Genetic secrets of rice pave way for future farming and conservation

Discovered genes provide strategies to protect rice crops against climate change and to domesticate wild relatives that can grow in currently unproductive habitats

King Abdullah University of Science & Technology (KAUST)

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A photo of one of the wild polyploid Oryza presented in this work (O. coarctata) described in the study.

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Credit: King Abdullah University of Science and Technology

A new study, seen in Nature Genetics and led by researchers at King Abdullah University of Science and Technology (KAUST; Saudi Arabia) and Wageningen University & Research (the Netherlands), provides new insights on rice evolution, showing how the DNA of this valuable crop has changed across species. The findings are expected to not only help with improving rice yields but also with the introduction of rice into regions where rice production is currently untenable.  

Rice is one of the first domesticated crops (approximately 10,000 years ago). The artificial selection farmers have made for nutrition and other traits that maximize profit have reduced its genetic diversity and thus its resilience to environmental stresses.  

On the other hand, the wild relatives of rice (i.e. Oryza) have experienced some 15 million years of evolution, which has given these relatives a remarkable array of genetic variation across their genomes (all the DNA in an organism) and thus an ability to adapt to all sorts of environmental conditions, like heat, drought, and salinity.  

"The genus Oryza has an incredibly rich collection of genomes. We were able to explain the consequences of the evolution on the collective genomes of rice and its wild relatives," explained KAUST Prof. Rod Wing, who led the study along with his postdoctoral research associate, Alice Fornasiero.  

Humans are diploid, meaning they inherit two sets of chromosomes—one from each parent. Anything more or less can be fatal. Plants can be polyploidy, meaning then can receive multiple sets of chromosomes from their parents. These extra sets result in a larger genome that can facilitate adaptation to new or stressful environments and the evolution of novel traits and even new species.   

The study examined nine tetraploid and two diploid wild relatives of rice. The researchers found that the species could be distinguished by subsets of the genomes. These differences were mostly due to transposable elements, also known as jumping genes because they are DNA sequences that move from one location in the genome to another and a common natural means for creating genetic diversity.  

Additionally, the existence of diploid and tetraploid species resulted in genomes that varied more than twice in size. In some of this massive DNA were genes that have strengthened the robustness of the plant against hotter temperatures, drier and saltier soil, and other environmental stresses common to the Middle East and increasing worldwide with climate change.  

The study was also able to determine the evolutionary tree of wild rice, showing when new species emerged. This history offers clues for when rice underwent significant stress that stimulated genomic changes for the plant to endure.  

"The genome analysis of this work provides a comprehensive understanding of how rice and its complex wild relatives have evolved. This work offers a comprehensive framework for future efforts for developing robust rice crops that can potentially withstand harsh environments," said Wageningen University Professor Eric Schranz, who also contributed to the study.  

With more than 3.5 billion people relying on it as the main staple of their diet, rice is one of the most important food crops in the world. 

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Journal

Nature Genetics

DOI

10.1038/s41588-025-02183-5 

Method of Research

Experimental study

Subject of Research

Not applicable

Article Title

Oryza genome evolution through a tetraploid lens

Article Publication Date

28-Apr-2025

Extreme monsoon changes threaten the Bay of Bengal's role as a critical food source

After examining 22,000 years of rainfall patterns, Rutgers researchers warn that climate conditions may reduce fish stock

Rutgers University

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Although the Bay of Bengal covers less than 1% of the global ocean, it supplies nearly 8% of the world’s fishery production. Scientists are looking to the past to predict the effect of monsoons on future marine life there.

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Credit: Kate Littler/International Ocean Discovery Program

New research involving Rutgers professors has revealed that expected, extreme changes in India’s summer monsoon could drastically hamper the Bay of Bengal’s ability to support a crucial element of the region’s food supply: marine life.

The study, published in Nature Geoscience, was conducted by scientists from Rutgers University, the University of Arizona and collaborators from India, China and Europe. To reach their conclusions, the scientists examined how the monsoon, which brings heavy rains to the Indian subcontinent, has influenced the Bay of Bengal’s marine productivity over the past 22,000 years.

