AI-powered UAV system uncovers new cotton defoliation gene for cleaner mechanical harvesting

Nanjing Agricultural University The Academy of Science

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By combining these refined phenotypic data with genome-wide association studies (GWAS) and transcriptome sequencing, researchers identified GhDR_UAV1, a previously unknown gene that positively regulates cotton leaf abscission.

Efficient pre-harvest defoliation is essential for modern cotton production, particularly in regions such as China’s Xinjiang, where large-scale mechanized harvesting dominates and relies on clean, uniform leaf drop to maintain efficiency and fiber quality. Although chemical defoliants are widely applied, their environmental, economic, and health risks underscore the importance of breeding varieties capable of strong natural or chemically induced leaf abscission. Yet progress in identifying defoliation-related genes has been constrained by traditional manual field surveys, which are slow, labor-intensive, and error-prone, yielding low-throughput phenotypic data that are insufficient for genome-wide association studies. These limitations have created an urgent need for scalable, precise, and synchronized phenotyping strategies to advance gene discovery and accelerate the development of defoliation-prone cotton cultivars.

A study (DOI: 10.1016/j.plaphe.2025.100109) published in Plant Phenomics on 17 September 2025 by Zuoren Yang’s team, Chinese Academy of Agricultural Sciences, provides a powerful new foundation for breeding defoliation-sensitive cotton lines.

In this study, cotton defoliation was assessed through an integrated high-throughput framework that combined top-down UAV multispectral scanning with bottom-up leaf area index (LAI) measurements, enabling rapid and precise field phenotyping across large populations. This dual-sensor strategy was evaluated against traditional manual surveys to quantify improvements in efficiency and accuracy. To identify the most informative predictors of defoliation, hierarchical segmentation analysis was applied to nine spectral indices and LAI across three statistical levels: leaf number (LN), leaf number difference (LND), and defoliation rate (DR). These selected indices were then used to train four deep learning architectures—1D-CNN, BiGRU, CNN-BiGRU, and CNN-BiGRU-Attention—for trait inversion. Model interpretability was further examined using SHAP analysis. Finally, model-derived phenotypes were incorporated into GWAS to identify genetic loci associated with defoliation, followed by transcriptome analysis and functional validation of candidate genes. Corresponding results demonstrated dramatic gains in efficiency: manual assessment of 214 plots would require 33 days for one investigator, whereas UAV flight required only 20 minutes and LAI measurements four days. UAV and LAI surveys also maintained high accuracy and, when combined, outperformed manual surveys for GWAS applicability. Hierarchical segmentation consistently identified MTCI, VDVI, CI, and LAI as core predictors. Among tested models, the CNN-BiGRU-Attention architecture achieved the highest accuracy (R² > 0.85), particularly for LN and LND. SHAP analysis revealed VDVI as the most influential feature, with chlorophyll-related indices (MTCI, CI) also contributing strongly. GWAS using LND-based predictions showed strongest concordance with manual measurements, identifying significant loci on chromosomes A08 and A10. Transcriptome profiling and functional assays confirmed GhDR_UAV1 as a key TDZ-responsive gene whose overexpression accelerates leaf wilting and abscission, establishing it as a positive regulator of cotton defoliation.

This new phenomics-genomics framework offers cotton breeders a scalable alternative to manual defoliation surveys, reducing weeks of labor to minutes of UAV flight time and enabling genetic studies that were previously infeasible. The discovery of GhDR_UAV1 provides a valuable molecular target for developing cotton varieties that defoliate rapidly and uniformly, reducing reliance on chemical defoliants and lowering production costs while improving fiber purity during mechanical harvesting. Beyond cotton, this approach demonstrates how AI-enabled remote sensing can transform the study of complex field traits, accelerating genomics-assisted breeding in other major crops.

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References

DOI

10.1016/j.plaphe.2025.100109

Original Source URl

https://doi.org/10.1016/j.plaphe.2025.100109

Funding information

This work was supported by National Key R&D Program of China (2022YFF1001400), National Natural Science Foundation of China (32360509), Natural Science Foundation of Xinjiang Uygur Autonomous Region (2024D01A150), Corps of agricultural science and technology innovation project special (NCG202316), Key Research and Development Program of Xinjiang (2022B02052).

About Plant Phenomics

Plant Phenomics is dedicated to publishing novel research that will advance all aspects of plant phenotyping from the cell to the plant population levels using innovative combinations of sensor systems and data analytics. Plant Phenomics aims also to connect phenomics to other science domains, such as genomics, genetics, physiology, molecular biology, bioinformatics, statistics, mathematics, and computer sciences. Plant Phenomics should thus contribute to advance plant sciences and agriculture/forestry/horticulture by addressing key scientific challenges in the area of plant phenomics.

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Journal

Plant Phenomics

DOI

10.1016/j.plaphe.2025.100109 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Establishment of a high-throughput field defoliation data survey strategy combined with genome-wide association studies to reveal the genetic basis of defoliation in cotton

 

Breakthrough in detection of deadly toxins in children’s medicines

University of East London

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A major scientific breakthrough has shown that deadly contaminants in medicinal syrups can be detected in seconds using simple, low-cost tests, offering a realistic way to prevent the deaths of children caused by poisoned medicines.

