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University of Adelaide researchers developing gene drive technology to combat invasive mice

ABC Rural

 / By Dylan Smith and Brooke Neindorf

Posted Thu 10 Nov 2022 at 1:49amThursday 10 Nov 2022 at 1:49am, updated Thu 10 Nov 2022 at 3:32pmThursday 10 Nov 2022 at 3:32pm

five mice on top of each other
The technology aims to make future females of invasive mice species infertile.(Supplied: University of Adelaide)

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Researchers at the University of Adelaide have released their findings about the potential effectiveness of gene drive technology to control invasive mice.

Key points:

  • A South Australian research team identifies new technology it hopes will eventually curb mice numbers
  • Co-author Luke Gierus says the technology is the first feasible genetic biocontrol tool for invasive mammals
  • Researchers believe the technology can be developed to work against other invasive pests

The technology — named t-CRISPR — uses sophisticated computer modelling on laboratory mice.

DNA technology is used to make alterations to a female fertility gene and, once the population is saturated with the genetic modification, the females that are generated will be infertile.

Research paper co-first author and post-graduate student Luke Gierus said the technology was the first genetic biological control tool for invasive animals.

“So we can do an initial seeding of a couple hundred mice and that will be enough, in theory, to spread and eradicate an entire population,” he said.

“We’ve done some modelling in this paper and we’ve shown using this system we can release 256 mice into a population of 200,000 on an island and that would eradicate those 200,000 in about 25 years.”

person with facial hair in their mid 20's smiles at the camera
Paper co-author Luke Gierus says the technology has a long way to go but signs are promising.(Supplied: Luke Gierus)

The team has been undertaking the research for five years.

Mr Gierus said the next step would be to continue testing in laboratories before releasing mice onto islands where the team could safely monitor the effects.

He said the method was far more humane than other methods, such as baiting.

“It’s potentially a new tool that can either be used alongside the current technology or by itself,” Mr Gierus said.

“This is quite a revolutionary technology that gives us another way to try and control and suppress mice.”

Mice scramble over a white background
Invasive mouse species have caused millions of dollars in damages to crops in recent years.(ABC News Video)

Technology welcomed

CSIRO research officer and mouse expert Steve Henry said wiping out mice from agricultural systems would be a wonderful outcome but he could not see it happening any time soon.

“The farming community are fantastic in terms of their willingness to adopt new ideas, so while it’s really important to do this research, the time frame is long and we need to make sure we don’t say we have a solution that’s just around the corner.”

But Mr Henry believed the technology would be welcomed with open arms when it did arrive.

A man in a hat weights a mouse at the end of a string
CSIRO researcher Steve Henry says farmers are keen on innovative solutions.(ABC News: Alice Kenney)

“While we need to be focusing on the stuff that we can use to control mice now, we also need to be looking outside of the box in terms of these new technologies … into the future,” he said.

Mr Henry said that while he did not have extensive knowledge about the technology, it was exciting.

“The other thing that is really cool is you can make it so it doesn’t affect native rodent species as well,” he said.

Farmers group welcomes research

Grain Producers South Australia chief executive officer Brad Perry said introduced mouse species could severely damage crops and equipment, and recent plagues had been destructive.

“When it comes to pests and diseases in grain and agriculture more broadly, we need to be innovative and think outside the square on prevention measures,” Mr Perry said.

He said technology such as this could help farmers save money in the long run.

a mouse held by the back of its neck stares into the camera lense
Invasive mice species can have a devastating impact on crops.(Supplied: Michael Vincent)

“Grain producers currently manage populations by minimising the food source at harvest, and if populations require [it] zinc phosphide baits are used,” Mr Perry said.

“However, using baits adds to input costs, it is not always readily available and there are limited windows to when this is effective.”

Mr Perry said many farmers would be keen to see the technology in the near future.

“We are supportive of additional tools that help reduce introduced mouse populations — particularly when it involves local world-leading research at the University of Adelaide — which is targeted, reduces inputs and is sustainable.”

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Posted 10 Nov 202210 Nov 2022, updated 10 Nov 202210 Nov 2022

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Insect DNA barcoding results delight UniSC entomologist

  • Education
  • 14 Nov 2022 2:18 pm AEST

University of the Sunshine Coast

Insect DNA barcoding results to be released publicly today show exciting progress in the tri-state Insect Investigators project, coordinated across regional Queensland by a UniSC entomologist.

“I’m absolutely blown away by the results to date, and by the enthusiasm of school students and teachers to engage in insect research,” said insect ecology researcher Dr Andy Howe of the University of the Sunshine Coast’s Forest Research Institute.

Seventeen Queensland schools (listed below) are among 50 schools involved in the ongoing citizen science project, led by the South Australian Museum.

Only about 30 percent of the estimated 225,000 insect species in Australia are formally named and described.

Thousands of new insects have now been successfully recorded in the project, which connects regional and remote school students with researchers to learn about Australia’s rich biodiversity.

Beerwah State High School was among those that set a Malaise trap on their grounds in March to collect and monitor local insects over a four-week period. It was one of many that Dr Howe has visited across the state to provide updates on insect species through the taxonomic process.

“It makes so much sense to engage our schools in research on insect taxonomy; schools are located throughout many environment types, which means they can collect a huge diversity of insects, simultaneously,” Dr Howe said.

“We can then use the data to not only name undescribed species, but importantly contribute to distribution maps of thousands of insects and spiders, which contributes to managing the environment sustainably.”

Overarching project leader Dr Erinn Fagan-Jeffries said more than 14,000 insect specimens were selected to be DNA barcoded by the Centre for Biodiversity Genomics at The University of Guelph in Canada, and today the DNA barcoding results will be released.

Dr Fagan-Jeffries said DNA barcoding involved sequencing a small section of the genome and using the variation among these barcodes to discriminate species.

“While the gold standard is always going to be identifying and describing insects using DNA data in combination with their physical characteristics, the DNA barcodes provide a fast and cost-effective way of shining a light on the remarkable diversity of insects in Australia that we know so little about,” she said.

