New Australian Chickpea pan-genome poised to boost Chickpea production

Murdoch University

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CCFI Director Rajeev Varshney and GRDC Senior Manager, Oilseeds and Pulses, Dr Francis Ogbonnaya, inspect Australian chickpeas

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Credit: CCFI

Researchers from the Centre for Crop and Food Innovation (CCFI) at Murdoch University have led the generation of a pan-genome tailored specifically to Australian chickpea varieties, paving the way for improved chickpea production.

The comprehensive genetic resource, composed of high-quality assemblies of the 15 most popular chickpea varieties grown by Australian farmers, uncovered previously uncharacterised genetic diversity that will prove essential in understanding and improving desirable agronomic traits that underpin the success of the nation’s Chickpea production, including yield, flowering time, acid soil tolerance and drought tolerance.

The pangenome analysis, published in Plant Biotechnology Journal and conducted in collaboration with Chickpea Breeding Australia (a Grains Research and Development Corporation and New South Wales Department of Primary Industries and Regional Development joint initiative), Agriculture Victoria Research, the WA Department of Primary Industries and Regional Development, the UWA Institute of Agriculture, and BGI Research, identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits.

The research pinpointed structural variations that influence flowering time, seed weight, disease resistance, drought resilience and acid soil resilience, highlighting a major opportunity to expand the genetic base of Australian chickpeas and ultimately support the long-term sustainability of chickpea production.

The researchers also discovered that Australian varieties could be further improved through the introduction of the “QTL hotspot” region for drought tolerance that has already demonstrated a 15- 22% yield advantage after its introgression in elite cultivars in India, Ethiopia, Kenya and Tanzania. CCFI is now working with industry partners to introgress the “QTL-hotspot” for drought tolerance into Australian varieties and deliver them to chickpea growers.   

Reporting on the findings, Professor Rajeev Varshney, CCFI Director and corresponding author of the study, explained that:

"The Australian chickpea pangenome marks a significant step in safeguarding future production, as it enables us to accelerate the development of chickpea varieties tailored to each region. That could mean varieties that are more drought-resilient and acid soil-tolerant in Western Australia and nationally, and more resistant to diseases like Ascochyta Blight. We look forward to working with breeding organisations to get new and improved varieties into the hands of Australian farmers.

"We can also leverage this genetic information to improve global chickpea breeding and agricultural sustainability efforts.

"I would like to thank all of our collaborators on this important piece of research, which we hope will ultimately boost farmer profitability and secure Australia's position as a globally leading chickpea producer."

GRDC Senior Manager for Oilseeds and Pulses, Dr Francis Ogbonnaya, added that:

"GRDC is proud to have invested on behalf of Australian grain growers in this ground-breaking research. It is fantastic to see the country's leading chickpea researchers unite to develop a significant genetic critical towards securing the future productivity and sustainability of chickpeas in increasingly challenging growing conditions.

"This landmark GRDC investment in the development of an Australian chickpea pan-genome represents a major leap forward in our understanding of chickpea genetics that underpins Australia's unique growing conditions. By unlocking the genetic diversity within the crop, this research provides a powerful foundation for breeding chickpea varieties with improved drought resilience and abiotic stresses, directly addressing some of the most pressing challenges for Australian grain growers. It exemplifies GRDC's commitment to delivering world-class science that drives real on-farm impact."

Summarising the findings, Dr Kristy Hobson, Chickpea Breeder at Chickpea Breeding Australia, said:

“Since the release of Australia’s first commercial chickpea variety in the 1970s, our industry has flourished into a billion-dollar sector that produced over 2 million tonnes of chickpea last season, and one of the world’s major chickpea exporters. However, there are significant challenges, including changes in agricultural practices, shifts in market demands, soil constraints, and significant disease pressures.

“These findings fill in some much-needed knowledge gaps regarding the genetic makeup of Australian chickpea varieties, which will be essential for further improvement through identifying the genes responsible for yields, stress tolerance and disease resistance.”

