Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection

Cao, Weilin; Gan, Li‐Ming; Shang, Kaijie; Wang, Chenchen; Song, Yunzhi; Liu, Hongmei; Zhou, Shumei; Zhu, Changxiang

doi:10.1007/s00425-020-03471-6

Cited by 16 publications

(16 citation statements)

References 65 publications

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“…Additionally, WGCNA is a reliable and effective method for the analysis of gene functions and has been successfully used in studying plant responses during pathogen infections. For example, the key genes that responded to Phytophthora infestans, Ralstonia solanacearum, and potato virus Y infections in potato were obtained using WGCNA (Cao et al, 2020). Therefore, transcriptome analysis and WGCNA were carried out to identify putative genes related to Fusarium wilt resistance using two mung bean lines in our study.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

Chang

Sun

et al. 2021

Front. Plant Sci.

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Fusarium wilt is a destructive soil-borne disease that threatens the production of mung bean. Mung bean lines Zheng8-4 and Zheng8-20 show high resistance and high susceptibility to Fusarium wilt, respectively. Transcriptome analysis was carried out to identify candidate genes involved in Fusarium wilt resistance using Zheng8-4 and Zheng8-20 at 0, 0.5, 1, 2, and 4 days post inoculation (dpi). Differential expression analysis showed that 3,254 genes responded to pathogen infection and were differentially expressed in the resistant and susceptible lines. Weighted gene co-expression network analysis (WGCNA) was also performed to identify five modules highly correlated with Fusarium wilt resistance, in which 453 differentially expressed genes (DEGs) were considered likely to be involved in Fusarium wilt resistance. Among these DEGs, we found 24 genes encoding resistance (R) proteins, 22 encoding protein kinases, 20 belonging to transcription factor families, 34 encoding proteins with oxidoreductase activity, 17 involved in stimulation/stress responses, and 54 annotated to pathogen resistance-related pathways. Finally, 27 annotated genes were further selected as candidate genes of Fusarium wilt resistance in mung bean. This study identifies novel potential resistance-related genes against Fusarium wilt and provides a theoretical basis for further investigation of Fusarium wilt resistance in mung bean breeding.

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Section: Discussionmentioning

confidence: 99%

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

Chang

Sun

et al. 2021

Front. Plant Sci.

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“…Comparison of syntenic genomic regions is a promising way to locate candidate R genes in the genomes of various crops [14,15]. Transcriptomic analysis is critically important for the reconstruction of molecular mechanisms of resistance to various pathogens (e.g., [16][17][18]). An integration of genomic and transcriptomic data may be useful for resolving complicated cases.…”

Section: Introductionmentioning

confidence: 99%

NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species

et al. 2021

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The long history of potato breeding includes the numerous introgressions of resistance genes from many wild species of South and Central America as well as from cultivated species into the breeding genepool. Most R genes belong to the NLR family with nucleotide-binding site–leucine-rich repeat. The aim of this research concerns an evaluation of NLR genes expression in transcriptomes of three potato cultivars (Evraziya, Siverskij, Sudarynya), which combine genetic material from wild and cultivated potato species, and each bears intragenic markers of RB/Rpi-blb1/Rpi-sto1 genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the Phytophthora infestans inoculation. The induction of RB/Rpi-blb1/Rpi-sto1 transcript after 24 h of inoculation was detected in the resistant cultivars Siverskij and Sudarynya but not in susceptible cv. Evraziya. This demonstrates the importance of transcriptomic assay for understanding the results of marker-assisted selection and phenotyping. Interestingly, assembling the transcriptomes de novo and analysis with NLR-parser tool revealed significant fractions of novel NLR genes with no homology to the reference genome from 103 (cv. Siverskij) to 160 (S. stoloniferum, 30514/15). Comparison of novel NLRs demonstrated a relatively small intersection between the genotypes that coincided with their complex pedigrees with several interspecific hybridization events. These novel NLRs may facilitate the discovery of new efficient R genes.

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“…In potato, global transcriptome analyses reveal comparable molecular signatures in the early response to either the oomycete Phytophthora infestans, the bacterium Ralstonia solanacearum or Potato virus Y infection. In addition, a weighted gene co-expression network analysis identified, amongst others, chitinases to regulate plant immune responses [19]. Several transcripts whose encoded proteins are involved in chitin signal perception and transduction were found to be induced.…”

Section: Biotic Stress Response Signallingmentioning

confidence: 99%

Transcriptional Changes in Potato Sprouts upon Interaction with Rhizoctonia solani Indicate Pathogen-Induced Interference in the Defence Pathways of Potato

Zrenner

Verwaaijen

Genzel

et al. 2021

IJMS

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Rhizoctonia solani is the causer of black scurf disease on potatoes and is responsible for high economical losses in global agriculture. In order to increase the limited knowledge of the plants’ molecular response to this pathogen, we inoculated potatoes with R. solani AG3-PT isolate Ben3 and carried out RNA sequencing with total RNA extracted from potato sprouts at three and eight days post inoculation (dpi). In this dual RNA-sequencing experiment, the necrotrophic lifestyle of R. solani AG3-PT during early phases of interaction with its host has already been characterised. Here the potato plants’ comprehensive transcriptional response to inoculation with R. solani AG3 was evaluated for the first time based on significantly different expressed plant genes extracted with DESeq analysis. Overall, 1640 genes were differentially expressed, comparing control (−Rs) and with R. solani AG3-PT isolate Ben3 inoculated plants (+Rs). Genes involved in the production of anti-fungal proteins and secondary metabolites with antifungal properties were significantly up regulated upon inoculation with R. solani. Gene ontology (GO) terms involved in the regulation of hormone levels (i.e., ethylene (ET) and jasmonic acid (JA) at 3 dpi and salicylic acid (SA) and JA response pathways at 8 dpi) were significantly enriched. Contrastingly, the GO term “response to abiotic stimulus” was down regulated at both time points analysed. These results may support future breeding efforts toward the development of cultivars with higher resistance level to black scurf disease or the development of new control strategies.

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Global transcriptome analyses reveal the molecular signatures in the early response of potato (Solanum tuberosum L.) to Phytophthora infestans, Ralstonia solanacearum, and Potato virus Y infection

Cited by 16 publications

References 65 publications

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species

Transcriptional Changes in Potato Sprouts upon Interaction with Rhizoctonia solani Indicate Pathogen-Induced Interference in the Defence Pathways of Potato

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