Through Insect Investigators, participating schools have added more than 12,500 new DNA barcodes to the international online repository, the Barcode of Life Database.

The variation among these barcodes suggests that there are more than 5,000 different species present among the specimens, and just over 3,000 of those are brand new records on the database.

Each of these DNA barcodes relates back to an individual insect specimen that will be deposited in the entomology collections at the South Australian Museum, Queensland Museum and the Western Australian Museum.

Taxonomists from around Australia will then be able to examine and determine if they represent undescribed species.

“It is highly likely that all contributing schools have found species new to Western science which is really exciting, but how many of these species we are actually able to describe is dependent on the resources and support available for taxonomy,” said Dr Fagan-Jeffries.

“Despite there currently being many more insect groups than taxonomists, we are hopeful that the taxonomists will be able to spot some new species that can be described, and in those cases, the students will then be invited to name the unique species that they have discovered.”

Participating Queensland schools:

  • ​Back Plains State School
  • ​Beerwah State High School
  • ​Belgian Gardens State School
  • ​Blackall State School
  • ​Cameron Downs State School
  • ​Columba Catholic College
  • ​Gin Gin State High School
  • ​Glenden State School
  • ​Kogan State School
  • ​Mornington Island State School
  • ​Mount Molloy State School
  • ​Prospect Creek State School
  • ​Springsure State School
  • ​St Patrick’s Catholic School, Winton
  • ​Tamborine Mountain State School
  • ​Yeppoon State High School
  • ​Yeronga State School

Dr Howe, whose PhD in 2016 examined an exotic ladybird in Denmark, said students enjoyed the information in his talks, designed to be entertaining as well as inspiring.

He said increasing Australia’s knowledge of its insect species could have benefits ranging from better management of the environment and effects of climate change and natural disasters to controlling pests and developing new medicines.

The DNA barcoding results will be released on the website https://insectinvestigators.com.au.

Insect Investigators received grant funding from the Australian Government, is led by the South Australian Museum, and involves 17 partner organisations.

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A gene from 28 million years ago protects today’s plants against caterpillars

Date:November 15, 2022Source:eLifeSummary:The defense mechanisms plants use to recognize and respond to a common pest — the caterpillar — has arisen from a single gene that evolved over millions of years, according to a new report.Share:

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The defence mechanisms plants use to recognise and respond to a common pest — the caterpillar — has arisen from a single gene that evolved over millions of years, according to a report published today in eLife.

The study finds that some plants, such as soybeans, have lost this protective gene over time, and suggests that breeding plants or genetically engineering them to reintroduce the gene could protect against crop failure.

The health status of a plant depends on the immune system it inherits. In plants, this means inheriting certain types of pattern recognition receptors that can recognise distinct pathogens and herbivore-derived peptides, and trigger an appropriate immune response.

“Inheriting the right types of pattern recognition receptors can allow plants to recognise threats and cope with diseases and pests,” explains lead author Simon Snoeck, postdoctoral researcher at the Department of Biology, University of Washington, US. ” Although we know many pest-derived molecules which activate immune responses in plants, our knowledge of how plants evolved the ability to sense new threats is limited.”

To address this gap, the team set out to define the key evolutionary events that allowed plants to respond to a common threat — the caterpillar. It was already known that species in a group of legumes — including mung beans and black-eyed peas — are uniquely able to respond to peptides produced from the mouths of caterpillars as they munch through plant leaves. So they looked at the genomes of this group of plants in depth to see whether a common pattern recognition receptor called the Inceptin Receptor (INR) had changed over millions of years, gaining or losing the ability to recognise caterpillars.

They found that a single, 28-million-year-old receptor gene perfectly corresponds with the plant immune response to the caterpillar peptides. They also found that among the descendants of the oldest plant ancestors that first evolved the receptor gene, a few species that could not respond to the caterpillar peptides had lost the gene.

To understand how this ancient gene acquired the ability to recognise new peptides from today’s pathogens, the team employed a technique called ancestral sequence reconstruction where they combined information from all modern-day receptor genes to predict the 28-million-year-old original sequence. This ancestral receptor was able to respond to caterpillar peptides. However, a slightly older version with 16 changes in the receptor sequence could not.

This genetic history, together with computer models showing how the ancient and current receptor structures may have differed, provide clues to how the receptor evolved. It suggests that there was a key insertion of a new gene into the ancestral plant’s genome more than 32 million years ago, followed by rapid evolution of diverse forms of the new receptor. One of these forms acquired the ability to respond to caterpillar peptides, and this new capability is now shared in dozens of descendant legume species.

“We have identified the emergence and secondary loss of a key immunity trait over plant evolution,” concludes senior author Adam Steinbrenner, Assistant Professor at the Department of Biology, University of Washington. “In the future, we hope to learn more about genome-level processes that generate new receptor diversity and identify as-yet unknown immune receptors within plant groups. As increasing genomic data becomes available, such approaches will identify ‘missing’ receptors that are useful traits to reintroduce into plants to help protect crops.”


Story Source:

Materials provided by eLifeNote: Content may be edited for style and length.


Journal Reference:

  1. Simon Snoeck, Bradley W Abramson, Anthony G K Garcia, Ashley N Egan, Todd P Michael, Adam Steinbrenner. Evolutionary gain and loss of a plant pattern-recognition receptor for HAMP recognitioneLife, 2022; 11 DOI: 10.7554/eLife.81050

Cite This Page:

eLife. “A gene from 28 million years ago protects today’s plants against caterpillars.” ScienceDaily. ScienceDaily, 15 November 2022. <www.sciencedaily.com/releases/2022/11/221115113928.htm>.

