How peach flowers survive winter: new spatial transcriptome insights revealed
image: t-SNE cluster analysis and cell type identification of flower bud samples at three different development stages. A Clusters were obtained of the first sample by unsupervised clustering using Seurat and visualized based on t-SNE algorithms. The figure on the right of panel A shows the specific distribution of different groups in the sample space slice position, and the color corresponds to A. C and E represent the second flower and third sample, respectively. The figures on the right of panel C and E show the specific distributions of different groups in the sample space slice position, and the color corresponds to C and E, respectively. B Number of detected genes in each cluster of sample Ad1. D corresponds to the Ad2 sample and F represents the Ad3 sample. G The development state of Ad3, its anther color turning yellowish.
Credit: Horticulture Research
Understanding how flower buds survive winter and resume growth in spring is crucial for fruit production, especially as climate change alters seasonal temperature patterns. This study maps the spatiotemporal gene expression landscape of peach flower buds across dormancy stages using high-resolution spatial transcriptomics. The researchers identified distinct cell types, developmental pathways, and regulatory genes involved in floral organ identity and bud dormancy transitions, with particular emphasis on key regulators in anther maturation. The work highlights how reproductive tissues continue differentiating even under low temperatures. These findings provide valuable molecular markers that can be used to predict dormancy release and support breeding strategies for climate-resilient fruit crops.
Dormancy enables perennial fruit trees to endure harsh winter conditions and bloom successfully in spring. However, insufficient chilling or premature bud break caused by warming climates increases the risk of frost damage and reduced yields. Although previous studies have suggested roles for hormonal and genetic pathways in dormancy regulation, cell-type-specific mechanisms remain poorly understood. The lack of spatial resolution has limited the ability to link gene expression patterns to developmental events, especially in reproductive tissues such as stamens, pistils, and pollen. Based on these challenges, there is a need to investigate peach flower buds at cell-level resolution to uncover regulatory programs underlying dormancy transitions.
Researchers from the Zhengzhou Fruit Research Institute and collaborating institutions have constructed a high-resolution spatial transcriptomic atlas of peach flower buds, according to a study published (DOI: 10.1093/hr/uhaf029) in Horticulture Research on May 1, 2025. The team analyzed three developmental stages spanning deep dormancy to eco-dormancy using the 10x Genomics Visium platform. Their analysis revealed spatial gene expression patterns across floral tissues and identified key regulatory modules that coordinate anther development and dormancy release.
The study identified 7–10 distinct cell clusters across different developmental stages, revealing an “outside-in” developmental progression, where sepals and petals completed differentiation earlier than stamens and pistils. Spatial gene expression patterns demonstrated the differential activity of major floral organ identity genes, including A-, B-, C-, and E-class MADS-box transcription factors. Among these, PpDAM4 and PpDAM6 showed reduced expression during dormancy release, consistent with their regulatory roles in maintaining dormancy.
A key finding centered on anther development. The researchers reconstructed regulatory pathways involving DYT1–TDF1–AMS–MS188–MS1, which control tapetum differentiation and pollen exine formation. Functional validation through virus-induced gene silencing of AMS led to earlier bud break and altered expression of MS188 and MS1, confirming the pathway’s importance in coordinating dormancy with reproductive development. Additionally, hormone-related genes exhibited distinct spatial behavior: abscisic acid (ABA) synthesis and receptor genes decreased as dormancy lifted, while gibberellin biosynthesis genes increased in reproductive cells. These results reveal how hormonal signaling interfaces with transcriptional networks to control the timing of flowering and pollen maturation.
“Our findings provide the first spatially resolved map of gene expression during peach bud dormancy and floral organ development,” said the study’s corresponding author. “This work demonstrates that reproductive tissues, particularly anthers, continue to differentiate during cold exposure. By identifying core regulatory genes and developmental checkpoints, we offer tools that can be used to model and predict floral phenology under changing temperature conditions.”
This dataset serves as a foundational resource for breeding fruit trees with stable flowering times under variable climates. Identifying early markers of anther development enables more accurate prediction of dormancy release, supporting crop management decisions to avoid frost injury. The study also provides molecular targets for manipulating hormonal and developmental pathways to enhance cold tolerance. Beyond peach, these findings offer broader insights into dormancy regulation in other perennial fruit species, contributing to long-term agricultural resilience and sustainability under global climate change.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhaf029
Funding information
This work was supported by the National Key Research and Development Program (2023YFE0105400, 2019YFD1000200), the National Natural Science Foundation of China (32341042), the Central Public-interest Scientific Institution Basal Research Fund (Y2022QC23, 1610192023310), the Agricultural Science and Technology Innovation Program (CAAS-ASTIP-2024-ZFRI-01), the Natural Science Foundation of Henan (232300421042), the National Science and Technology Major Project of Yunan (202302AE090005-3), and the Crop Germplasm Resources Conservation Project (2016NWB041).
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, 2023. 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.