The findings were made by a research team led by scientists at the University of Oxford and including the University of East London, and published in Nature’s Scientific Reports.

The team has demonstrated, for the first time, that simple, ultra-low-cost tests already used for alcohol detection can be repurposed to identify lethal toxic contaminants in medicinal syrups and their raw materials.

The findings open a realistic new way to prevent contaminated medicines from reaching children, particularly in low- and middle-income countries.

The breakthrough addresses a long-standing and deadly problem. Ethylene glycol (EG) and diethylene glycol (DEG) - industrial chemicals used in antifreeze and brake fluid - have repeatedly entered pharmaceutical supply chains, often through mislabelled or substituted raw ingredients.

In 2022 alone, contaminated syrups caused the deaths of more than 300 children across Indonesia, The Gambia, Uzbekistan and Cameroon. More recently, at least 24 further child deaths were reported in India.

Until now, detecting EG and DEG has depended on formal laboratory techniques that are expensive, time consuming, require highly qualified and trained personnel, and are often unavailable where the risk is greatest.

The research team has shown that this barrier can be overcome by repurposing everyday tools:

• Alcohol test strips, commonly used to detect alcohol in saliva or breast milk, can identify ethylene glycol contamination in under two minutes.
• Disposable breathalysers can distinguish ethylene glycol and diethylene glycol in raw materials in as little as ten seconds.

Both methods cost less than £1 per test, require minimal training, use no hazardous solvents, and can be deployed outside laboratory environments - representing a step-change in what is possible for medicine safety screening across supply chain.

Project leader, Professor Paul Newton of the Centre for Tropical Medicine and Global Health at the University of Oxford said, "Urgent interventions are needed to be implemented to prevent these recurring tragedies of childhood deaths and screening devices for detecting the toxins offer great promise in enabling this."

Dr Merchant, from the University of East London's Department of Bioscience, is a co-author on the study.

He said, “More than 80 years have passed since the sulfanilamide disaster, when diethylene glycol was mistakenly used in a liquid medicine - later infamously termed the ‘elixir of death’. That tragedy led to the introduction of the most stringent pre-market safety regulations for medicines in the United States and subsequently across Europe.

“Yet, it is deeply concerning that lives continue to be lost today due to illicit contamination with ethylene glycol (EG) and diethylene glycol (DEG), compounded by inadequate regulatory oversight in parts of the developing world.

“Global regulators must act decisively and collaboratively to ensure that no one ever dies from such preventable failures again. By lowering the barrier to detection, this work has the potential to stop contaminated medicines at source and prevent avoidable child deaths.”

The paper, ‘Rapid screening of ethylene glycol and diethylene glycol in raw materials and medicinal syrups using low-cost field deployable assays’, is published in Nature’s Scientific Reports

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Journal

Scientific Reports

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Rapid screening of ethylene glycol and diethylene glycol in raw materials and medicinal syrups using low-cost field deployable assays

Article Publication Date

13-Dec-2025

 

Archaeologists use AI to create prehistoric video game

Archaeologists from the University of Copenhagen and the University of Bergen have used AI and free digital tools to create a dynamic and educational video game about the Stone Age

University of Copenhagen

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image: 

Dolmen Debbie. Screenshot from the game.

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Credit: University of Copenhagen

Historians and archaeologists are constantly looking for new ways to bring the past to life. And in museums, audiovisual and digital solutions have long been a part of the presentation of cultural heritage.

However, until now, developing immersive digital content about the past has been very expensive and has required specialized labour. At the same time, it has been difficult to update the content if needed.

For this reason, only large commercial game developers have been successful in making (pre-)history-based video games. Popular examples are Assassin's Creed and Civilisation, which are great, but don't always place a high value on historical accuracy.

But in a new research paper (link), archaeologists from the University of Copenhagen show that by using AI, the free tool Unreal Engine and tutorials on YouTube, they have been able to create an educational dynamic 3D computer game - in a short time and for very little money.

“We believe that these free tools that are now available to everyone have the potential to revolutionize digital cultural heritage communication. And with the research article about our game, we give other professionals the recipe for how to get started with digital storytelling without spending huge resources on it," says archaeologist Mikkel Nørtoft from the University of Copenhagen.

Small talk with a Stone Age woman

The 3D game developed by the researchers is based on the Deep Histories of Migration research project about the Neolithic period in Northern Europe. The game is centred around the archaeologists' own video recordings of two well-preserved long dolmens from Lindeskov Hestehave on Funen.

“The aim of the game is to learn more about the Neolithic Age and the burial monuments that were built back then in a dramatised universe. You do this by exploring the site, and talking to two AI-driven characters, an archaeologist and a Stone Age woman, whom we have prompted with background stories,” explains Mikkel Nørtoft and continues:

 "In other words, we haven't had to write detailed manuscripts because the characters speak using generative AI and can therefore express themselves - optionally in

several different languages - based on our prompts and our own compiled archaeological knowledge banks.”