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Video: UNESCO examines the environmental and biodiversity impacts of gene-edited plants and animals

UNESCO | November 8, 2022

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Credit: UNESCO
Credit: UNESCO

Genome editing is a powerful tool. It allows us to modify genes not only to treat human diseases but also to change characteristics of animals and plants within a very short period of time at a much larger scale than any other methods that humans had ever used in the past. A technique called “gene drive” that uses genome editing to spread certain genes in the entire population of a target species could eradicate diseases caused by insects such as malaria and other vector borne diseases. Plants and animals could be more resistant to diseases and grow quicker. But is it safe? What would be the impact on the environment and biodiversity?

The third of the series of Ethics of Genome Editing “3. Impact of Genome editing on plants, animals and environment” is now available in English, French, Japanese, Spanish and other languages subtitles.

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Genomic analyses suggest three mysterious ancestors contributed DNA to the modern-day banana

An unusual type of banana cut in half showing white flesh with dark seeds
Breeding helped get rid of wild bananas’s seeds to create the fleshy fruit cherished today.JULIE SARDOS

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People like to know where their food comes from, but even experts are throwing up their hands when it comes to the origins of the modern banana. An extensive genetic analysis of more than 100 varieties of wild and cultivated bananas unpeels the fruit’s tangled history of domestication and reveals the existence of three previously unknown—and possibly still living—ancestors. Banana experts want to track down those mysterious forebears to see whether their genes might help keep modern banana crops healthy.

“Banana domestication is much more complicated than I had realized previously,” says Loren Rieseberg, an evolutionary biologist at the University of British Columbia, Vancouver, who was not involved in the study.

About 7000 years ago, bananas were not the seedless, fleshy fruits we know today. The flesh was pitted with black seeds and nearly inedible. Instead, people ate the banana tree’s flowers or its underground tubers. They also stripped fibers from the trunklike stem to make rope and clothes. Banana trees back then were “very far from the bananas we see in people’s fields today,” says Julie Sardos, a genetic resources scientist at the Alliance of Bioversity International, which stockpiles banana varieties.

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Scientists do know the banana’s predominant wild ancestor is a species named Musa acuminata, which occurs from India to Australia. Most researchers agree that Papua New Guinea is where domesticated bananas as we know them first appeared. Today, there are many banana varieties—more than 1000 at last count. Over the course of their domestication, the modern bananas available in supermarkets lost their seeds and became fleshier and sweeter. But it’s been hard to pin down exactly how and when that domestication occurred. Complicating matters, some bananas have the usual two sets of chromosomes, whereas others have three sets or more, suggesting at least some modern bananas are hybrids that resulted from the interbreeding of two or more varieties, or even different species.

There’s good reason to try to tap into the modern banana’s deep historical gene pool: The $8 billion banana industry, which produces 100 billion bananas annually, is threatened by diseases such as Panama disease and banana bacterial wilt. Banana breeders are scrambling to find ways to combat such pathogens, particularly the ones that attack the Cavendish banana, which accounts for more than half of all the bananas exported to the United States and Europe. Some are collecting wild relatives and obscure varieties that are more resistant to disease. But introducing genes from distant ancestors could also help steel modern-day bananas. Genetic analyses can help piece together the history of domestication and pin down living members of those ancestral fruits.

Nabila Yahiaoui, a banana genomics scientist at the French Agricultural Research Centre for International Development in Montpellier, and colleagues previously compared DNA from 24 collected samples of wild and domestic bananas. In a few of them, they found something puzzling: DNA that didn’t match that from any of the other samples. Based on that finding, they proposed in 2020 that, in addition to M. acuminata and other known wild relatives, two unknown species contributed DNA to the modern banana.

In the new study, Sardos and her colleagues expanded on that work, focusing on banana varieties with two sets of chromosomes, as they are likely more closely related to the first domesticated bananas. (The Cavendish has three sets.) They sampled the DNA of 68 samples of wild relatives and of 154 types of cultivated bananas, including 25 varieties Sardos’s team collected in Papua New Guinea. That’s an impressive number of cultivars, some of which can be hard to obtain, says Tim Denham, an archaeologist at Australian National University who was not involved with the work.

The comparison provided more evidence that bananas were originally cultivated on New Guinea and suggested an M. acuminata subspecies named “banksia” was the first to be domesticated. The same subspecies subsequently contributed to more widespread cultivated varieties, Sardos and colleagues report this month in Frontiers in Plant Science. “This [conclusion] is significant,” Denham says. “It confirms previous archaeological, botanical, linguistic, and genetic studies.”

The samples also pointed to the existence of a third unknown source of banana genetic material, the team reported. Scientists have yet to identify the three species; their data suggest one came from New Guinea, one from the Gulf of Thailand, and the third from somewhere between northern Borneo and the Philippines.

Denham was surprised to find that the modern banana varieties on New Guinea are more genetically diverse than their wild ancestor. “This runs counter to most genetic arguments that speculate that initial domestication results in a bottleneck,” he says. He suspects that even as banana growers worked to improve bananas, there was rampant interbreeding with wild relatives, leading to bunches of varieties with different genetic ancestries.

“This work further confirms the importance of hybridization in the evolution of [certain] crops,” says Rieseberg, whose work with sunflowers has demonstrated that interbreeding can be important for evolution.

The field remains ripe with possibility: Sardos and other banana aficionados are hoping to visit small farms and other sites in the ancestral bananas’ homelands to see whether they can find more modern descendants. They, too, may yield a stock resistant to disease that can be crossbred with commercial bananas. “There is a lot of unsampled banana diversity out there,” Rieseberg says.


doi: 10.1126/science.adf3420

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PLANTS & ANIMALS

ABOUT THE AUTHOR

Elizabeth Pennisi

Elizabeth Pennisi

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Liz Pennisi is a senior correspondent covering many aspects of biology for Science

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It takes three: the genetic mutations that made rice cultivation possible

kobe.ac

  • July 1, 2022
  • Graduate School of Agriculture
  • News

Applications in preventing seed scattering and increasing rice yield

Rice has a long history as a staple food in Japan and other parts of Asia. The results of a new study by an international research collaboration suggest that the emergence of cultivated rice from wild rice plants is the result of three gene mutations that make the seeds (i.e. the grains of rice) fall from the plant less easily.