 

ENDS
 

Notes to editor:

This research output stems from two GRDC-funded projects (Code:  UMU2303-003RTX and UMU2403-009RTX).

In this study, researchers generated high-quality genome assemblies and annotations for 15 leading Australian chickpea cultivars using single-tube long-fragment read technology. The pan-genome analysis identified 34,345 gene families, including 13,986 dispensable families enriched for genes associated with key agronomic traits. Comparative genomic analysis revealed ~2.5 million single-nucleotide polymorphisms, nearly 200,000 insertions/deletions, and over 280,000 structural variations.
 

The full study and its implications can be found here.

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Journal

Plant Biotechnology Journal

DOI

10.1111/pbi.70192 

Method of Research

Meta-analysis

Subject of Research

Not applicable

Article Title

An Australian chickpea pan-genome provides insights into genome organization and offers opportunities for enhancing drought adaptation for crop improvement

Article Publication Date

18-Jun-2025

 

Decoding the molecular commonality underlying lip hypertrophy in cichlids

Proteoglycans and Wnt signaling pathway drive lip hypertrophy in cichlids of East African Great Lakes

Institute of Science Tokyo

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Scientists from Institute of Science Tokyo have discovered the role of wingless-related integration site signaling pathway in regulating lip hypertrophy in cichlids of East African Great Lakes. The involvement of versican and periostin proteins in lip hypertrophy provides vital clues to tackle skin diseases affecting humans.

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Credit: Institute of Science Tokyo, Japan

In a recent study, researchers have discovered that the genes related on extracellular matrix (ECM) and the Wnt signaling pathway characterize the independently acquired lip hypertrophy in cichlids of East African Great Lakes. Through advanced omics-based experiments and comparative histological analyses, they found that hypertrophied lips of cichlids had a larger proteoglycan-rich layer. This study provides vital insights into the evolutionary biology of lip hypertrophy in cichlids of East African Great Lakes.

Cichlids, a diverse family of freshwater fishes, are well-documented for their remarkable evolutionary traits. Over the years, these fishes have acquired unique facial features such as diverse snouts and varying jaw morphologies. Several reports indicate that the ability to adapt to a new environment has been a key feature of their evolution.

The cichlid fishes, especially those within the three East African Great Lakes of Victoria, Malawi, and Tanganyika, have independently evolved to achieve hypertrophied lips. The enlarged lips in these cichlids, which are a result of adaptive parallel evolution, are beneficial for foraging and detecting prey by providing a larger area of taste receptors. While different genetic influences and environmental factors are attributed to cause lip hypertrophy, the underlying molecular mechanisms are yet to be discovered.

To shed light on lip hypertrophy in cichlid fishes, researchers from Institute of Science Tokyo (Science Tokyo), Japan, collaborated with researchers from the Tanzania Fisheries Research Institute (TAFIRI), Tanzania, and conducted an in-depth study by comparing the genetic profiles and molecular pathways of cichlids with hypertrophied lips to those with normal lips. The research team led by Associate Professor Masato Nikaido comprised graduate students Nagatoshi Machii and Ryo Hatashima, Researcher Mitsuto Aibara, Assistant Professors Tatsuya Niwa and Tatsuki Nagasawa, Professor Hideki Taguchi, and researchers from the TAFIRI. Their findings were published online in eLife on April 22, 2025.

Initially, the researchers investigated the histological differences between hypertrophied lips and normal lips of cichlids from Lake Victoria, Lake Malawi, and Lake Tanganyika. They observed a significantly larger proteoglycan-rich layer within the extracellular matrix (ECM) of hypertrophied lips of cichlids from all lakes.

In subsequent proteomics-based analyses, the researchers found that 133 proteins were upregulated while the expression of 5 proteins was downregulated in the hypertrophied lips. “Interestingly, the tip of hypertrophied lips contained high amounts of proteoglycans and their related proteins such as versican and periostin,” remarks Nikaido.

