Using single-nucleus RNA sequencing, the researchers mapped over 50,000 individual cells from both aerial and subterranean pegs, identifying distinct cell types and gene expression patterns that guide the downward growth of fertilized ovaries into the soil. Their analysis revealed that hormone signaling, particularly the auxin pathway, plays a critical role in regulating gravity-responsive growth and tissue differentiation.
Peanut (Arachis hypogaea L.) produces flowers above ground, but its fertilized ovaries extend downward to form subterranean pods—a process known as pegging. The peg, or gynophore, is a positively geotropic organ that senses gravity and directs seed formation underground. Previous studies have implicated plant hormones such as auxin, ethylene, cytokinin, and gibberellins in this process, but the molecular details have remained elusive. Advances in single-cell RNA sequencing now allow scientists to dissect cell-specific transcriptional activity and reconstruct developmental trajectories. Given the peg’s hybrid nature—combining stem-like structure with root-like behavior—cell-level resolution is critical to reveal the genetic and hormonal mechanisms underlying its formation.
A study (DOI:10.48130/ph-0025-0019 ) published in Plant Hormones on 16 September 2025 by Hao Liu’s & Wenyi Wang’s team, Guangdong Academy of Agricultural Sciences & South China Agriculture University, provides a detailed molecular blueprint of peg formation, offering valuable insights into the mechanisms that ensure successful pod development and potentially paving the way for higher-yield peanut varieties.
To dissect how peanuts drive fertilized ovaries into the soil to form underground pods, the researchers combined single-nucleus/single-cell RNA sequencing (snRNA-seq) and bulk RNA sequencing on both aerial and subterranean pegs, generating high-resolution transcriptional maps of 23,539 aerial peg cells and 27,364 subterranean peg cells. They clustered these cells (20 aerial clusters and 22 subterranean clusters) using UMAP and t-SNE, then annotated nine major cell types in each peg type through marker-gene expression and RNA in situ hybridization, including ovule, cortex, xylem, epidermis/exodermis, and phloem/cambium. With these cell identities established, they reconstructed developmental “pseudo-time” trajectories to model how peg cells differentiate as the peg grows downward and enters the soil. In aerial pegs, this analysis resolved 11 developmental states and 7,086 pseudo-time differentially expressed genes (DEGs), including 87 key transcription factors (TFs) such as members of the MYB, AP2/ERF, WRKY, and AGL families. Network analysis highlighted TFs like AP2/ERF and WRKY41/53/70 as central regulators of aerial peg growth. A similar pseudo-time reconstruction in subterranean pegs identified 4,830 DEGs and 42 core TFs, with enriched pathways in secondary metabolism, fatty acid degradation, and flavonoid biosynthesis, suggesting metabolic reprogramming after soil penetration. Integrating single-cell and bulk datasets revealed cell type–specific regulators of cortex differentiation, including auxin transport and response genes such as PIN3 and ARF8, and showed that hormone signaling pathways—especially auxin signaling—shift sharply between aerial and subterranean pegs. Hormone profiling confirmed major differences in indole-3-acetic acid (IAA), ABA, salicylic acid, and cytokinins between aboveground and belowground tissues. Together, these methods produced the first cell-by-cell regulatory atlas of peanut peg development and showed that auxin-driven transcriptional programs underlie gravity-guided peg penetration and pod initiation.
This single-cell atlas provides a powerful resource for understanding the gene regulatory networks controlling peanut reproduction. By elucidating the hormonal and transcriptional mechanisms that mediate peg differentiation and soil penetration, the findings offer molecular targets for breeding peanut cultivars with improved pod-setting efficiency and yield stability under variable environmental conditions. The data also open possibilities for manipulating hormone signaling pathways to optimize gravity responses and enhance reproductive success in other legume crops.
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References
DOI
10.48130/ph-0025-0019
Original Source URL
https://doi.org/10.48130/ph-0025-0019
Funding Information
This work was supported by the Guangdong Provincial Key Research and Development Program-Modern Seed Industry (2022B0202060004), the National Key Research and Development Project (2023YFD1202800), the Open Competition Program of Top 10 Critical Priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan in Guangdong Province (2022SDZG05), The National Natural Science Foundation of China (32272121, 32172051, 32301869), the Guangdong Science and Technology Plan Project (2023B1212060038), the Guangdong Basic and Applied Basic Research Foundation (2021A1515010811, 2023A1515010098, 2023A1515010569, 2023A04J0776), the China Agriculture Research System of MOF and MARA (CARS-13), the Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science (R2020PY-JX004, R2020PY-JG005, R2021PY-QY003, R2022YJ-YB3025), the Foundation of Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences (202101, 202201, 202306), Special Funds for the Revitalization of Agriculture through Seed Industry under the Provincial Rural Revitalization Strategy (2022-NPY-00-022), the Project of Collaborative Innovation Center of GDAAS (XTXM202203), the Special Support Program of Guangdong Province (2021TX06N789), Science and Technology Planning Project of Heyuan City (Heyuan She Nong Da Zhuan Xiang 2022002), and the Science and Technology Project of Qingyuan City 2023 (2023KJJ002).
About Plant Hormones
Plant Hormones (e-ISSN 3067-221X) is an open access, online-only, academic journal publishing rigorously peer-reviewed original articles, reviews, break-through methods, editorials, and perspectives on broad aspects of plant hormone biosynthesis, signal transduction, and crosstalk. The journal primarily publishes fundamental research that represents significant advances or new insight into specialized areas of plant hormones, and review articles that provide comprehensive and critical review of current research areas and offer directions or perspectives for future research. The journal publishes applied research that has significant implications for the development of agriculture, horticulture, and forestry. Plant Hormones also provides a community forum by publishing editorials and perspective papers for expressing opinions on specific issues or new perspectives about existing research on particular topics. Plant Hormones is hosted by Chongqing University, and published by Maximum Academic Press.