In their investigations, the researchers discovered that each of the three mutations individually have little effect but when all three mutations are present the panicles of the rice plant retain more of their seeds- resulting in a greater crop yield.

It is believed that the domestication of wild rice began when our ancestors discovered and started to cultivate rice plants that do not drop their seeds easily, paving the way for stable rice production. It is hoped that these research results can contribute towards future improvements to the ease in which rice seeds fall (i.e. making the crop easier to thresh) and the development of high-yield rice cultivars where every grain can be harvested, reducing waste.

This discovery was made by an international collaboration which included researchers from Kobe University’s Graduate School of Agriculture (Japan), the National Institute of Genetics (Japan), University College London (UK), the University of Warwick (UK), Yezin Agricultural University (Myanmar) and the Cambodian Agricultural Research and Development Institute.

These research findings were published online in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) on June 23 (JST).

Main points

  • The researchers discovered the causal mutation in the qSH3 gene that is necessary to prevent rice seeds from falling (referred to as seed shattering).
  • In the qSH3 gene mutation, there is a single nucleotide substitution on the gene (YABBY). This mutation is found in the vast majority of cultivars for the world’s most widely farmed rice species (indica and japonica).
  • The researchers found that plants with only the qSH3 gene mutation dropped their seeds naturally. However when the qSH3 mutation was combined with the previously reported sh4 gene mutation, the abscission layer (which is required for seed shattering) was partially inhibited.
  • Seeds still fell with the qSH3 and sh4 mutation-mediated partial inhibition of the abscission layer, however the addition of a mutation at SPR3 that causes closed panicle structure resulted in the majority of seeds remaining on the plant, thus increasing the crop yield.
  • An analysis of structural mechanics was performed to determine the relationship between panicle opening and closing and inhibition of the abscission layer. The results showed that with all three mutations present, shattering was suppressed and the seeds remained stably attached to the panicles.
  • It is thought that our hunter-gatherer ancestors happened to observe the visual characteristics (i.e. closed panicles) of certain rice plants that had a higher yield and began to cultivate them, paving the way for rice to become a staple crop.

Research Background

Figure 1: Cultivated rice was developed from wild rice, which is a weed.

Oryza sativa (often referred to as Asian rice in English) is widely grown and consumed worldwide. It is known to have originated from the wild rice weed Oryza rufipogon (Figure 1). It is believed that rice began to be cultivated when hunter gatherers in ancient times chose individual wild rice plants that had suitable characteristics for this purpose. Wild rice plants perform a seed shattering process which scatters their seeds, enabling them to propagate efficiently. However, when cultivating rice, this seed shattering must be suppressed in order to obtain a stable crop (Figure 2A). In 2006, the sh4 gene was discovered: this gene is necessary for the commencement of seed shattering in plants including rice, and it was proposed that a mutation in this gene enabled the cultivation of rice. However the current research team showed that this sh4 mutation alone is insufficient to prevent seed shattering loss, suggesting that other gene mutations are also involved. With a focus on the early history of rice cultivation, this study brought together specialists in plant genetics, archaeobotany and structural mechanics to elucidate how increasing yields of rice came to be cultivated.

Figure 2: Seed shattering in wild rice and cultivated rice.A. Comparison of the panicles of wild rice and cultivated rice:
When wild rice seeds ripen, seed shattering occurs in which they naturally fall to the ground.
B. Comparison of the seed bases between wild rice and cultivated rice:
Seed shattering is caused by the breakdown of the abscission layer that forms at the base of the seed.
C. Comparison of the structural positioning of the abscission layer in wild rice and cultivated rice:
In wild rice, abscission layers are fully formed around the vascular bundles. However, in cultivated rice (japonica), the abscission layer isn’t formed at all.

Research Methodology

Figure 3: Discovery of the qSH3 gene related to seed-shattering loss in wild rice

Seed shattering is caused by a structure called the abscission layer that is formed at the base of each rice seed (Figure 2 B and C). The researchers found that a single nucleotide substitution (from cytosine to thymine) in the DNA of the qSH3 gene is required to inhibit the abscission layer (Figure 3), in addition to the aforementioned sh4 gene mutation. This qSH3 gene mutation is found in the main types of rice that is cultivated worldwide (indica and japonica). Individual mutations related to seed shattering, for example in genes sh4 and qSH3, cannot prevent shattering in wild rice plants on their own. However, the researchers discovered that when sh4 and qSH3 mutations were combined, this partially inhibited the formation of the abscission layer, which is required for seed shattering (Figure 4). Despite this, they concluded that such a small inhibition would not be enough to produce a stable crop yield, as seeds drop easily in a natural environment. Thus, they decided to focus on panicle shape next. Panicle refers to the clusters of thin branches at the top of the rice plant that carry the seeds.

Figure 4: Combining qSH3 and sh4 gene mutations partially inhibited the abscission layerWild rice plants with the double mutation exhibited slight abscission layer inhibitions around the vascular bundles (as indicated by the arrowhead) and it was determined that the seed was attached to the rachis. However even with this partial abscission layer junction, the seeds still tend to fall easily in a natural environment.
Figure 5: Panicle shape in wild rice (open panicles)When wild rice produces seeds, the panicles open to allow the seeds (i.e. grains of rice) to be efficiently shattered. On the other hand, the panicles on cultivated rice are closed.
Figure 6: Seed gathering rate results for rice plants with a combination of three genetic mutations (in sh4qSH3 and SPR3)The panicle shapes of 8 plants (above) and the seed gathering rate for each plant when grown on cultivated land (below).

Wild rice has an open panicle structure which enables the seeds to fall easily (Figure 5). Through hybridization, the researchers produced 8 wild rice plants, each with a different combination of three gene mutations: a mutation at the SPR3 that causes the panicles to close, and the aforementioned sh4 and qSH3 mutations. They then investigated the yield of each plant. They found that individual mutations had little effect and that even combining two mutations did not result in a large yield increase. However, when all three gene mutations were present, the yield increased exponentially (Figure 6).

