Category Archives: Genetic Engineering

Beer, with roots dating to before 6000 B.C.E., is one of the oldest drinks in history. It has been vital to human culture since antiquity: Mesopotamians praised a Sumerian goddess of brewing, Ninkasi, in a 3800-year-old hymn that includes a recipe for brewing beer with barely. We havent lost our fondness for the stuff. Today, the beer industry is worth an estimated $768.17 billion and could grow to as much as $989.48 billion by 2028.

But, especially since the the 1970s when brewers adopted new manufacturing techniques, beer may have lost some of its past flavor. Beer had historically been brewed in open, horizontal vats, but the industry switched to the larger, closed vessels, as seen on any present-day brewery tour. These containers are easier to fill, empty, and clean, and they enable larger brewing volumes to save costs. But this modern method can reduce the flavor produced in the process.

[Related: How Evolution Determines The Flavor Of Beer and Whiskey.]

There may be a way to revive some of that taste, thanks to new developments in gene editing. Belgian scientists report improving the flavor of contemporary beer by identifying and engineering a gene in yeast and some other alcoholic drinks, in a new study out in the journal Applied and Environmental Microbiology.

During the fermentation process, yeast converts 50 percent of the sugar in the mash to ethanol, and the other half to carbon dioxide. The carbon dioxide pressurizes the closed vessels, dampening the flavor and causing the problem.

Johan Thevelein, an emeritus professor of molecular cell biology at Katholieke Universiteit in Leuven, Belgium, and his team first figured out how to identify the genes responsible for commercially important traits in yeast. (Thevelein is also founder of NovelYeast, which works with other companies on industrial biotechnology projects.) They used this technique to identify the genes responsible for flavor in beer by screening large numbers of yeast strains and evaluating which was best at preserving flavor while under pressure. According to Thevelein, they focused on a gene for a banana-like flavor, because it is one of the most important flavors present in beer, as well as in other alcoholic drinks.

[Related: How have non-alcoholic beers gotten so good?]

In a press release, Thevelein explained, To our surprise, we identified a single mutation in the MDS3 gene, which codes for a regulator apparently involved in production of isoamyl acetate, the source of the banana-like flavor that was responsible for most of the pressure tolerance in this specific yeast strain.

The team used CRISPR/Cas9, the groundbreaking gene editing technology, to create this gene mutation in other brewing strains. The genetic engineering improved the strains ability to tolerate carbon dioxide pressure and enriched the beers flavor.

The mutation is the first insight into understanding the mechanism by which high carbon dioxide pressure may compromise beer flavor production, said Thevelein.

He noted that the MDS3 protein is likely part of an important regulatory pathway that might inhibit carbon dioxide in banana flavor production, but the team is not sure how it does so. The same technology has also identified the genetic elements that are important for rose flavor production by yeast in alcoholic drinks.

This specific beer isnt on the market just yet, but it is not out of the realm of possibility, as the world becomes more interested in the future of genetically modified foods. A Japanese study from 2021 relied on CRISPR to edit barley, used in beer, to help the crop thrive despite climate change. And if youre hankering for a gene-edited burger with your gene-edited cold one, in May the FDA cleared the sale of beef from gene-edited cattle.

Read more:
The key to tastier beer might be mutant yeastwith notes of banana - Popular Science

According to Cain, via Per NPR, cotton candy grapes don't simply grow on vines. To generate growth, scientists have to extract the embryos from baby grape hybrids and fertilize them in test tubes. It probably won't come as much of a surprise, then, that they're notoriously expensive. At a Whole Foods Market in Brooklyn, cotton candy grapes run for $4.99 per pound, compared to $1.99 per pound for red seedless grapes. But, the high cost of production isn't the only reason this wine will probably never happen.

In 2016, Jim Beagle, CEO and co-founder of Grapery, said some grape farmers tried making cotton candy grape wine via Bon Apptit and it was a disaster. As Beagle puts it, "It's so bad. It tastes nothing like cotton candy... no acidity structure to give you [a] balanced mouthfeel. It tastes like the flabbiest Chardonnay you've ever had. And it smells like stale donuts." Scientifically, this feedback makes sense. Most wine grapes belong to the "Vitus vinifera" grape species, says Cain, but cotton candy grapes are a hybrid specie of V. vinifera and a yet-undisclosed Concord-adjacent specie. Therefore, not only do cotton candy grapes taste super unique, but they're also fundamentally different from other grapes at a biological level. So, perhaps cotton candy grapes should remain the super-sweet superstar of the fruit bowl and leave wine-making to the others. (If you're super into the idea, luckily, cotton candy-flavored dessert wine is still a thing.)

