Genome-wide association study and functional validation of CsAGD6 conferring drought tolerance in tea plant

Abstract

Drought stress significantly threatens tea production and quality worldwide. To elucidate the genetic basis of drought tolerance in tea plant, we evaluated 11 physiological traits across 115 diverse tea accessions under drought conditions. A comprehensive drought resistance index (D-value) was constructed through principal component analysis and fuzzy membership function. Genome-wide association studies identified 67 significant SNPs and pinpointed four candidate genes associated with drought-responsive traits. Integrated transcriptome and qRT-PCR analyses revealed that three genes, including CsAGD6, were significantly upregulated under drought stress. Functional assays confirmed that CsAGD6, encoding a nucleus-localized ARF-GAP protein, positively regulates drought tolerance by modulating photosynthetic efficiency and membrane stability. Haplotype analysis identified favorable alleles Hap-P1 and Hap-C1 in the promoter and coding regions of CsAGD6, respectively. Moreover, an SNP-kompetitive allele-specific PCR marker targeting chr10:206216541 (C/T) was developed and validated in 104 accessions, demonstrating high efficacy for early selection of drought-tolerant genotypes. This study provides novel insights into the molecular mechanisms of drought tolerance in tea plant and offers valuable genetic resources and tools for marker-assisted breeding.

Acknowledgements

This work was funded by the National Natural Science Foundation of China (No. 32272767).

Author contributions

J.Y.: Formal Analysis, Data curation, and Writing—Review & Editing. S.H.: Data curation, Software, and Writing—Review & Editing. S.L.: Software and Methodology. Y.W.: Conceptualization and Supervision. H.W. and X.L.: Validation and Investigation. K.F., J.H., J.S., L.S., and S.D.: Supervision. Z.D.: Supervision, Guidance, and Support. W.Q.: Project administration, Funding Acquisition, Supervision, and Writing—review & editing.

Data availability

The transcriptome data and original sequencing of 107 tea accessions were deposited in the NCBI Sequence Read Archive database under accession numbers PRJNA1297129, PRJNA1304154 and PRJNA1314853. The tea reference genome ‘Lucha 6’, was deposited in the National Genomics Data Centre database (https://ngdc.cncb.ac.cn/gwh) under the BioProject is PRJCA049695 and accession number GWHGZIG00000000.1. The data that support the results are provided in this paper and its supplementary files.

Conflicts of interest statement

The authors declare no conflict of interest.

Supplementary material

Supplementary material is available at Horticulture Research online.

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