An analysis of the structural mechanics of the closed panicle alteration and the abscission layer inhibition revealed a complementary relationship between the two. The burden of gravity on the seed base’s abscission layer is lower in closed panicle plants than in open panicle plants, which potentially brings about an even greater crop yield by further reducing seed shattering. ‘Non-seed-shattering behavior’ caused by sh4 and qSH3 mutations and ‘closed panicles’ caused by the SPR3 mutation are completely unrelated characteristics, however the incidental collaboration between these characteristics is considered to be what enabled rice to become a crop.

In the three arrows parable, 16th century Japanese warlord MORI Motonari gave each of his three sons an arrow and they were able to break the individual arrows easily. However, a bundle of three arrows is stronger and by showing his sons that three arrows together could not be broken, he explained that the three of them should work together govern the land. In rice cultivars, three mutations that have little effect on their own incidentally work together – an important stepping stone towards the success of rice as a crop.

Rice has been a source of daily energy for people for thousands of years and some Japanese rice cultivars are considered cultural works of art. These research results not only reveal the seed shattering mechanism, they also give us insight into the long history behind the improvement of rice growing.

Further Developments

Even though rice is an essential crop worldwide, it is still not fully understood how it was domesticated. Advances in agricultural techniques were accompanied by the development of rice cultivars that dropped their seeds less and less easily, suggesting that the acquirement of non-seed shattering behavior is the result of multiple gene mutations. It is hoped that by further investigating these mutations, the cultivation process for rice can be elucidated. In addition the amount of seed shattering could be controlled utilizing genes with many of these mutations, leading to the development of new rice cultivars where all the seeds produced by the plant can be harvested.

Acknowledgements

This research was funded by the following:

  • Japan Society for the Promotion of Science (JSPS) Grant-In-Aid for Scientific Research (C) (JP 18KO5594)
  • JSPS Postdoctoral Fellowship for Research in Japan  (JP 16F16095)
  • JSPS Fund for the Promotion of Joint International Research (JP 15KK0280)
  • JSPS Bilateral Open Partnership Joint Research Projects (JPJSBP120189948/JPJSBP120219922)
  • Nikki Saneyoshi Foundation
  • Kinoshita Foundation
  • National Institute of Genetics (Japan) Joint Research Fund (NIG-JOINT 82A 2016-2018)

In addition, the wild rice accessions used in this study were provided by the National Institute of Genetics (Japan) and the National Bioresource Project (NBRP) of the Ministry of Education, Culture Sports, Science and Technology, Japan.

Journal Information

Title“A stepwise route to domesticate rice by controlling seed shattering and panicle shape”DOI:10.1073/pnas.2121692119AuthorsRyo Ishikawa, Cristina Cobo Castillo, Than Myint Htun, Koji Numaguchi, Kazuya Inoue, Yumi Oka, Miki Ogasawara, Shohei Sugiyama, Natsumi Takama, Chhourn Orn, Chizuru Inoue, Ken-Ichi Nonomura, Robin Allaby, Dorian Q Fuller and Takashige IshiiJournalProceedings of the National Academy of Sciences of the United States of America (PNAS)

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USDA-ARS Releases Genome of the Voracious Desert Locust

USDA Agricultural Research Service sent this bulletin at 06/27/2022 09:16 AM EDT

View as a webpageARS News ServiceARS
News ServiceTwo desert locustsARS has produced the first high-quality, highly detailed genome of the desert locust. Photo by Brandon WooUSDA-ARS Releases Genome of the Voracious Desert LocustFor media inquiries contact: Kim Kaplan, 301-588-5314June 27, 2022—The first high-quality genome of the desert locust—those voracious feeders of plague and devastation infamy and the most destructive migratory insect in the world—has been produced by U.S. Department of Agriculture Agricultural Research Service scientists.The genome of the desert locust (Schistocerca gregaria) is enormous at just under 9 billion base pairs, nearly three times the size of the human genome.”We were concerned that, faced with this huge and very likely complex desert locust genome, it was going to be an extremely long and difficult job. However, we were able to go from sample collection to a final assembled genome in under 5 months,” said entomologist Scott M. Geib with the ARS Tropical Crop and Commodity Protection Research Unit in Hilo, Hawaii, and one of the team leaders. “The desert locust is one of the largest insect genomes ever completed and it was all done from a single locust.”The size of the desert locust’s chromosomes is remarkable; compare them to those of the model fruit fly Drosophila melanogaster, the first insect genome ever assembled. Many of the desert locust’s individual chromosomes are larger than the entire fruit fly genome.”With the desert locust, we were dealing with a much larger genome in many fewer pieces about 8.8 Gb in just 12 chromosomes. Next to the fruit fly, it’s like an 18-wheeler next to a compact car,” Geib said. “It was like sequencing a typical insect genome many, many times over. But with today’s advances in DNA sequencing technologies, we are now able to generate extremely accurate genomes of insects that previously would have been unapproachable.”ARS has made the genome available to the international research community through the National Center for Biotechnology Information at https://www.ncbi.nlm.nih.gov/bioproject/814718.Desert locust plagues are cyclic and have been recorded since the times of the Pharaohs in ancient Egypt, as far back as 3200 B.C. In recent decades, there have been desert locust swarms in 1967-1969, 1986-1989 and most lately 2020-2022. They cause devastation in East Africa, the Middle East, and Southwest Asia, threatening food security in many countries.Their damage can be massive. A small swarm can eat as much food in a day as would feed 35,000 people; a swarm of historic proportions covering the area of New York City eats in one day the same amount as the population of New York, Pennsylvania and New Jersey combined, according to the Food and Agriculture Organization of the United Nations.Current desert locust control mostly depends on locating swarms and spraying them with broad-spectrum pesticides. Ultimately, this genomics work could decrease dependence on such pesticides.”Having a high-quality genome is a big step toward finding targeted controls,” Geib said. “It will also give us valuable information about relatives of the desert locust that are major pests in the Americas such the Mormon cricket, another swarming species that can impact U.S. food security.”This work is part of the Ag100Pest Initiative, an ARS program to develop high quality genomes for the top 100 arthropod pests in agriculture as a foundation for basic and applied research.USDA Foreign Agricultural Service coordinated this research opportunity and provided funding from the U.S. Agency for International Development Africa Bureau through an interagency agreement.Five Desert Locust FactsThe Desert Locust (Schistocerca gregaria) is a species of short-horned grasshopper that periodically changes its body shape, behavior, and reproduction rate in response to environmental conditions such as an abundance of rainfall and moisture.Plague is actually a technical term. Desert locust infestations are identified in a sequence of increasing severity based on magnitude and geographical scale of the swarm size: recession (calm), outbreak, upsurge, plague (maximum intensity and scope).Swarms can stay in the air for long periods of time. They regularly cross the Red Sea, about 300 km. They can also cover long distances: For example, Northwest Africa to the British Isles in 1954 and from West Africa to the Caribbean in about ten days in 1988. Swarms can travel up to 1,000 km in one week, about the distance between San Francisco and Seattle.A one-square-kilometer swarm can contain up to 80 million adult desert locusts.Each new generation in a swarm can be up to 20 times larger than the previous one.The Agricultural Research Service is the U.S. Department of Agriculture’s chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in agricultural research results in $17 of economic impact.Interested in reading more about ARS research? Visit our news archiveU.S. DEPARTMENT OF AGRICULTURE
Agricultural Research Service

