Supplementary Figures S1–S11. Additional analyses and visualizations, Supplementary Tables S1–S4. Supporting data for RNA isolation and enrichment analyses

Developing resistant chickpea varieties is crucial for combating Fusarium wilt, caused by Fusarium oxysporum, a disease leading to chickpea yield loss. Our transcriptome analysis revealed gene expression changes in resistant and sensitive genotypes of C. arietinum L. and C. reticulatum chickpeas upon Foc0 inoculation. RNA sequencing revealed that sensitive genotypes exhibited a significantly higher number of differential expressions. Genes for defense were activated in all plants upon infection. However, resistant plants specifically upregulate genes acting outside the cell while downregulating internal functions, unlike sensitive plants. Sensitive chickpea plants showed a preference for specific isoforms of 6 genes compared to resistant ones. These genes encode E3 ubiquitin-protein ligase, plastid-lipid-associated protein 11, callose synthase 5-like, enoyl-acyl-carrier-protein reductase, and cell division cycle-associated protein 7-like. Notably, a gene linked to leaf rust resistance (LOC101515334) also exhibited isoform switching. These findings shed light on chickpea Fusarium wilt resistance and open doors for breeding-resistant varieties.