See the original post:
Why You'll Probably Never See Cotton Candy Grape Wine - Tasting Table

GEOSCIENCEMichael Uglo

By MICHAEL JOHN UGLOWELCOME all to our sixth lecture on the sciences of the earth.The sciences of the earth also involve living things of all sorts that contribute to the formation of the earth and its earth structures through geologic time.Hence working smarter in this time we call the technology age, we have to make greater use of what is available rather than letting it to the earth to allow the earths natural processes to take place through the lithification processes whereby once-living matter and non-living matter such as silts, shells, sediments and bones are turned into rocks.Materials in the living world are a major source of materials and resources that can be used applications to do with biogeotechnology or geobiotechnology in both the commutative and associative as well in their applications.For instance, in the biology of evolutionary applications, it is the huge area of biotechnology and genetic engineering that are a resource on the earth. Natural selection and genetic drift result in the species and populations of organisms and biodiversity seen on the planet earth both in the past for extinct life and in the present.

As a link, people have been doing artificial selections of organisms for so many years to contain the favourable characters of the organisms. There were cross-breedings done in plants to produce hybrid plants that produce good yields as well as producing plants that are drought-resistant and plants that can thrive in lengthy wet seasons and water-logged areas.Cross-breeding is also done in the rice plant as an example, to come up with the hybrid rice to grow in the dry ground instead of only water-logged areas and wetlands.The natural immunity to counter cancer is no longer effective. Cancers have evolved to decimate populations of organisms. Microbes such as bacteria, fungi and viruses have evolved to outpace the available effective drugs for their treatment. Soon microbes will become resistant to all the effective available drugs because they are continually evolving.In the field of agriculture, pests and weeds have become resistant to available pesticides and weedicides. The trend is continuing and the industry is going through a chemical treadmill to treat resistant weeds and pests.

Hence, understanding the evolutionary genetics at the molecular level in the nucleotides of the DNA and RNA is vital. Knowing how the genes programme the enzymes and proteins to produce parts of plants, animals and microbes will result in the understanding of the first-hand information on how the nitrogen bases and genes programme the synthesis of the organic polymers. This will also help in the understanding of the basis of genetic mutations and protein alterations to find a cure for cancer as well as the effective diagnosis of the problems arising in medicine, agriculture as well as in botany and other fields.For instance, in engineering an evolutionary computer-algorithm results in solving very complex and multi-faceted engineering problems. The algorithms programmed by man are not so multi-dimensional like the evolutionary algorithm in superiority.Materials found naturally on the earth are the rocks, soil, minerals and water. There are also metals and precious stones that are found on the earth such as gold, silver and gemstones. Other important materials are diamonds which are allotropes of carbon just like graphite and the fullerenes Buckminster as a resource base for carbon nanotubes.These materials become very important resources for life, agriculture, industry and technology.Specific areas have various resources of those earth materials. The rocks become a resource for construction work such as in buildings and roads. Materials such as sandstone, mud, soil, granite, limestone and marble are very important for civil works and engineering construction. For instance, marble can be quarried and cut at site for construction like a local resource.Caliche is a soft limestone material that can be used as a resource. It is found at the site of limestone bedrock as well as calcium carbonate soils. Caliche are collected and squashed to be mixed with cement for making building structures as well as structural walls.The rammed earth that is 30 per cent mud and 70 per cent sand is also made to be used for buildings and other structures in civil constructions and engineering. Like caliche, their porosity is very important for holding water and creating chemical bonds with the additives like the cement which are to be used as the structures of walls which adds the compression.

The caliche and rammed earth structures as well as stone products can be used as finishing characteristics of constructions. They can become good heat radiators or thermal bodies in winter. These structures can also be used for providing cool environments in summer. Further, these materials are fire-proof.At the sites of the clay soil, brick plants can be located to make and supply bricks for constructions. Bricks are made by conditioning and heating the clay or it is baked for uses such as structural tiles, roof tiles, pavers and floor tiles.The caliche block, rammed earth and stone with brick structures become very useful for structural constructions such as structural walls, road constructions as well as buildings.Soils are always tested in laboratories to see their structures for construction work. Some soils are not so suitable for constructions, especially soils with very high expansibility factor.s And example opf such soils is bentonite. AAll rocks and soil resources are good to use locally because these reduces the cost of transport. The material cost will come down because of the low transport costs. Also, non-renewable resources are to be used whereby the ecology of the site must not be affected with more extractions. They have to be used sustainably.My Prayer for PNG today is: I will proclaim to all your people, the wonders you have done for me. You are indeed a God of goodness, you draw me gently to your heartNext week: Physical events

Read the original here:
Earth materials in technology The National - The National

Published 7:47 am Monday, October 10, 2022

Does your fall dcor feature sunflowers, burlap and orange leaves? Or super-scary-creepy things for All Hallows Eve?