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Following a fungus from genes to tree disease: a journey in science

Published: June 30, 2022 9.36am EDT

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  1. Brenda WingfieldPrevious Vice President of the Academy of Science of South Africa and DSI-NRF SARChI chair in Fungal Genomics, Professor in Genetics, University of Pretoria, University of Pretoria

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Brenda Wingfield receives funding from the South African Department of Science and Innovation via the National Research Foundation (NRF). She is a fellow of the Academy of Science of South Africa, African Academy of Science and the Third World Academy of Science She is the Secretary General of the International Society of Plant Pathology and a fellow of the American Phytopathological Society She is the current chair of the NRF Executive Evaluation Committee

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Anyone who reads even a little about science and technology will be familiar by now with the idea of genome sequencing. This process involves breaking an organism’s DNA into fragments to study their compositions or sequences. Then the fragments are aligned and merged to reconstruct the original sequence.

But why sequence an organism’s genome? What’s the value for ordinary people and the world more broadly? The answers are immediately obvious when it comes to the medical field. Understanding what makes a disease “tick” offers scientists a way to treat or prevent it. Sequencing the genome of a crop or animal can improve agricultural yields or make species hardier in shifting climates.

It’s a little tougher to explain the value of sequencing the genome of plant pathogens, the organisms that cause diseases in plants. But this has become a critical part of the work of microbiologists and plant pathologists. And it is important, far beyond the laboratory: by carefully studying plant pathogens’ genomes, researchers have been able to design specific double stranded RNA fungicides to short circuit some pathogens’ abilities to harm plants.

These fungicides have not yet been deployed commercially but have huge potential – only targeted species will be affected and so the process is likely to be more environmentally friendly than any involving chemical fungicides. This research has the potential to protect crops, benefiting agriculture and contributing to food security.

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For the past 13 years I’ve focused on sequencing one plant pathogen’s genome. Here’s where that scientific journey has led.

Pine trees at risk

sequenced the genome of a fungus called Fusarium circinatum in 2009; it was the first fungal genome sequence to be conducted on the African continent.

I started studying this pathogen more than 20 years ago because it was killing seedlings in South African pine nurseries. Fusarium circinatum causes pitch canker on pine trees, which makes trees exude pitch or resin. In severe cases the fungus causes tree death. This fungus is considered to be the most important pathogen threat to the global plantation pine industry. It is also potentially devastating in some areas of the southern US, Central America, Europe and Asia, where pines are found naturally.

Trees are extremely important in carbon sequestration. They also produce oxygen – it is estimated that, daily, one tree can produce enough oxygen for four people. Trees have huge economic value, too, providing timber for our homes and paper and packaging for many uses in our daily lives. It is difficult to estimate the total value of pine plantations globally but the South African industry is estimated to contribute more than US$2 billion to the country’s Gross Domestic Product annually.

Sequencing the genome was just the beginning. Follow-up studies published in 2021 involved knocking genes out of the genome and studying what happened. This process is a bit like first identifying and lining up all the parts, then removing these parts one at a time to see what difference they make to the functioning of the fungus. Sometimes we need to understand how gene products (proteins) interact with each other and then more than one gene might be removed from a genome.

In this way, my colleagues and I can learn which genes are important to the processes that Fusarium circinatum uses to cause pitch canker and which are not. Now we’re working to target the important genes in studies to manage the pathogen.

It’s time-consuming work: this fungus has around 14,000 genes. This is more than the yeast that is used to ferment beer, which has 6000 genes, but less than the estimated 25,000 genes in the human genome. Luckily technologies are evolving rapidly to enable routine gene knock-outs. This involves a protein which acts a bit like DNA-specific scissors allowing deletion of a specific sequence of DNA. The position where the protein cuts is guided by using small pieces of RNA sequence that are identical to the target DNA sequence.


Read more: What is CRISPR, the gene editing technology that won the Chemistry Nobel prize?


Another of our key findings is that Fusarium circinatum has acquired, through horizontal gene transfer from other organisms, a group of five genes that apparently enhance its growth.

This discovery has been very useful in developing a specific diagnostic tool using LAMP PCR (Loop-mediated isothermal amplification) to identify this pathogen. This is a special kind of highly sensitive test that was developed to allow for in-field detection of pathogens. It also doesn’t require specialised training. This is useful because trees only recently infected with Fusarium circinatum can be asymptomatic. It’s crucial to determine the presence of the pathogen as early as possible so its spread can be better managed.

