Mung Bean Pan-Genome Study Maps Key Genes for Yield, Nutrition, and Pest Resistance

Because Mung beans (Vigna radiata) are nutritious, inexpensive, have nitrogen-fixing capacity, and are relatively easy to grow with a short growing cycle, they are an important crop for food security in many parts of Asia, Africa, and other regions. Now, researchers have made a significant contribution to a landmark international study that has uncovered tens of thousands of previously hidden structural variations influencing yield, nutritional quality, insect resistance, and other relevant mung bean traits.

The study entitled, “Graph-based pan-genome reveals structural variations associated with agronomic traits in mung bean,” published in Nature Genetics, presents the world’s first graph-based pan-genome for the pulse crop (a legume grown specifically for its dry edible seeds) offering a comprehensive resource for understanding the genetic basis of key agronomic traits and accelerating crop improvement.

The international research team, co-led by researchers at the Chinese Academy of Agricultural Sciences and Murdoch University’s Centre for Crop and Food Innovation (CCFI), assembled chromosome-scale genomes from genetically diverse mung bean accessions and analyzed genomic variation across 580 global accessions. The resulting graph-based pan-genome captures more than 75,000 gene families and identifies over 66,000 structural variants, offering important insights that will help breeders target key agronomic traits and accelerate crop improvement.

More specifically, the authors note that, “integrating these structural variants and single nucleotide polymorphisms, genome-wide association studies across five environments identified candidate genes for 20 agronomic traits, underscoring the pivotal roles of these variants in driving mung bean domestication and improvement.”

Mechanistically, they add, the work demonstrates that “a 68-bp promoter insertion in VrTIFY6B and a 136-bp promoter deletion in VrPGIP1 regulate flavonoid content and confer bruchid resistance, respectively.”

In Australia, mung bean generates over $100 million annually in export revenue. At roughly three times the price of wheat, it represents a highly profitable break crop opportunity for Australian growers; however, seasonal rainfall variability continues to drive significant year-to-year swings in the size and value of the crop.

By cataloging tens of thousands of previously invisible structural variations and linking them to agronomic traits through genome-wide association analysis, this new genomic resource gives breeders a far more complete map of the genetic variation they can work with.

Globally, where mung bean underpins the diets and incomes of millions of smallholder farmers across Asia and Africa, the study’s findings on genes governing seed nutritional compounds and resistance to bruchids, a major storage pest, have direct implications for global food security.

Rajeev Varshney FRS FAA, CCFI director, said the research represents a major advance in crop genomics and demonstrates how next-generation genomic technologies are transforming plant breeding. “Traditional reference genomes capture only part of the genetic diversity within a crop species. By constructing a graph-based pan-genome, we can now identify structural variations that were previously invisible but often have profound effects on important agricultural traits.

“These discoveries provide breeders with powerful new genomic tools to accelerate the development of higher-yielding, more nutritious and climate-resilient mung bean varieties,” Varshney continues. “The genomic resources generated through this work will support marker-assisted breeding, genomic selection and genome editing, enabling breeders to deliver improved varieties to farmers much faster.”

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Very Low Uptake in Workplace Semen Analysis Research: Formative Web-Based Cross-Sectional Follow-Up Survey Distinguishing Employees With Self-Reported Unawareness From Aware Nonparticipants