Driven by their findings, the research team conducted transcriptome analysis to reveal commonality of hypertrophied lips among the three East African Great Lakes. Notably, the expression pattern of ECM-related genes reflected differences in lip morphology (hypertrophied and normal), regardless of the genetic closeness. In other words, the researchers identified the gene set that characterizes the hypertrophied lip among the independently acquired in the three lakes.

To decipher the molecular machinery involved in lip hypertrophy, the scientists examined advanced transcriptome analysis of the different developmental stages of cichlids. The results showed that genes involved in the Wnt signaling pathway were highly expressed in cichlids with hypertrophied lips at both the juvenile and adult stages.

Elaborating on the importance of the present study, Nikaido states, “The same ECM-related genes implicated in lip hypertrophy—such as versican and periostin—are also known to play key roles in human fibrotic skin diseases like keloids. Therefore, our study not only advances the current understanding of evolutionary biology in cichlids but also offers insights into skin diseases affecting humans.”

Taken together, this study reveals a shared molecular mechanism underlying the parallel evolution of lip hypertrophy in East African cichlid fishes.

 

***

 

About Institute of Science Tokyo (Science Tokyo)
Institute of Science Tokyo (Science Tokyo) was established on October 1, 2024, following the merger between Tokyo Medical and Dental University (TMDU) and Tokyo Institute of Technology (Tokyo Tech), with the mission of “Advancing science and human wellbeing to create value for and with society.”

 

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Journal

eLife

DOI

10.7554/eLife.99160.3 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Pronounced expression of extracellular matrix proteoglycans regulated by Wnt pathway underlies the parallel evolution of lip hypertrophy in East African cichlids

 

Vaping exposes pregnant women to fewer toxins than smoking

City St George’s, University of London

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Pregnant women are exposed to lower levels of toxic chemicals if they vape during pregnancy compared with if they smoke cigarettes, according to new research led by scientists at City St George’s, University of London and published today in Nicotine and Tobacco Research.

Stopping smoking during pregnancy is a key health priority for both the mother and developing baby, with more pregnant women choosing to vape as a way to stop smoking.

Until now, there’s been a lack of reliable data on exposure to harmful substances that can result from vaping during pregnancy.

In the first study to rigorously compare exposure to toxic chemicals from smoking and vaping during pregnancy, a total of 140 pregnant women were recruited to the study from five UK hospitals. They were divided into five groups: those who exclusively smoke (38 people), who only vape but previously smoked (35), who smoke and vape (25), who smoke and use nicotine replacement therapy (10) and those who have no history of using any nicotine or tobacco products (32).

Urine samples were taken at a routine antenatal appointment and analysed to measure levels of nicotine and harmful substances. These included 14 different chemicals called volatile organic compounds (VOCs) – one of the main toxicants inhaled when smoking or vaping. VOCs are major risk factors for cancer, and for respiratory and cardiovascular disease.

Compared with the women who exclusively smoked, urine levels of 10 VOCs were significantly lower in those who exclusively vaped, ranging from a 44% to 97% reduction. They also found that levels of 13 VOCs were similar among women who exclusively vaped compared with those who had never used nicotine or tobacco products.

Professor Michael Ussher, Professor of Behavioural Medicine from the School of Health and Medical Sciences at City St Georges, University of London, who led the study, said:

“Just because mothers-to-be are exposed to fewer harmful chemicals by opting to vape instead of smoking cigarettes, does not mean vaping during pregnancy is safe.”

“Understanding exposure to these toxins in pregnant women is only one half of the picture. We’re now embarking on the most rigorously designed study, to date, to look at whether vaping during pregnancy has any harmful health outcomes for mother or baby.”

Although the team investigated the main known toxins at the time of the study starting, they highlight that some of the toxins were similar for smoking and vaping and there could be other toxic substances found in vaping products that were not analysed in the study.

