Mapping garlic’s cellular battle: How viruses shape clove development
image: Cell-specific expression of garlic virus genes. (a) UMAP shows the expression of genes from six viruses in swelling cloves. GarVAgp6, QY65.gp6, X660.gp6, GvEgp8, GarVXgp6, and GarLVgp6 were used to estimate the activity of garlic viruses A, B, D, E, and X, and the shallot latent virus, respectively. (b) Violin plots showed the expression of virus genes X660-GP6 (Garlic viruses D), GvEgp8 (Garlic viruses E), GarVXgp6 (Garlic viruses X), and QY65-gp6 (Garlic viruses B). (c), Relative expression level for genes of garlic virus A (GarVAgp6), D (X660.gp6), and X (GarVXgp6) in six stages of clove swelling growth. The bulb figures show the state of clove growth at the beginning (S1) and finishing sampling (S6). (d) Relatively expressed levels of GarVAgp6 (GarA), X660.gp6 (GarD), and GarVXgp6 (GarX) in virus-accumulated (CO) and virus-free garlic. The virus-free garlic used is produced by a culture in vitro of young cloves. The y axis indicates a relative expression level. Image link: https://academic.oup.com/view-large/figure/507917944/uhae365f3.tif
Credit: Horticulture Research
Garlic propagation depends on vegetative reproduction, leading to the accumulation of multiple viruses such as garlic viruses A, B, D, E, and X. These infections cause reduced bulb size and compromised quality, yet the molecular mechanisms behind virus–host interactions remain elusive. Previous transcriptomic or histological studies could not distinguish the responses of different cell types, masking the spatial dynamics of viral invasion. Single-cell RNA sequencing (scRNA-seq) offers a transformative approach to dissect plant defense at single-cell resolution, enabling the discovery of cell-type-specific immune mechanisms. Due to these challenges, it is necessary to conduct an in-depth investigation into garlic’s cellular differentiation and viral infection dynamics.
Researchers from Yangzhou University, in collaboration with the Chinese Academy of Agricultural Sciences and Shandong Dongyun Research Center of Garlic Engineering, published (DOI: 10.1093/hr/uhae365) their findings in Horticulture Research on April 1, 2025. Using single-cell RNA sequencing, the team generated a comprehensive cellular map of garlic cloves and tracked viral activity within each cell type. The study reveals how garlic’s meristem cells resist viral intrusion while differentiated cells become vulnerable, identifying glutathione metabolism and RNA-silencing genes as core components of garlic’s antiviral defense strategy.
The team performed scRNA-seq on garlic cloves collected from three developmental stages, yielding 19,681 single-cell profiles classified into 11 clusters. Cell trajectory analysis revealed that clove cell differentiation begins from meristematic cells (clusters C7 and C11) and proceeds along two developmental branches, culminating in mature parenchyma cells. Viral gene mapping uncovered the presence of six major viruses, with minimal activity in meristem cells but high expression in mature clove tissues. Two infection patterns emerged—some viruses such as garlic virus D increased in activity with development, while others like virus A and X declined in mature cloves. Co-expression analysis identified 2,060 garlic genes linked to viral genes, including glutathione synthase and reductase genes that were upregulated in infected tissue. Metabolomic profiling further showed a decline in glutathione and its derivatives, implying oxidative imbalance during infection. Additionally, several RNA-silencing-related genes (AGO, DCL, RDR) were found to be co-expressed with viral genes, suggesting multi-layered antiviral mechanisms at the cellular level.
“Garlic’s clonal propagation makes it uniquely vulnerable to cumulative viral infection,” said Prof. Touming Liu, corresponding author of the study. “By dissecting the infection landscape at single-cell resolution, we now understand that meristem cells serve as protected zones against viral invasion, while differentiated cells become active sites of infection. This cellular-level insight not only deepens our understanding of plant antiviral immunity but also opens new avenues for virus-free propagation strategies through meristem tissue culture.”
This study provides a powerful single-cell framework for understanding virus-host interactions in clonally propagated crops. The discovery that viruses remain inactive in meristem cells supports the development of efficient virus-elimination methods through meristem culture or in vitro young clove regeneration, reducing dependence on traditional shoot-tip culturing. Insights into glutathione-mediated defense and RNA-silencing mechanisms can also guide molecular breeding for enhanced viral resistance. Beyond garlic, this single-cell approach offers a blueprint for exploring complex plant-pathogen relationships and improving yield and quality across vegetatively propagated horticultural crops.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae365
Funding information
This study was supported by the program of NSFC [32060700], the National Guidance Foundation for Local Science and Technology Development of China [[2023] 009] and [2022-1-52], Guiyang Science and Technology Plan Project [Construction Technology Contract [2023] 48–21], the Science and Technology Project of Guizhou Province, China (Qiankehe Foundation-ZK [2022]) (Grant No.702076222101).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2024. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.