New skills, new possibilities

The rise in studies that sequence plant pathogens’ genomes has also opened up opportunities for scientists to develop new skills. The data generated by genome sequencing sometimes outstrips the number of researchers available to analyse it. During pandemic lockdowns in South Africa, some students in my research programme learned how to code and developed skills in bioinformatics, using computers to capture and analyse biological data rather than working in a laboratory.

With these new skills, as well as fast-improving technology, we may well crack Fusarium circinatum’s code once and for all. And that will help to guard pine trees against a dangerous, costly pathogen.

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Two Genes Crucial for Plants Colonizing the Earth 470 Million Ago Have Been Identified

TOPICS:EvolutionFungiGene TransferPlant SciencePlantsPopularUniversity Of Copenhagen

By UNIVERSITY OF COPENHAGEN – FACULTY OF SCIENCE JUNE 27, 2022

Earth DNA Genetics

Scientists believe it likely that the two genes, PEN1 and SYP122, paved the way for all terrestrial plant life.

Researchers shed new light on how plant life became established on the surface of the Earth

Researchers from the University of Copenhagen have shed new light on how plant life got established on the surface of our planet. They specifically demonstrated that two genes are crucial for terrestrial plants to protect themselves against fungal attack – a defense mechanism that dates back 470 million years. These defenses most likely paved the way for all terrestrial plant life.

Mads Eggert Nielsen, a University of Copenhagen biologist.

Plants evolved from aquatic algae to being able to survive on land roughly half a billion years ago, laying the groundwork for life on land. Fungi were one of the obstacles that made this dramatic transition so difficult:

“It is estimated that 100 million years prior, fungi crept across Earth’s surface in search of nourishment and most likely found it in dead algae washed up from the sea. So, if you, as a new plant, were going to establish yourself on land, and the first thing you encountered is a fungus that would eat you, you needed some sort of defense mechanism,” says Mads Eggert Nielsen, a biologist at the University of Copenhagen’s Department of Plant and Environmental Sciences.

According to Mads Eggert Nielsen and his research colleagues from the Department of Plant and Environmental Sciences and the University of Paris-Saclay, the essence of this defense mechanism can be narrowed down to two genes, PEN1 and SYP122. Together, they help form a kind of plug in plants that blocks the invasion of fungi and fungus-like organisms.

https://96c34ecf13edaf76976bebcf48263872.safeframe.googlesyndication.com/safeframe/1-0-38/html/container.html

“We found out that if we destroy these two genes in our model plant thale cress (Arabidopsis), we open the door for pathogenic fungi to penetrate. We found that they are essential to form this cell wall-like plug that defends against fungi. Interestingly, it appears to be a universal defense mechanism that is found in all terrestrial plants,” says Mads Eggert Nielsen, senior author of the study, which is published in the journal eLife.

Originated in a 470-million-year-old plant

The research team has tested the same function in liverwort, a direct descendant of one of Earth’s very first land plants. By taking the two corresponding genes in liverwort and inserting them into thale cress, the researchers examined whether they could identify the same effect. The answer was yes.

“Even though the two plant families that Arabidopsis and liverwort belong to evolved in divergent directions 450 million years ago, they continue to share genetic functions. We believe that this gene family emerged with the unique purpose of managing this defense mechanism and has thus been one of the foundations for plants to establish themselves on land,” says Mads Eggert Nielsen.

A symbiosis between plants and fungi

While fungi posed an obstacle for plants in their transition from an algal marine stage to becoming land plants – they were also a prerequisite. As soon as plants could survive attacks from fungi seeking to eat them on land, the next problem they faced was to find nutrients, Mads Eggert Nielsen explains:

“Dissolved nutrients like phosphorus and nitrogen are easily accessed by plants in aquatic environments. But 500 million years ago, soil as we know it today did not exist – only rocks. And, nutrients bound in rocks are extremely difficult for plants to get a hold of. But not for fungi. On the other hand, fungi cannot produce carbohydrates – which is why they consume plants. This is where a symbiotic relationship between plants and fungi is believed to have arisen, which then became the basis for the explosion of terrestrial plant life during this period.”

The defense structures that form in a plant do not kill either the plant or the fungus, they simply stop a fungus from invading.

“Since a fungus can only gain partial entry into a plant, we believe that a tipping point arises where both plant and fungus have something to gain. Therefore, it has been an advantage to maintain the relationship as is. The theory that plants tamed fungi to colonize land is not ours, but we are providing fodder that supports this idea,” says Mads Eggert Nielsen.

Can be applied in agriculture

The new results add an important piece to the puzzle of the evolutionary history of plants. More importantly, they could be used to make crops more resistant to fungal attacks, which is a major problem for farmers.

“If all plants defend themselves in the same way, it must mean that the microorganisms capable of causing diseases – such as powdery mildew, yellow rust, and potato mold – have found a way to sneak in, turn off or evade the defenses of their respective host plants. We want to find out how they do it. We will then attempt to transfer defensive components from resistant plants to those plants that become diseased, and thereby achieve resistance,” says Mads Eggert Nielsen.

Mads Eggert Nielsen is involved in a research project at the Department of Plant and Environmental Sciences led by Hans Thordal-Christensen and supported by the Novo Nordisk Foundation that focuses on making crops more resistant by identifying the defense mechanisms in plants that pathogenic microorganisms are trying to shut down.

Reference: “Plant SYP12 syntaxins mediate an evolutionarily conserved general immunity to filamentous pathogens” by Hector M Rubiato, Mengqi Liu, Richard J O’Connell and Mads E Nielsen, 4 February 2022, eLife.
DOI: 10.7554/eLife.73487

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What role can genetics play in ‘designing’ more sustainable crops, livestock and trees?