Although the Bay of Bengal covers less than 1% of the global ocean, it supplies nearly 8% of the world’s fishery production. Its coastal waters support densely populated regions that rely heavily on marine resources for food and livelihoods. 

“Millions of people living along the Bay of Bengal rely on the sea for protein, particularly from fisheries,” said Yair Rosenthal, a Distinguished Professor in the Department of Marine and Coastal Sciences and the Department of Earth and Planetary Sciences at Rutgers University and an author of the study. “The productivity of these waters – the ability of the ocean to support plankton growth – is the foundation of the marine food web. If ocean productivity declines, it will powerfully affect the ecosystem, ultimately reducing fish stocks and threatening food security for coastal communities.”

The monsoon is essential for providing freshwater to the region, but the researchers found that both extremely strong and extremely weak monsoon periods over the centuries caused a significant disruption – a 50% reduction in food available for marine life at the surface. This occurred because these extreme conditions inhibited mixing between the deep and surface zones of the ocean, preventing nutrients from reaching the upper region where marine life thrives.

With climate change expected to make the monsoon more intense and variable, and those extremes provoking stratification of the ocean layers, the food supply produced by the Bay of Bengal may be threatened, researchers said.

To understand how the Indian summer monsoon and ocean productivity have changed over time, scientists studied the fossil shells of foraminifera – tiny single-celled plankton that live in the ocean and build calcium carbonate shells. The shells preserve information about the environment they grew in, acting like natural recorders of past ocean and climate conditions. 

“By analyzing their chemistry and tracking the abundance of certain types that thrive in productive waters, we reconstructed long-term changes in rainfall, ocean temperatures and marine life in the Bay of Bengal,” said geoscientist Kaustubh Thirumalai, an assistant professor at the University of Arizona and lead author of the study. “Together, these chemical signals helped us understand how the monsoon and ocean conditions responded to global climate changes over the past 22,000 years.”

The sediments analyzed were recovered from the seafloor by scientists aboard the National Science Foundation-funded research vessel JOIDES Resolution as part of the International Ocean Discovery Program.

The researchers found that productivity of the Bay of Bengal’s waters collapsed during periods of very weak monsoons, such as Heinrich Stadial 1, and very strong monsoons, such as those in the early Holocene. The period known as Heinrich Stadial 1, a significantly cold period, occurred between 17,500 and 15,500 years ago. The early Holocene, a time marked by rapid warming and sea level rise because of melting glaciers, occurred between about 10,500 and 9,500 years ago.

The amount of monsoon rainfall controls the volume of river discharge into the Bay of Bengal. The freshwater significantly changes oceanographic conditions and affects the feeding cycle of fish and plankton. When monsoon rains are too intense, a freshwater layer can cap the ocean surface, blocking nutrients from below. Without nutrients, plankton growth drops – and with it, the entire food chain, including fish. Weaker monsoons also suppress nutrient delivery by reducing ocean circulation and wind-driven mixing.

“Both extremes threaten marine resource availability,” Thirumalai said.

When researchers compared ancient patterns with modern ocean data and model projections, they found an unsettling parallel: Future scenarios project warmer surface waters and stronger freshwater runoff, conditions that match past intervals when marine productivity dropped sharply. Compounding the risk, future winds may not be strong enough to counteract the stratification that suppresses mixing.

Looking at past climate patterns helps scientists understand how the interconnected components and processes that compose the physical Earth, including its atmosphere and biosphere, affect the climate, environment and all organisms over long timescales.

“The relationship between monsoons and ocean biology we have uncovered in the Bay of Bengal gives us real-world evidence of how marine ecosystems have reacted to warming and monsoon shifts and may do so in the future,” Rosenthal said. “These insights can help refine projections and inform sustainable management of fisheries and coastal resources as the impacts of climate change accelerate.”

Kaixuan Bu, an assistant research professor with the Department of Marine and Coastal Sciences at Rutgers-New Brunswick, also contributed to this study.

Explore more of the ways Rutgers research is shaping the future.