Background: Very low uptake in workplace semen analysis research is difficult to interpret, particularly in employer-adjacent settings, where nonparticipation may reflect limited recruitment reach, limited understanding of the occupational rationale, low perceived relevance, or procedure-related concerns. Objective: This post hoc formative study described self-reported awareness of a parent workplace semen analysis study as an indicator of effective recruitment reach, reported reasons for nonparticipation under the implemented survey condition, and design issues for exposure-defined workplace reproductive health research. Methods: In April-May 2025, we conducted an anonymous web-based cross-sectional follow-up survey among male employees in Japan who had been eligible for, but had not completed, a parent workplace semen analysis study. The parent study invited approximately 2000 male employees from 3 companies between November 2024 and January 2025; 6 completed the protocol. The follow-up survey invited approximately 900 male employees from 1 company. Part 1 assessed awareness, reasons for nonparticipation, interest in male reproductive health information, and general openness to future related research. Optional Part 2 assessed age, knowledge, concerns, expected reactions, and willingness under simplified conditions. Responses were summarized descriptively using Wilson 95% CIs; no hypothesis testing was performed. Results: We analyzed 108 submitted questionnaires; 83 respondents completed Part 2. Overall, 74/108 (68.5%; 95% CI 59.3‐76.5) respondents reported no awareness of the parent study. Among unaware respondents, 68/74 (91.9%; 95% CI 83.4‐96.2) selected “did not know the study existed.” Among aware nonparticipants, the most frequent reasons were perceived irrelevance and resistance to collecting semen (each 9/34, 26.5%; 95% CI 14.6‐43.1), embarrassment or reluctance (8/34, 23.5%; 95% CI 12.4‐40), and hassle (7/34, 20.6%; 95% CI 10.3‐36.8). In Part 2, anxiety about unfavorable results was reported by 52/83 (62.7%; 95% CI 51.9‐72.3) respondents, concerns about collection location or privacy protection by 48/83 (57.8%; 95% CI 47.1‐67.9), and self-reported resistance by 42/83 (50.6%; 95% CI 40.1‐61.1). Under simplified conditions, 36/83 (43.4%; 95% CI 33.2‐54.1) respondents indicated willingness to undergo semen analysis. Conclusions: Very low uptake in this employer-adjacent semen analysis study was not interpretable as a single phenomenon. This post hoc formative process evaluation identified limited awareness, suggesting limited effective recruitment reach under the implemented procedures, and characterized the reason profile among aware nonparticipants, including low perceived relevance and semen collection–related concerns. Rather than identifying primary causal determinants of nonparticipation, the findings support a bounded recruitment-methodological interpretation and highlight recruitment-cascade components for prospective measurement: objective exposure to recruitment materials, information access, understanding of the occupational rationale, voluntary postinformation declination, privacy concerns, logistical burden, and specimen-return completion. Informed acceptability after occupational reproductive-hazard education should be evaluated in future designs that include such education and comprehension assessment.
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Autism-Related Information on Websites and General-Purpose Artificial Intelligence Chatbots: Comparative, Bilingual Study

Background: Parents increasingly consult the internet, both websites and, more recently, artificial intelligence chatbots, for information on autism spectrum disorder (ASD). However, the comparative quality of these two source types, especially across languages, remains underexplored. Objective: This study aimed to assess the completeness and accuracy of ASD information delivered by websites and 5 popular artificial intelligence chatbots and determine whether performance differs between English and Romanian content. Methods: In a cross-sectional design, 25 English-language and 25 Romanian-language websites and the responses of ChatGPT, Gemini, Claude, Copilot, and DeepSeek were evaluated. Content was benchmarked against a 24-item checklist, yielding completeness and accuracy scores. Chatbots were tested in 2 scenarios: a single broad query (A) and 24 item-specific queries (B). Results: Websites achieved higher completeness in English than in Romanian (6.9 vs 5.1; =.007) and marginally higher accuracy (6.9 vs 6.1; =.045). In scenario A, chatbot completeness (English: 5.3 vs Romanian: 6.2; =.15) and accuracy (English: 6.0 vs Romanian: 5.6; =.32) did not show significant differences by language. In the single-query scenario, websites showed higher accuracy than chatbots in both English (6.9 vs 6.0; =.19) and Romanian (6.1 vs 5.6; =.53), with neither difference reaching statistical significance. Conversely, item-specific questioning favored chatbots, which yielded higher accuracy scores than websites in English (8.3 vs 6.9; =.053) and Romanian (8.0 vs 6.1; =.007). Accuracy scores improved significantly from the single-query to the item-specific scenario (English: 6.0 vs 8.3; =.002; Romanian: 5.6 vs 8.0; =.001). While an initial analysis suggested variation in performance between chatbots (repeated measures ANOVA; =.005), pairwise differences between individual models did not remain significant after adjustment for multiple testing. Conclusions: This exploratory study indicates that the quality of online ASD information varies by language and source context. English-language websites are more complete than Romanian-language websites. Among chatbots, targeted questioning yields more accurate answers than single broad queries in both languages. The findings should be interpreted cautiously due to the temporal gap between website and chatbot data collection.
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What Anthropic’s latest AI discovery does—and doesn’t—show

This story originally appeared in The Algorithm, our weekly newsletter on AI. To get stories like this in your inbox first, sign up here.

Anthropic—currently the world’s most valuable AI company, with a nearly $1 trillion valuation—has a reputation for publishing strange and heady research. It’s looking into whether AI models can feel pain, for example, and will sometimes cut off chatbot conversations if it suspects users are “abusing” the model. 