Rodolphe Barrangou | National Academy of Engineering | July 1, 2022

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Plants, animals and microbes can be improved with gene editing. Credit: Carys-ink
Plants, animals and microbes can be improved with gene editing. Credit: Carys-ink

The ability to engineer genomes and tinker with DNA sequences with unprecedented ease, speed, and scale is inspiring breeders of all biological entities. Genome engineers have deployed CRISPR tools in species from viruses and bacteria to plants and trees (whose genome can be 10 times larger than the human genome), including species used in food and agriculture (Zhu et al. 2020).

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Starting small, bacteria used in food fermentations have had their genomes enhanced to optimize their functional attributes linked to the flavor and texture of fermented dairy products such as yogurt and cheese. The fact that CRISPR-Cas systems provide adaptive immunity against viruses in dairy bacteria led to the commercial launch, more than a decade ago, of bacterial starter cultures with enhanced phage immunity in industrial settings. Most fermented dairy products are now manufactured using CRISPR-enhanced starter cultures. Since then, a variety of bacteria, yeast, and fungi (figure 2) involved in the manufacturing of bioproducts has also been CRISPR enhanced to yield commercial products such as enzymes, detergents, and dietary supplements.

Moving along the farm-to-fork spectrum, most commercial crops—from corn, soy, wheat, and rice to fruits and vegetables—have had their genomes altered (figure 2). Genome engineering is used to increase yield (e.g., meristem size, grain weight) and improve quality (e.g., starch and gluten content), pest resistance (e.g., to bacteria, fungi, viruses), and environmental resilience (e.g., to drought, heat, frost). For instance, nonbrowning mushrooms with extended shelf life can be generated, and tomatoes with increased amounts of gamma aminobutyric acid (GABA) to enhance brain health have been commercialized. In addition, efforts are underway to enhance nutritional value.

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Credit: NAE

Livestock breeders have joined the fray, with genome engineering of main farm species such as swine (leaner bacon), poultry (CRISPR chicken), and cattle (for both meat and dairy). Swine have also been edited with a viral receptor knockout to prevent porcine reproductive and respiratory syndrome; the approach is being evaluated for regulatory approval (Burkard et al. 2017). Breeding applications include hornless cows (for more humane treatment), resistance to infectious disease (tuberculosis in cattle), and removal of viral sequences in the genome of elite commercial livestock,[1] notably swine. The CRISPR zoo also encompasses genetically diverse species—fish (tiger-puffer and red sea bream), cats (efforts are underway to develop hypoallergenic variants), and even butterflies (wing pattern)—illustrating the ability to deploy this technology broadly.

This is an excerpt. Read the original post here

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new soil viruses

Scientists discover new soil viruses

by Sarah Wong, Pacific Northwest National Laboratory

seedling
Credit: Unsplash/CC0 Public Domain

Soil is the unsung hero of our lives. It provides nourishment to crops to provide us with food, offers drainage for rainwater into aquifers, and is a habitat for a variety of organisms. On the microscopic level, soil thrives with life, harboring microbes, such as fungi and bacteria that work cooperatively with plants. Despite being such an important part of our lives, not much is known about exactly what exists just below the Earth’s surface.

In new research from Pacific Northwest National Laboratory (PNNL), scientists used bioinformatics and deep sequencing to identify soil viruses and better understand their roles in the Earth. Most of these viruses infect bacteria, and are thus thought to play an important part in maintaining microbial populations.

“Viruses are abundant in nature,” said Janet Jansson, chief scientist for biology and PNNL Laboratory Fellow. “Because there are so many of them in every soil sample, identifying different viruses becomes a challenge.”

Jansson worked with Computational Scientist Ruonan Wu and Earth Scientist and Microbiome Science Team Leader Kirsten Hofmockel in the Biological Sciences Division at PNNL to meet this challenge.

Along with collaborators from Washington State University; Oregon Heath & Science University; Iowa State University; and EMSL, the Environmental Molecular Sciences Laboratory, a Department of Energy Office of Science user facility at PNNL; the PNNL scientists collected soil samples from grasslands in Washington, Iowa, and Kansas and began a deep dive into the soil composition. They leveraged the massive DNA sequencing abilities of the Joint Genome Institute, computing power of the National Energy Research Scientific Computing Center, and multi-omics expertise from EMSL to unearth previously unknown soil viruses. Their results were published in mBio and Communications Biology.

Different viruses for different climates

The scientists chose Washington, Iowa, and Kansas for their soil samples because each location gets a different amount of rainfall. Eastern Washington is much drier compared to Iowa, while Kansas sits in the crossroads between the two in terms of soil moisture.

“We chose to take samples from places with different amounts of soil moisture to see if this made a difference in the types and amounts of viruses there,” said Wu. “Wetter soil contains more bacteria, and many soil viruses infect bacteria.”

The scientists noticed that certain viruses are much more abundant in dry soil than wet soil.

“In drier climates, there tend to be fewer, but more diverse, microbes in the soil,” said Wu. “The relative scarcity of bacterial hosts means that it’s in the virus‘s best interest to keep the host alive.”

The researchers also discovered that in drier soil, viruses were more likely to contain special genes that they could potentially transfer to their bacterial hosts.

“These genes could potentially give their bacterial hosts ‘superpowers'” said Jansson. “These virus genes could be passed to their bacterial hosts to help them survive in dry soils.”

Though more research is necessary to better understand the role of these special viral genes, the possibility that they could be useful to bacteria living in the soil is exciting. These genes could be useful to bacteria by increasing their ability to recycle carbon and thus increase soil health.


Explore further

Distribution of soil bacterial community in surface and deep layers reported along elevational gradient


More information: Ruonan Wu et al, DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes, mBio (2021). DOI: 10.1128/mBio.02595-21

Ruonan Wu et al, Moisture modulates soil reservoirs of active DNA and RNA viruses, Communications Biology (2021). DOI: 10.1038/s42003-021-02514-2

Journal information: Communications Biology  mBio 

Provided by Pacific Northwest National Laboratory 

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