Wednesday, October 29, 2025

Single-cell atlas reveals gene networks shaping peanut peg formation and subterranean pod development




Maximum Academic Press





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.

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Arts-based methods are transforming leadership education – new study highlights the importance of creativity and empathy for future leaders



University of Eastern Finland






Arts-based methods can significantly enhance leadership education and better prepare students to address the major societal challenges of our time, a new study from the University of Eastern Finland shows. The study examined a course on innovation cultures delivered at the University of Eastern Finland between 2013 and 2023, where students employed visual arts, music, drama and play as part of their learning process.

According to the study, arts-based methods support the development of students’ emotional intelligence, creativity and critical thinking. They encourage students to reflect on their experiences, question their assumptions and explore leadership from new perspectives. Arts-based methods also promote collaborative learning and create learning environments that mirror the complexity and demands of workplaces.

“Students felt that the course helped them gain a deeper understanding of innovation cultures, while encouraging them to apply creative thinking both in their studies and in their future careers. Many reported increased confidence and greater courage to experiment with new things, even in cases where they did not have a strong background in the arts,” says University Lecturer Pasi Hirvonen, one of the course teachers.

The study shows that arts-based methods are not only beneficial in leadership education, but they also offer broader opportunities to develop pedagogical approaches that support students in becoming responsible and empathetic change leaders. Arts-based methods strengthen students’ ability to navigate uncertainty, work in teams and networks, and harness emotions and creativity as drivers of change.

According to the course teachers, successful implementation of the course requires robust pedagogical expertise, the ability to navigate uncertainty and, above all, institutional support.

“Creating a safe and encouraging learning environment is essential for students to feel confident enough to engage with creative learning methods,” Professor Hanna Lehtimäki notes.

The study highlights the need to reform business education to better respond to current and future challenges. Traditional teaching methods should be supplemented by approaches that support students’ holistic growth.

“Arts-based methods offer students a unique opportunity to develop skills that are urgently needed in modern workplaces. Empathy, critical thinking and creative problem-solving are not just academic goals but essential skills that enable future professionals to thrive in a rapidly changing and increasingly complex world,” Hirvonen concludes.

 

Scientists develop an efficient method of producing proteins from E. coli



This development could enhance microbial protein production and drive progress in biomanufacturing



Nagoya University

Translation process accelerated to produce proteins more efficiently 

image: 

Proteins are synthesized through two processes involving DNA: transcription, which converts DNA into mRNA; and translation, where ribosomes read the mRNA and sequentially link amino acids to form proteins. This image illustrates the translation process accelerated to produce proteins more efficiently.

 

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Credit: Teruyo Ojima-Kato




Proteins sourced from microorganisms are attracting attention for their potential in biomanufacturing a variety of products, including pharmaceuticals, industrial enzymes, and diagnostic antibodies. These proteins can also be used for converting resources into biofuels and bioplastics, which could serve as viable alternatives to petroleum-based fuels and products. Therefore, efficiently producing microbial proteins could make a significant contribution to sustainable manufacturing.

Producing proteins from Escherichia coli (E. coli) has become popular due to its cost-effectiveness and efficiency. However, yields of protein production in E. coli may be reduced depending on the specific gene sequence of the target protein.

In a study published in the journal RSC Chemical Biology, a research group in Japan has successfully developed a new technology that improves the efficiency of protein production in E. coli.

The reduction in protein production is believed to be a contributing factor to  ribosome stalling. Ribosomes synthesize proteins using genetic information carried by messenger RNA (mRNA). However, when ribosomes are unable to continue the translation process for some reason, protein synthesis is halted.

"In our previous research, we found that adding a short peptide sequence composed of four amino acids—serine, lysine, isoleucine, and lysine—to the N-terminus of a protein reduces ribosomal stalling and significantly improves translation efficiency in E. coli," said Associate Professor Teruyo Ojima-Kato from Nagoya University's Graduate School of Bioagricultural Sciences.

Based on this finding, Kato and Professor Hideo Nakano of Nagoya University, in collaboration with researchers from the National Institute of Advanced Industrial Science and Technology and Waseda University, conducted a study to identify short translational-enhancing peptides (TEPs) that can prevent ribosome stalling.

The researchers first created a tetrapeptide library, a collection of random peptide sequences formed by all possible combinations of the four amino acids. This library contains the arrangements of the 20 amino acids that make up proteins, totaling 160,000 distinct tetrapeptides. Using this library, they conducted a comprehensive analysis and identified several novel TEPs that effectively prevent ribosome stalling.

Next, the researchers attempted to evaluate the translation-enhancing effects of the 160,000 tetrapeptides. To assess such large numbers of tetrapeptides, they developed an artificial intelligence (AI) prediction model based on data from about 250 experiments.

The research group conducted three rounds of AI predictions, demonstrating that their AI model accurately predicts the strength of translation enhancement for all 160,000 tetrapeptides. This result suggests that AI-based predictive models could be helpful in the rational design of peptide sequences that can be readily translated into target proteins.

"We present a novel approach for efficient production of proteins using short peptide sequences," said Kato. "This technique can be applied to more efficient production of enzymes, which play a significant role in the biorefinery sector that generates chemicals and fuels from renewable resources. Our findings could provide fundamental technology to support sustainable manufacturing that does not depend on petroleum."