Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Karma L Bhutia; Mahtab Ahmad; Anima Kisku; R A Sudhan; Nangsol D Bhutia; V K Sharma; Bishun Deo Prasad; Mahendar Thudi; Oliver Obročník; Viliam Bárek; Marian Brestic; Milan Skalicky; Ahmed Gaber; Akbar Hossain

doi:10.3389/fmicb.2023.1265265

Shoot transcriptome revealed widespread differential expression and potential molecular mechanisms of chickpea (Cicer arietinum L.) against Fusarium wilt

Front Microbiol. 2024 Feb 1:14:1265265. doi: 10.3389/fmicb.2023.1265265. eCollection 2023.

Authors

Affiliations

¹ Department of Agricultural Biotechnology and Molecular Biology, CBS&H, Dr. Rajendra Prasad Central Agricultural University, Pusa, Bihar, India.
² College of Horticulture and Forestry, Central Agricultural University (Imphal), Pasighat, Arunachal Pradesh, India.
³ Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Nitra, Slovakia.
⁴ Institute of Plant and Environmental Sciences, Slovak University of Agriculture, Nitra, Slovakia.
⁵ Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia.
⁶ Department of Biology, College of Science, Taif University, Taif, Saudi Arabia.
⁷ Division of Soil Science, Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh.

Abstract

Introduction: The yield of chickpea is severely hampered by infection wilt caused by several races of Fusarium oxysporum f. sp. ciceris (Foc).

Methods: To understand the underlying molecular mechanisms of resistance against Foc4 Fusarium wilt, RNA sequencing-based shoot transcriptome data of two contrasting chickpea genotypes, namely KWR 108 (resistant) and GL 13001 (susceptible), were generated and analyzed.

Results and discussion: The shoot transcriptome data showed 1,103 and 1,221 significant DEGs in chickpea genotypes KWR 108 and GL 13001, respectively. Among these, 495 and 608 genes were significantly down and up-regulated in genotypes KWR 108, and 427 and 794 genes were significantly down and up-regulated in genotype GL 13001. The gene ontology (GO) analysis of significant DEGs was performed and the GO of the top 50 DEGs in two contrasting chickpea genotypes showed the highest cellular components as membrane and nucleus, and molecular functions including nucleotide binding, metal ion binding, transferase, kinase, and oxidoreductase activity involved in biological processes such as phosphorylation, oxidation-reduction, cell redox homeostasis process, and DNA repair. Compared to the susceptible genotype which showed significant up-regulation of genes involved in processes like DNA repair, the significantly up-regulated DEGs of the resistant genotypes were involved in processes like energy metabolism and environmental adaptation, particularly host-pathogen interaction. This indicates an efficient utilization of environmental adaptation pathways, energy homeostasis, and stable DNA molecules as the strategy to cope with Fusarium wilt infection in chickpea. The findings of the study will be useful in targeting the genes in designing gene-based markers for association mapping with the traits of interest in chickpea under Fusarium wilt which could be efficiently utilized in marker-assisted breeding of chickpea, particularly against Foc4 Fusarium wilt.

Keywords: Fusarium wilt; RNA sequencing; chickpea; energy metabolism; environmental adaptation; transcriptome.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This experiment was funded by the Science and Engineering Research Board (SERB), DST-Government of India (Project Id No. EEQ/2020/000535). The study was also financially supported by the Slovak Research and Development Agency under contract no. APVV-15-0562, APVV-20-0071 and Science grant agency under contract no. VEGA-1/0300/22. The study received funding from the Deanship of Scientific Research, Taif University.