Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses

Abstract

The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.

Keywords: Differentially expressed genes; Late blight resistance; Potato; RNAseq; Transcriptome.

Fig. 1

(a) Hypersensitive response (HR) on the leaves of Ando cultivar resistant to P. infestans and (b) Disease symptoms on Arielle susceptible cultivar with expanding sporulating lesion in response to P. infestans.

Fig. 2

Venn diagram of differentially expressed genes (DEGs) between the resistant and susceptible potato cultivars in response to P. infestans infections. (a) DEGs distribution between Arielle at D3 vs Arielle at D0 and Ando at D3 vs Ando at D0 sets. (b) Venn diagram of common and specific significantly up-and down-regulated genes. (c) DEGs distribution among Arielle at D3 vs Arielle at D0, Ando at D3 vs Ando at D0, Ando at D3 vs Arielle at D3, and Ando at D0 vs Arielle at D0 sets. D0 and D3 are before, and 72 h after infection (72 hpi). up: upregulated; down: downregulated.

Fig. 3

Gene ontology (GO) classification of upregulated DEGs in Ando_D3 vs Ando_D0. X-axis, three major functional categories of top 20 GO terms: biological process, molecular function, and cellular component; Y-axis, terms with percentages of DEGs in the major category. The percentage of genes is the ratio of the DEGs number to the background number in a certain process expressed in percentage. D0 and D3 are before and 72 h post-inoculation (72 hpi), respectively.

Fig. 4

Gene ontology (GO) classification of downregulated DEGs in Ando_D3 vs Ando_D0. X-axis, three major functional categories of top 20 GO terms: biological process, molecular function, and cellular component; Y-axis, terms with percentages of DEGs in the major category. The percentage of genes is the ratio of the DEG number to the background number in a certain process expressed in percentage. D0 and D3 are before and 72 h post-inoculation (72 hpi), respectively.

Fig. 5

KEGG pathways assignment to differentially expressed genes (DEGs) in the resistant cultivar Ando for upregulated (a) and downregulated (b) differentially expressed genes compared to the healthy. Dot size and colour refer to the number of genes and the corrected P-value, respectively. The gene ratio is the ratio of the number of DEGs annotated in a given pathway term to the number of all genes annotated in the pathway term. A higher gene ratio indicates greater intensity. The padj value is the corrected P-value and ranges from 0 to 1, and a lower value indicates greater intensity. Only significantly enriched pathways are shown.