This also means that researchers can continuously change the back stories as they gain new knowledge. In this way, they can ensure that the communication always stands on solid academic ground, while at the same time appearing immediate and natural to the players.

“Our game is primarily an example of what is technically possible for beginners, so we recommend that museums and other interested parties build their own scenarios with their expert knowledge. With a little help, most people will be able to learn how to build a simple scenario with characters within a few days and start experimenting with this type of dissemination.”

For Mikkel Nørtoft and his colleagues, their attempt to create a computer game shows that archaeologists and historians no longer have to depend on expensive commercial developers. They can now take control of the communication of their subject and create their own research-based digital version of prehistory.

See a demonstration of the archaeologists' game on YouTube: https://www.youtube.com/watch?v=6h4KqFgoPv4.

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Journal

Advances in Archaeological Practice

DOI

10.1017/aap.2025.10106 

Method of Research

Computational simulation/modeling

Subject of Research

Not applicable

Article Title

Gamifying the past: embodied LLMs in DIY archaeological video games

Article Publication Date

10-Dec-2025

 

Most parents aware of early peanut introduction guidelines, but confused about details

Interviews reveal parents need more clarity to boost peanut allergy prevention efforts

Ann & Robert H. Lurie Children's Hospital of Chicago

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Feeding babies peanut-containing foods as early as possible can help prevent peanut allergy, but a new study published in JAMA Network Open found that parents need more support to get it right. Interviews with parents revealed widespread confusion about the purpose, risks, and timing of early peanut introduction guidelines.

“While some parents we talked to understood correctly that starting their baby on peanut foods trains the immune system in order to prevent the development of peanut allergy, other parents mistakenly believed that the purpose is to test if their baby is allergic – a misconception that fueled fears of severe allergic reaction, leading to hesitation and delays in peanut introduction,” said lead author Waheeda Samady, MD, a hospital-based pediatrician at Ann & Robert H. Lurie Children’s Hospital of Chicago and Associate Professor of Pediatrics at Northwestern University Feinberg School of Medicine.

“For prevention of peanut allergy, timing and consistency are of the essence,” she said. “We encourage peanut introduction as soon as the baby starts eating solids, before or around 6 months of age. It’s also important to continue peanut exposure twice a week through the first year and into toddler years. Feeding babies peanut foods just once or twice is not enough.”

Early peanut introduction guidelines were issued in 2017 following groundbreaking research showing over 80% reduction in peanut allergy development. Peanut allergy affects approximately 2% of U.S. children and is the least likely food allergy to be outgrown, making prevention through early introduction an important public health strategy.

Dr. Samady and colleagues analyzed 49 interviews with Chicago parents of infants aged 8-13 months from diverse backgrounds. Participants were recruited from primary care academic clinics, federally qualified health centers and private clinics.

Researchers also found that parents mostly did not understand that eczema places their baby at high risk for developing food allergy, making early peanut introduction even more critical.

“If a baby has eczema, peanut introduction should start early, around 4 months of age, if possible, to maximize peanut allergy prevention coupled with good skincare,” said Dr. Samady. “Pediatricians need to reinforce this message, given that most parents we interviewed were not aware that eczema increases the baby’s chances of developing food allergies.”

In the study, parents reported that pediatricians were their primary source of information about early peanut introduction.

“Pediatricians are key to successful guideline implementation, but they need better resources for families to provide comprehensive information during busy well-child visits," Dr. Samady noted. "Overall, we found that parents are accepting of early peanut introduction, but they need clearer guidance and more support.”

Dr. Samady emphasized that improved messaging and resources for families should clarify that early peanut introduction prevents peanut allergy through regular dietary exposure, address the connection between eczema and food allergy risk, provide specific guidance on timing and frequency, and reassure parents about the low risk of severe allergic reactions in infants.

“Parents need to be reassured that if their baby is allergic to peanut, they may see hives, some swelling, or vomiting, but allergic reactions in infancy are usually mild,” she explained. “We should empower parents with information and action plans so this does not stop them from participating in early peanut introduction.”

This research was funded by the National Institute of Allergy and Infectious Diseases (NIAID K23AI159517).

Ann & Robert H. Lurie Children’s Hospital of Chicago is a nonprofit organization committed to providing access to exceptional care for every child. It is the only independent, research-driven children’s hospital in Illinois and one of less than 35 nationally. This is where the top doctors go to train, practice pediatric medicine, teach, advocate, research and stay up to date on the latest treatments. Exclusively focused on children, all Lurie Children’s resources are devoted to serving their needs. Research at Lurie Children’s is conducted through Stanley Manne Children’s Research Institute, which is focused on improving child health, transforming pediatric medicine and ensuring healthier futures through the relentless pursuit of knowledge. Lurie Children’s is the pediatric training ground for Northwestern University Feinberg School of Medicine. It is ranked as one of the nation’s top children’s hospitals by U.S. News & World Report.

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Journal

JAMA Network Open