Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 Feb 4;26(1):106.
doi: 10.1186/s12864-025-11308-3.

The transcriptional response to yellow and wilt disease, caused by race 6 of Fusarium oxysporum f. sp. Ciceris in two contrasting chickpea cultivars

Aliakbar Faramarzpour  1   2 , Sara Dezhsetan  3 , Hamid Hassaneian Khoshro  4 , Raheleh Mirdar Mansuri  2 , Hamid Reza Pouralibaba  4 , Zahra-Sadat Shobbar  5
Affiliations

The transcriptional response to yellow and wilt disease, caused by race 6 of Fusarium oxysporum f. sp. Ciceris in two contrasting chickpea cultivars

Aliakbar Faramarzpour et al. BMC Genomics. .

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 548 genes (332 upregulated and 216 downregulated) in the resistant genotype (Ana) and 1115 genes (595 upregulated and 520 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 131 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 insights into the molecular mechanism underlying resistance to FW and could be valuable for breeding programs aimed at developing FW-resistant chickpea varieties.

Keywords: Biotic stress; Chickpea; Fusarium wilt (race 6); RNA sequencing.

PubMed Disclaimer

Conflict of interest statement

Declarations. Ethics approval and consent to participate: We declare that the plants used in this study complied with local or national guidelines. All plant materials used in this article are cultivated crop varieties (i.e. two Iranian chickpea cultivars) belonging to the Iranian Dryland Agricultural Research Institute (DARI). According to the rules of this institute, the researchers are permitted to use the plant materials for research purposes. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Venn diagram of the DEGs under Fusarium wilt stress revealed the genes that were either exclusively or commonly differentially expressed in the resistant (Ana) and susceptible (Hashem) cultivars. Up: Upregulated; Down: Downregulated
Fig. 2
Fig. 2
Gene Ontology (GO) classification of differentially expressed genes (DEGs) in the Ana and Hashem cultivars based on three main categories: biological process (BP), molecular function (MF) and cellular component (CC). (A) bubble diagram: upregulated genes, (B) bubble diagram: downregulated genes: The X-axis represents the percentage of genes (%), and the Y-axis represents the GO terms. The color scales indicate the different thresholds for the q-values, and the sizes of the dots represent the number of genes corresponding to each GO term
Fig. 3
Fig. 3
The top eight pathways with the greatest number of genes in the KEGG protein database. The X-axis represents the ratio of genes with significant differential expression (DEGs) involved in the specified KEGG pathway to the total number of DEGs assigned to KEGG pathways in each genotype, and the Y-axis represents the KEGG pathways
Fig. 4
Fig. 4
Validation of twelve candidate genes via qRT‒PCR in root tissue of Ana and Hashem under FW disease stress; Bar graphs illustrate the relative transcript abundance of the selected genes in the chickpea cultivars under different conditions (RNA-seq (blue) and qRT-PCR (light green)). Data points are demonstrated as log2 fold change values
Fig. 5
Fig. 5
Heatmap analysis of DEGs involved in disease resistance pathways with a Q value cutoff of ≤ 0.01 and a − 1 ≤ Log2-fold change ≥ 1 under Fusarium wilt (race 6) stress conditions at 48 hpi in the resistant versus susceptible chickpea cultivars. (A) pathogen sensing, (B) signaling pathways, (C) transcription regulation, (D) cell wall integrity, (E) Transport-related DEGs, (F) metabolism. Blue indicates upregulated expression, and green indicates downregulated expression upon stress. Cluster method and ‌distance method was single and Euclidean, respectively
Fig. 6
Fig. 6
A schematic representation of candidate genes and pathways might be involved in resistance to race 6 of Fusarium wilt in the resistant cultivar (Ana). Up arrow: upregulation; down arrow: downregulation under FW disease stress
See this image and copyright information in PMC

References

    1. Rani A, Devi P, Jha UC, Sharma KD, Siddique KHM, Nayyar H. Developing Climate-Resilient Chickpea Involving Physiological and Molecular Approaches With a Focus on Temperature and Drought Stresses. Front Plant Sci. 2020;10(February):1–29. Available from: 10.3389/fpls.2019.01759. - PMC - PubMed
    1. Wood JA, Grusak MA. Nutritional value of chickpea. Chickpea Breed Manag. 2007;101–42. Available from: 10.1079/9781845932138.005.
    1. Shiade G, Roghie S, Fathi A, Kardoni F, Pandey R, Pessarakli M. Nitrogen contribution in plants: recent agronomic approaches to improve nitrogen use efficiency. J Plant Nutr. 2024;47(2):314–31. Available from: 10.1080/01904167.2023.2278656. Cited 2021 Oct 16.
    1. FAO, FAOSTAT. FAOSTAT. 2021. Available from: https://www.fao.org/faostat.
    1. Hamida D, Gowda VT, Kundu A, Kaur R. Bag. and TK. Effect of culture filtrate containing fusaric acid of Fusarium oxysporum f. sp. ciceris on defence enzymes in chickpea. Indian Phytopathol. 2024;1–9. Available from: 10.1007/s42360-023-00702-0.

Supplementary concepts

LinkOut - more resources