Professor Michael Ussher added: “Vaping products are constantly evolving, and so we need to keep an eye on any new toxins that we need to check for. It’s an ever-evolving field of research.”

The research was a collaboration between scientists at City St George’s, University of London, University of Nottingham, University College London, Kings College London, The US Centers for Disease Control and Prevention and The UK Health Security Agency. It was funded by Cancer Research UK.

ENDS

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Journal

Nicotine & Tobacco Research

Method of Research

Observational study

Subject of Research

People

Article Title

Toxicant and Nicotine Exposure in Pregnant Smokers, Vapers, and Nicotine-Replacement Users: Cross-Sectional Study

Article Publication Date

18-Jun-2025

 

New test will help driverless cars make ‘moral’ decisions

WHO TO HIT, WHO NOT TOO HIT

North Carolina State University

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Researchers have validated a technique for studying how people make “moral” decisions when driving, with the goal of using the resulting data to train the artificial intelligence used in autonomous vehicles. These moral psychology experiments were tested using the most critical audience researchers could think of: philosophers.

“Very few people set out to cause an accident or hurt other people on the road,” says Veljko Dubljević, corresponding author of the study and a professor in the Science, Technology & Society program at North Carolina State University. “Accidents often stem from low-stakes decisions, such as whether to go five miles over the speed limit or make a rolling stop at a stop sign. How do we make these decisions? And what constitutes a moral decision when we’re behind the wheel?

“We needed to find a way to collect quantifiable data on this, because that sort of data is necessary if we want to train autonomous vehicles to make moral decisions,” Dubljević says. “Once we found a way to collect that data, we needed to find a way to validate the technique – to demonstrate that the data is meaningful and can be used to train AI. For moral psychology, the most detail-oriented set of critics would be philosophers, so we decided to test our technique with them.”

The technique the researchers developed is based on the Agent Deed Consequence model, which posits that people take three things into account when making a moral judgment: the agent, which is the character or intent of the person who is doing something; the deed, or what is being done; and the consequence, or the outcome that results from the deed.

Specifically, the technique tests how people judge the morality of driving decisions by sharing a variety of traffic scenarios with test subjects, and then having the test subjects answer a series of questions about moral acceptability and various aspects of what took place in each scenario.

For this validation study, the researchers enlisted 274 study participants with advanced degrees in philosophy. The researchers shared driving scenarios with the study participants and asked them about the morality of the decisions that drivers made in each scenario. The researchers also used a validated measure to assess the study participants’ ethical frameworks.

“Different philosophers subscribe to different schools of thought regarding what constitutes moral decision-making,” Dubljević says. “For example, utilitarians approach moral problems very differently from deontologists who are very focused on following rules. In theory, because different schools of thought approach morality differently, results on what constituted moral behavior should have varied depending on which framework different philosophers used.

“What was exciting here is that our findings were consistent across the board,” Dubljević says. “Utilitarians, deontologists, virtue ethicists – whatever their school of thought, they all reached the same conclusions regarding moral decision-making in the context of driving.

“That means we can generalize the findings,” says Dubljević. “And that means this technique has tremendous potential for AI training. This is a significant step forward.

“The next step is to scale up testing among broader populations and in multiple languages, with the goal of determining the extent to which this approach can be generalized both within western culture and beyond.”

The paper, “Morality on the road: the ADC model in low-stakes traffic vignettes,” is published in the journal Frontiers in Psychology. First author of the paper is Michael Pflanzer, a Ph.D. student at NC State. The paper was co-authored by Dario Cecchini, a postdoctoral researcher at NC State; and by Sam Cacace, an assistant professor of psychology at the University of North Carolina at Charlotte.

This work was done with support from the National Science Foundation under grant 2043612.

