Single-cell transcriptome atlas unveils transcriptional regulation networks of banana root tips in response to Fusarium oxysporum infection

Abstract

Fusarium wilt caused by Fusarium oxysporum (Foc) is one of the most destructive diseases in global banana production. The response of root system to Foc infection through gene expression in multiple cell types is crucial for understanding the disease resistance mechanism in banana. Here, we reported a single-cell transcriptional landscape of banana root tips in response to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) infection. We characterized 10 major cell types from 19 cell clusters. We explored differentiation trajectories of meristematic cells, root cap cells, and pericycle cells through pseudotime analysis, and identified pericycle cell as the dominant root cell type under Foc TR4 infection. Moreover, we identified 11 co-expression regulatory networks, of which eight were significantly associated with Foc TR4 response. Specifically, MaKAN4 was co-expressed with two Zn ²⁺-dependent genes (MaACA7 and MaADH3) in M5 module, which was associated with pericycle cell type and responded to Foc TR4 infection. Further analysis demonstrated that MaKAN4 protein could interact with the promoters of MaACA7 and MaADH3 to promote their expression levels, highlighting a crucial role of MaKAN4 in banana disease resistance by regulating the Zn ²⁺-dependent MaACA7/MaADH3 module. These findings provide a comprehensive view of cell fate determination in banana root tips and highlight novel insights into the regulatory mechanisms of major cell types in response to Foc TR4 infection, laying a useful foundation for developing disease-resistant banana cultivars.

Acknowledgements

This work was supported by the Project of State Key Laboratory of Tropical Crop Breeding (No. SKLTCBQN202512), National Key Laboratory for Tropical Crop Breeding (No. NKLTCB-HZ03, NKLTCB-ZX02, NKLTCB202307, NKLTCBCXTD05), the Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (No. 1630052024002, 1630052023014), the Hainan Provincial Natural Science Foundation of China (No. 325QN444, 323QN282), the National Natural Science Foundation of China (No. 32272675), the Project of Sanya Yazhou Bay Science and Technology City (No. SCKJ-JYRC-2024-80), the Hainan Provincial Science and Technology Talent Innovation Program of China (KJRC2023A04).

We thank Professor Jun Niu for this support in cell type classification. Special thanks to Guangzhou Kidio Biotechnology Co., Ltd. for support with single-cell sequencing.

Author contributions

W.H. J.H.X and Z.H.D. conceived and designed the project. K.S.H. completed a full single cell transcription map. M.Y.L. W.W and D.X.L. finished the molecular biology experiment. X.X.Y, Z.N.X and Y.Y. collected the samples. W.W.T., C.C.L. and J.X.M. performed pseudotime analyses. W.H., Z.H.D. and K.S.H. wrote the manuscript with contributions from all authors.

Data availability

The dataset has been uploaded to National Genomic Data Center (BioProject: PRJCA038648).

Conflict of interests

The authors declare no competing interests.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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