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Journal

Nature Geoscience

DOI

10.1038/s41561-025-01684-6 

Method of Research

Observational study

Subject of Research

Not applicable

Article Title

Extreme Indian summer monsoon states stifled Bay of Bengal productivity across the last deglaciation

Article Publication Date

28-Apr-2025

 Empathic comforting varies more within bonobo and chimpanzee species than between them

Durham University

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Juvenile bonobo embraces a distressed companion during post-conflict consolation.  

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Credit: Zanna Clay/Lola ya Bonobo Sanctuary

Psychologists from Durham University, UK, observed the behaviour of 90 sanctuary-living apes to establish whether bonobos were more likely than chimpanzees to comfort others in distress. 

The study, led by Dr Jake Brooker, found that both species consoled their peers at similar rates, with the greatest variation actually occurring within each species. 

This challenges long-held assumptions that bonobos are the more empathic ape and instead highlights the variation within each species. 

It is the first time that the two species’ consolation tendencies have been directly compared. 

The study has been published in the journal Evolution and Human Behavior. 

The researchers studied 40 bonobos at the Lola ya Bonobo sanctuary in the Democratic Republic of Congo and 50 chimpanzees at the Chimfunshi Wildlife Orphanage in Zambia. 

In total, the team logged 1,400 hours of observation across the two species, focussing on how individuals reacted to a group member that had experienced a naturally occurring moment of distress such as a fight. 

They found that older apes were less likely to console than younger apes in both bonobos and chimpanzees. 

This suggests that emotional sensitivity to others emerges early in ape development. 

In bonobos, younger individuals were more likely to console others and be consoled. 

In chimpanzees, young males and close social partners consoled the most. 

Both species console each other in a similar way to humans, with behaviours including embracing, hand grasping, and touching. 

Dr Brooker, of Durham University’s Department of Psychology, said: “For a long time, bonobos have been thought of as the more empathic ape, whilst chimpanzees are typically spoken about as the violent, despotic ape. 

“However, we found that chimpanzees are just as likely to console one another as bonobos.  

“Instead, like recent studies comparing bonobos and chimpanzees in aggression, social tolerance, and sexuality, our findings highlight the important individual and social variation within each species. 

“Just like humans, bonobos and chimpanzees may flexibly show empathy depending on the individual, the group, and the surrounding social culture.” 

Senior author of the study, Professor Zanna Clay of Durham University’s Department of Psychology, added: “Although empathy is very important for our own species, our findings show that empathic behaviours, like consolation, appear to be a common trait we also share with our two closest ape relatives.  

“Finding these overlaps between our two close cousins suggests our last common ancestor likely showed these empathic capacities too. 

“A next step will be to see how much these patterns are also observed in other settings, particularly in the wild.” 

The research team say that collecting more data on different groups of apes in a variety of settings would help further our understanding of our closest living relatives, which in turn could shed light on the evolution of human social behaviour.  

This study was funded by the Templeton World Charity Foundation. 

ENDS 

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Journal

Evolution and Human Behavior

DOI

10.1016/j.evolhumbehav.2025.106682 

Method of Research

Observational study

Subject of Research

Animals

Article Title

Within-species variation eclipses between-species differences in Pan consolation

Article Publication Date

25-Apr-2025

Two young bonobos embracing

Victim bonobo with pout face being consoled by a juvenile bystander

Credit

Zanna Clay/Lola ya Bonobo Sanctuary

Mother chimpanzee embracing her distressed juvenile son

At Chimfunshi, chimpanzees live in large naturalistic miombo woodland forest enclosures

Juvenile chimpanzee holding the hand of adult following social conflict

Adult chimpanzee embracing juvenile chimpanzee

Adult chimpanzee embracing juvenile chimpanze

Credit

Jake Brooker/Chimfunshi Wildlife Orphanage Trust

 

Many paths to an angry bird

Uncovering the roots of aggressiveness in female cavity-nesting birds

Duke University

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Among the pairs of species compared in the study are the Yellow Warbler (left) and the Prothonotary Warbler— an obligate cavity nester. 

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Credit: Photos courtesy of Shelby Lawson and Michael Jeffords

“Get off my lawn!”

