Abstract
Potato cyst nematodes (PCNs) are major pests worldwide that affect potato production. The molecular changes happening in the roots upon PCN infection are still unknown. Identification of transcripts and genes governing PCN resistance will help in the development of resistant varieties. Hence, differential gene expression of compatible (Kufri Jyoti) and incompatible (JEX/A-267) potato genotypes was studied before (0 DAI) and after (10 DAI) inoculation of Globodera rostochiensis J2s through RNA sequencing (RNA-Seq). Total sequencing reads generated ranged between 33 and 37 million per sample, with a read mapping of 48–84% to the potato reference genome. In the infected roots of the resistant genotype JEX/A-267, 516 genes were downregulated, and 566 were upregulated. In comparison, in the susceptible genotype Kufri Jyoti, 316 and 554 genes were downregulated and upregulated, respectively. Genes encoding cell wall proteins, zinc finger protein, WRKY transcription factors, MYB transcription factors, disease resistance proteins, and pathogenesis-related proteins were found to be majorly involved in the incompatible reaction after PCN infection in the resistant genotype, JEX/A-267. Furthermore, RNA-Seq results were validated through quantitative real-time PCR (qRT-PCR), and it was observed that ATP, FLAVO, CYTO, and GP genes were upregulated at 5 DAI, which was subsequently downregulated at 10 DAI. The genes encoding ATP, FLAVO, LBR, and GP were present in > 1.5 fold before infection in JEX-A/267 and upregulated 7.9- to 27.6-fold after 5 DAI; subsequently, most of these genes were downregulated to 0.9- to 2.8-fold, except LBR, which was again upregulated to 44.4-fold at 10 DAI.
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All datasets analyzed in this study are included in the manuscript. Additional data is available in the supplementary data files.
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Acknowledgements
We thank the Director, ICAR-CPRI, Shimla, for facilitating the study.
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We acknowledge the financial help from the Centre for Agricultural Bioinformatics CABin project (1006448).
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Conceptualized and designed the experiments: SS, VB and AB. Performed the experiments: AB, VB, SS, BD, AK, and BS. Phenotyping: EPV, PHM, AKS and SSh. Genotyping: SS, VB, AB, and SuS. Contributed material/facility: SSh, AKS, and VK. Analyzed the data: SS, SR, and TT. Wrote the manuscript: AB and SS. All authors read and approved the manuscript.
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ESM 1
Table S1. Differentially expressed genes (DEGs) and their functional annotation in resistant genotype after inoculation (XLSX 2179 kb)
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Table S2. Differentially expressed genes (DEGs) and their functional annotation in susceptible genotype after inoculation (XLSX 2169 kb)
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Table S3. Gene Ontology (GO) of upregulated genes in the resistant genotype (XLSX 10 kb)
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Table S4. Gene Ontology (GO) of downregulated genes in the resistant genotype (XLSX 10 kb)
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Table S5. Gene Ontology (GO) of upregulated genes in the susceptible genotype (XLSX 10 kb)
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Table S6. Gene Ontology (GO) of downregulated genes in the susceptible genotype (XLSX 10 kb)
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Fig. S1 Heat map of differentially expressed genes (DEGs) in control KJC and JC samples (JPG 324 kb)
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Fig. S2 Heat map of differentially expressed genes (DEGs) in inoculated KJT and JT samples (JPG 400 kb)
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Bairwa, A., Sood, S., Bhardwaj, V. et al. Identification of genes governing resistance to PCN (Globodera rostochiensis) through transcriptome analysis in Solanum tuberosum. Funct Integr Genomics 23, 242 (2023). https://doi.org/10.1007/s10142-023-01164-3
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DOI: https://doi.org/10.1007/s10142-023-01164-3