Comparative transcriptome analysis reveals candidate genes and defence pathways associated with resistance to potato cyst nematodes in potato (Solanum tuberosum)

Globodera rostochiensis and Globodera pallida are two nematode species responsible for are potato cyst nematode (PCN) that significantly reduce potato (Solanum tuberosum) productivity worldwide. To elucidate the molecular basis of PCN resistance, we compared transcriptomic responses of the highly resistant potato breeding clone SM/11-120 with the susceptible cultivar Kufri Jyoti following simultaneous infection with both PCN species. Nematode penetration assays showed that SM/11-120 completely restricted nematode invasion up to 7 days post-inoculation (dpi), whereas Kufri Jyoti was susceptible to nematode penetration within 24 h post-inoculation (hpi) and supported juvenile development at 72 hpi and 7 dpi. RNA-sequencing (RNA-Seq) generated 18–27 million high-quality paired-end reads per library, of which 51.6–68.3% mapped uniquely to the potato reference genome. Comparative transcriptome analysis identified 724, 795, 694, and 899 differentially expressed genes (DEGs) between SM/11-120 and Kufri Jyoti at 0 hpi, 24 hpi, 72 hpi, and 7 dpi, respectively. The resistant genotype exhibited enhanced expression of genes involved in immune signalling (NRC1, NBS-LRR), transcriptional regulation (WRKY, MYB), calcium signalling, pathogenesis-related proteins (PR1), hormone and defence metabolism (ACO1, geraniol 10-hydroxylase), and cell wall reinforcement (HRGP, XTH3, pectinesterase, β-expansin). Gene Ontology analysis revealed stronger enrichment of stress response, biological regulation, nitrogen compound metabolism, and response to biotic stimulus in SM/11-120 than in Kufri Jyoti. Expression patterns of selected defence-related genes were validated by quantitative reverse transcription (qRT)-PCR, confirming their rapid and sustained induction in the resistant genotype.