Funny as a meme but maybe scary in real life, this short sentence is synonymous with an elderly man shouting at kids whose bikes have gotten too close to a well-manicured front yard. But it could just as well represent a female bird, aggressively chasing whatever intruder gets too close to her nest.

Not any female bird, though. An international team of researchers led by Sara Lipshutz, assistant professor of Biology at Duke University, found that female birds who can only nest in cavities are far more aggressive than those who don’t have this restriction on their nesting real estate.

Called obligate secondary cavity nesters, these are species that build their nests in pre-existing cavities in tree trunks, fence posts or rocky outcrops. “They can't excavate that cavity themselves, and they can’t just build a nest anywhere,” explained Lipshutz. “They have to find a hole in a tree, and this is the only way they can reproduce.”

These specific needs — and the fact that they do not create these cavities themselves — mean that females with good nest sites have a precious resource to defend. And they do, with beaks and claws, and quite a bit of angry vocalizing.

Lipshutz’s federally-funded team focused on five families of birds: swallows, wood warblers, sparrows, thrushes and wrens, and on two closely related species per family — one an obligate secondary cavity nester, and one not. The researchers then strategically placed decoys corresponding to each species and Bluetooth speakers playing their call in the vicinity of nests and observed how the resident birds responded.

As with so many other traits, one could expect aggressiveness to run in families, being more prevalent in some branches of birds’ evolutionary tree than in others. What Lipshutz and her team found, however, was that aggressiveness is far more related to nest strategy than to family. With the exception of never-aggressive sparrows and always-aggressive wrens, obligate cavity nesters were far more determined to get intruders off their lawn than their more versatile cousins. Among the obligate cavity-nesters, females were also more aggressive than males, possibly reflecting the higher cost they’d bear if their nest was lost.

“It was a really striking behavioral pattern,” said Lipshutz.

“The pressure to compete led to higher aggressiveness,” added Kimberly Rosvall, a Duke alumna whose lab at Indiana University contributed to the project. “And this was especially strong for the females.”

The team also looked at another frequent culprit of aggressiveness: testosterone. Once again, the results were surprising. Females from cavity-nesting species didn’t have higher levels of testosterone.

If family and hormones can’t explain why obligate cavity-nesters are particularly aggressive, could it be that aggressiveness is associated with specific genes? Lipshutz and her team looked at how genes are expressed — turned on or off — in each of their study species, to understand whether certain genes are repeatedly used in cavity-nesters. Their findings indicate both yes and no. Cavity-nesters expressed many of the same genes in the same manner, but fewer genes seemed to be consistently associated with aggression across all species.

“We always want to find the genes, a handful of genes that make a lot of sense, previously known genes that are associated with aggression and maybe have even been experimentally manipulated to impact aggression,” said Lipshutz. “And we didn't find any of those usual suspects.”

Lipshutz is far from disappointed, though. “There are probably several hundred genes associated with aggression and they're probably all working together in subtle ways. Those combinations are not the same for each species, which is really interesting from an evolutionary perspective,” she said. “It shows that there are independent ways to get to the same behavioral outcome.

“As our team likes to say, ‘There are many possible routes to build an aggressive bird.’”

This work was funded by the U.S. National Science Foundation (DBI-1907134, DBI-2146866, IOS-1953226 and IOS-1942192).

CITATION: “Repeated Behavioral Evolution Is Associated With Convergence of Gene Expression in Cavity-Nesting Songbirds,” Sara E Lipshutz, Mark S Hibbins, Alexandra B Bentz, Aaron M Buechlein, Tara A Empson, Elizabeth M George, Mark E Hauber, Douglas B Rusch, Wendy M Schelsky, Quinn K. Thomas, Samuel J. Torneo, Abbigail M Turner, Sarah E Wolf, Mary J Woodruff, Matthew W Hahn, Kimberly A Rosvall. Nature Ecology and Evolution, April 28, 2025. DOI: 10.1038/s41559-025-02675-x

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Journal

Nature Ecology & Evolution

DOI

10.1038/s41559-025-02675-x 

Method of Research

Experimental study

Subject of Research

Animals

Article Title

Repeated behavioural evolution is associated with convergence of gene expression in cavity-nesting songbirds

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