Elucidating early immune signaling pathways underlying chickpea resistance to necrotrophic fungi: a comparative transcriptomic and hormonal analysis

Chickpea is a major protein source in dry and semi-arid regions, but diseases caused by necrotrophic fungi strongly limit yield and the early immune signaling mechanisms remain unclear. This study used one resistant and one susceptible chickpea line inoculated with a dominant Ascochyta isolate and collected leaf samples at 0, 6, 12 and 24 h, combining RNA-seq with quantification of JA, ACC, SA and ABA to compare time-course responses between genotypes. The resistant line showed large-scale transcriptional reprogramming by 12 h with many more up-regulated genes than the susceptible line and strong enrichment in receptor-like kinases, WRKY/ERF transcription factors and cell wall modification pathways. JA and ACC in the resistant line increased rapidly and showed high correlations with key co-expression modules, whereas the susceptible line showed weaker activation and a rise in ABA. The work proposes an early immune signaling framework for chickpea challenged by necrotrophic fungi and identifies a set of candidate hub genes tightly linked to JA/ethylene pathways that can support mechanistic studies and marker-based selection.