Unraveling the transcriptional response mechanisms to yellow and wilt disease, caused by race 6 of Fusarium oxysporum f.sp. ciceris in two contrasting chickpea cultivars

Abstract

Background Chickpea (Cicer arietinum L.) ranks as the third most crucial grain legume worldwide. Fusarium wilt (Fusarium oxysporum f. sp. ciceri (Foc)) is a devastating fungal disease that prevents the maximum potential for chickpea production. Results To identify genes and pathways involved in resistance to race 6 of Foc, this study utilized transcriptome sequencing of two chickpea cultivars: resistant (Ana) and susceptible (Hashem) to Foc race 6. Illumina sequencing of the root samples yielded 133.5 million raw reads, with about 90% of the clean reads mapped to the chickpea reference genome. The analysis revealed that 518 genes (317 upregulated and 201 downregulated) in the resistant genotype (Ana) and 1063 genes (587 upregulated and 476 downregulated) in the susceptible genotype (Hashem) were differentially expressed under Fusarium wilt (FW) disease stress caused by Foc race 6. The expression patterns of some differentially expressed genes (DEGs) were validated using quantitative real-time PCR. A total of 127 genes were exclusively upregulated under FW stress in the resistant cultivar, including several genes involved in sensing (e.g., CaNLR-RPM1, CaLYK5-RLK, CaPR5-RLK, CaLRR-RLK, and CaRLP-EIX2), signaling (e.g., CaPP7, CaEPS1, CaSTY13, and CaPR-1), transcription regulation (e.g., CaMYBs, CaGLK, CaERFs, CaZAT11-like, and CaNAC6) and cell wall integrity (e.g., CaPGI2-like, CaEXLs, CaCSLD and CaCYP73A100-like). Conclusions The achieved results could provide significant insights into the molecular mechanism underlying resistance to FW and could be valuable for breeding programs aimed at developing FW-resistant chickpea varieties.