One niche that Anthropic spends more time and money on than other AI companies is called mechanistic interpretability, which means looking inside the complex math of an AI model to learn why it comes up with one particular output and not another. It’s complicated stuff; there are millions of data points that might contribute to any result, and wading through them can look more like word salad than anything useful. It’s also controversial. Describing AI models with terms borrowed from psychology and neuroscience can make their behavior seem more sophisticated than we might otherwise judge it to be.

That’s why, when Anthropic announced last week that it had found a new window into its models’ “internal thoughts” as they reason through answers, there was one colleague I had to talk to. Senior editor Will Douglas Heaven, aside from having a PhD in computer science, has spent a lot of time digging into what we can say about how AI models work. I spoke with him about what we should take from Anthropic’s new (and predictably quirky) research.

What did Anthropic learn here, exactly?

Anthropic has been trying to understand how large language models (LLMs) work for a few years now. Anthropic isn’t the only one looking at this, but I think the company has made it part of its core mission more than most. Anthropic’s CEO, Dario Amodei, has said we won’t be able to control LLMs fully unless we learn more about how they work. 

So this new research is very much in that context. It goes deeper into the weird mechanisms inside LLMs than ever before. What Anthropic learned was that LLMs have a space inside them—which Anthropic calls the J-space—filled with words that don’t appear in their output but that seem to influence the way they puzzle through problems. All this was hidden until Anthropic developed a new technique to probe its model Claude, so it’s a genuine discovery. 

Sometimes these words keep track of where the LLM has got to in a particular task, sometimes they look more like flashes of recognition (for example, “protein” might pop up when you give an LLM only the letters of a protein sequence), and sometimes they represent a kind of internal commentary on the model’s decision-making. In my favorite example, Claude decided to cheat on a coding test when the word “panic” appeared.

Anthropic also found that LLMs are able to describe and manipulate the words in this space. So somehow they seem to be making use of it. 

Let’s step back for a second. I don’t think of large language models as simple, but they’re also not magic. There’s a bunch of math that learns relationships between words, right? So why is it so hard to “peer” into an LLM to know what’s going on?

Yeah, they’re not magic! I think the fact we don’t fully understand them plays into the mythmaking. And it’s worth noting that the whole narrative that Anthropic is leaning into here—that they’ve built this really mysterious technology, but don’t worry, because they’re also the ones to figure it out—very much fits with the company’s vibe. [See how Anthropic warned that its new models were so good at coding they posed a global cybersecurity risk, only for the US government to shut them down shortly thereafter.]

So yes: LLMs are just math. And yet it’s vastly complex math. Not only are today’s LLMs made out of hundreds of billions of numbers, but running them triggers a cascade of millions and millions of calculations. I wrote last year that if you printed out even a medium-size LLM on pieces of paper, it would cover a city the size of San Francisco

It’s impossible to make sense of any of that math without specialist tools that highlight specific parts of an LLM at specific times. You need to know where to look and how to look. And building those tools requires understanding something of that complex math in the first place. 

You’ve written elsewhere about this concept of studying LLMs the way one might study an organism’s brain. Is it fair to use “brain-like” terms when talking about how an LLM works?

I don’t love using those kinds of terms. LLMs are not brains. Talking like this is misleading because it can suggest that LLMs are capable of more human-like things than they are or that we can make assumptions about how they might behave that we shouldn’t. The whole anthropomorphization thing is also tied up with a bunch of strong ideological positions about what this technology is and what it’s going to be

But at the same time, we lack a good alternative vocabulary for talking about what these models are doing. I can understand why people reach for words like “think” and “understand” and “brain-like”—they’re convenient shorthand. 

Anthropic compares this new space it found inside LLMs to the space that some neuroscientists think our brains use to keep track of conscious thoughts. I asked the company how seriously we should take that comparison and it said in a statement: “Drawing these analogies was helpful to us in designing our experiments, as they allowed us to make many non-obvious experimental predictions about the J-space that turned out to be true. At the same time, it’s important to note that there are some important differences between the J-space (and language models in general) and the human brain, so we don’t mean to claim there’s a perfect correspondence.” 

What’s a problem in AI that this new concept of the J-space might be used to solve?

Anthropic has said that monitoring the J-space could be a way to catch models doing something they shouldn’t. Because words pop up in this space that don’t appear in a model’s output, they can tell you things about its behavior that you might not have noticed otherwise—such as when it is giving biased responses or when it is weighing the pros and cons of cheating. 

That’s the theory, at least. I think it’s better to think of this result as one more step on the path to understanding this technology overall than as something that will be useful by itself. 

Read more in Will’s full story about the new research

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