present study, we used high-throughput RNA sequencing to investigate the comprehensive resistance mechanisms induced by PCN infestation in the resistant cultivar Kufri Swarna and the susceptible cultivar Kufri Jyoti. PCN infestation induced 791 differentially expressed genes in resistant cultivar Kufri Swarna, comprising 438 upregulated and 353 downregulated genes. In susceptible cultivar Kufri Jyoti, 2225 differentially expressed genes were induced, comprising 1247 upregulated and 978 downregulated genes. We identified several disease resistance genes (KIN) and transcription factors (WRKY, HMG, and MYB) that were upregulated in resistant Kufri Swarna. The differentially expressed genes from several enriched KEGG pathways, including MAPK signaling, contributed to the disease resistance in Kufri Swarna. Functional network analysis showed that several cell wall biogenesis genes were induced in Kufri Swarna in response to infestation. This is the first study to identify underlying resistance mechanisms against PCN and host interaction in Indian potato varieties.

Keywords: RNA-seq; cyst nematode; differentially expressed genes; disease resistance; potato.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Development of Globodera spp. on susceptible Kufri Jyoti (A) and resistant Kufri Swarna (B) at 55 days after planting in potato-cyst-nematode-infested soil.
Figure 2
Figure 2
(A) MDS plot showing the correlation of expression values among the RNA-seq libraries. (B) Venn diagrams showing differentially expressed genes (DEGs) shared between resistant Kufri Swarna and susceptible Kufri Jyoti.
Figure 3
Figure 3
Summary plot of gene expression values for the cultivars Kufri Swarna and Kufri Jyoti. The red points represent genes with expression significant at p ≥ 0.9.
Figure 4
Figure 4
Significantly enriched KEGG pathways among the (A) upregulated and (B) downregulated DEGs of resistant cultivar Kufri Swarna. The color and size of the dots represent the different functionally enriched clusters and the number of DEGs mapped to the indicated pathways, respectively.
Figure 5
Figure 5
Significantly enriched KEGG pathways among the (A) upregulated and (B) downregulated DEGs of susceptible cultivar Kufri Jyoti. The color and size of the dots represent the different functionally enriched clusters and the number of DEGs mapped to the indicated pathways, respectively.
Figure 6
Figure 6
MapMan visualization of DEGs mapped to the biotic stress pathway in resistant Kufri Swarna (A) and susceptible Kufri Jyoti (B) in response to PCN infestation. DEGs are binned to MapMan functional categories and values are represented as log2 fold change values. Red represents upregulated DEGs and green represents downregulated DEGs. R, response; PR, pathogen-related.
Figure 7
Figure 7
Heatmap showing the expression of DEGs for transcription factors (A) and plant disease resistance genes (B) in resistant Kufri Swarna and corresponding expression in susceptible Kufri Jyoti in response to PCN infestation. Plant disease-resistance gene classes are included in the gene name. Gene expression values are presented as log2 fold change.
Figure 8
Figure 8
Top 20 terms under the Gene Ontology categories of biological process (BP), molecular function (MF), and cellular components (CC) enriched among the DEGs upregulated in resistant Kufri Swarna.
Figure 9
Figure 9
Functional network analysis of DEGs in resistant Kufri Swarna showing the functionally grouped terms with nodes linked based on their kappa score (≥0.3); only the label of the most significant term per group is shown. The node size represents the enrichment significance of the term.
Figure 10
Figure 10
Validation of RNA-seq results with qRT-PCR findings. SC, control susceptible cultivar; ST, treated susceptible cultivar; RC, control resistant cultivar; RT, treated resistant cultivar.
See this image and copyright information in PMC

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