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Journal

Frontiers in Psychology

DOI

10.3389/fpsyg.2025.1508763 

Method of Research

Experimental study

Subject of Research

People

Article Title

Morality on the road: the ADC model in low-stakes traffic vignettes

Article Publication Date

18-Jun-2025

‘Starter packs’ have played a central role in Bluesky’s rapid growth – new study shows

Lancaster University

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Starter packs’—curated user lists that new users can follow with a single click—played a key role in helping Bluesky grow to over 30 million users, according to a new study.

Launching new social media platforms is notoriously difficult, as users risk leaving familiar content and, most importantly, their established connections. This challenge has reinforced the dominance of existing platforms. 

However, new research, led by computer scientists at Lancaster University, TU Darmstadt and City St George's, University of London, reveals how Bluesky overcame this barrier using starter packs – an onboarding feature that helped Bluesky address the "cold start" problem and rapidly grow its user base.

“Our findings go beyond Bluesky: they point to a new framework for launching successful social platforms,” said Dr Onur Ascigil, Lecturer in Computer Science at Lancaster University and Principal Investigator of the study. “Starter packs are becoming a vital onboarding strategy for the emerging social media systems that are seeking to attract users from dominant platforms.”

The researchers believe their findings could help platform designers and policymakers promote more equitable and trustworthy online spaces.

Starter packs can be created by anybody on the platform and generally aim to rapidly create new, or recreate existing, communities.

Starter packs were adopted rapidly by Bluesky users, with more than 335,000 created in the first six months of their launch, the researchers found. They accounted for up to 43% of people following others in Bluesky during peak periods, and contributed to nearly 20% of all follow relationships across the full study period, from June 2024 to January 2025. Users included in starter packs received up to 85% more followers and posted 60% more than similar users not included.

“While only 6.25% of users were members of a starter pack at the time of the study, the outsized impact of these starter packs highlights how a relatively small mechanism can significantly influence network formation and user visibility,” said Dr Ascigil.

However, the researchers also found that starter packs tend to reinforce existing communities rather than create new ones. They help users with already-large followings grow even more. The researchers say this raises concerns about deepening popularity inequalities.

“Starter packs quickly became central to Bluesky’s network of social connections,” said Leonhard Balduf of TU Darmstadt, co-lead author of the study. 

Saidu Sokoto, also a co-lead author from City St George's, University of London, said: “We also observed risks, such as reinforcing popularity gaps and enabling misuse, including harassment or pay-for-inclusion practices. There was anecdotal evidence that some users may be paying to be added to high-visibility starter packs.”

The study also tracked spikes in Bluesky’s growth that aligned with real-world events like the US elections and changes at X (formerly Twitter). The researchers say starter packs played a crucial role during these waves of migration, helping newcomers quickly establish social connections.

“During peak migration periods—corresponding to the 2024 US elections and Twitter/X’s controversial decision to make content visible to users who had been blocked—between 20% and 40% of daily follow actions came from one-click starter pack follows,” said Dr Ascigil.

Using machine learning, the researchers analysed starter pack themes and found the largest communities centred around art, politics, gaming, sports, and activism. Many starter pack members were public figures such as journalists, politicians, and activists, i.e., groups that tend to rebuild influence early on emerging platforms.

The study, Bootstrapping Social Networks: Lessons from Bluesky Starter Packs, will be presented at the International Conference on Web and Social Media (ICWSM) in Copenhagen this June.

The study’s authors are: Leonhard Balduf and Björn Scheuermann of TU Darmstadt; Saidu Sokoto, Andrea Baronchelli and Michal Krol of City St George’s University of London; Ignacio Castro of Queen Mary University of London; Gareth Tyson of Queen Mary University of London and Hong Kong University of Science and Technology; George Pavlou of University College London and Onur Ascigil of Lancaster University.

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Journal

Proceedings of the International AAAI Conference on Web and Social Media

DOI

10.1609/icwsm.v19i1.35810 

Method of Research

Data/statistical analysis

Subject of Research

Not applicable

Article Title

Bootstrapping Social Networks: Lessons from Bluesky Starter Packs