We do things differently. Ive got a bunch of shiny discarded CDs making beautiful rainbows as they spin from a magnolia tree. Its a fall tradition that seems to amuse and get compliments from neighbors walking their dogs.

On the inside, its a different story. Sugar skulls in the Dia De Los Muertos tradition adorn my house from candles and towels to salt and pepper shakers. People give me these colorful pieces of Mexican heritage.

Thats how I got hot sauce in a skull jar. My original intent was to go through the store-bought stuff so I could always make my own and keep it in the jar.

Spooky right?

Its a warning to others: I like it hot. I usually go red, but Ive gone green of late.

One hot green version: Simply cut up fresh jalapenos and run them through the blender with garlic and a little vinegar. The green stuff can be mixed in to yogurt to cool it down.Play around with that. Have fun. Dont be scared.

Monkeys and Sea Creatures Laid-back monkeys, skulls and sea creatures announce some tasty canned beverages that will take you into the season. No reason to say goodbye to island flavors in our mild winter area.

Osena is spiked coconut water cocktail as close as a pop of the top Lush Dragon Fruit, Exotic Pineapple and Pure Original are smooth flavors that allow you 100 calories of beachy feeling. The electrolytes just come naturally. Cute little monkeys are sharing a coconut drink with straws on the label. Try @drinkosena on social media.

Our friends at Fire Dept. Coffee have always meant businesses. The skull in a fire hat just calls me in for some adventure. Now Nitro-Charged Shellback Espresso with a dual-trident armed sea king is taking no prisoners.

Theres no alcohol in Spirit-Infused Irish Coffee and Nitro Latte is right in there with the new cans that arent for novice coffee drinkers. Its in good fun and based on the concept our fire fighters need to stay alert. Read atfiredeptcoffee.com how efforts help those hurt on the job.

Soil to shelf and not sketchy I truly enjoyed a meal of Chi, which is fake meat to haters. To Culinary Thrill Seekers looking for new flavors and some healthy fun, I say give this 100 percent plant-based meat a go.

It impressed a guest who found the good texture and flavor familiar. He guessed that nuts played a role in the good texture. I served it with tortilla and beans and we all felt good about our choices.

It cooks in 4 minutes and the box says theres No Sketchy Stuff like genetic engineering and artificial flavors or dyes. I cant wait to see how a box ofCHI-rizo upgrades my next Taco Tuesday. Italian Herb comes after that. Join in the fun fromchifoods.us.

Pork Yeah! Its Plants.

Darragh Doiron is a Port Arthur area foodie looking for her one sweater she pulls out each of our brief autumn seasons. Share your foodie finds with her atdarraghcastillo@icloud.com.

Read more:
CULINARY THRILL SEEKING Proceed with caution. It's hotter than blazes season. - Port Arthur News - The Port Arthur News

Granting legal rights and protections to non-human entities such as animals, trees and rivers is essential if countries are to tackle climate breakdown and biodiversity loss, experts have said.

The authors of a report titled Law in the Emerging Bio Age say legal frameworks have a key part to play in governing human interactions with the environment and biotechnology.

Ecuador and Bolivia have already enshrined rights for the natural world, while there is a campaign to make ecocide a prosecutable offence at the international criminal court. The report for the Law Society, the professional body for solicitors in England and Wales, explores how the relationship between humans and mother earth might be recalibrated in the future.

Dr Wendy Schultz, a futurist and report co-author, said: There is a growing understanding that something very different has to be done if our children are going to have a planet to live on that is in any way pleasant, much less survivable, so this is an expanding trend. Is it happening as fast as any of us would want? Possibly not, which is why its important to get the word out.

Her co-author, Dr Trish OFlynn, an interdisciplinary researcher who was previously the national lead for civil contingencies at the Local Government Association, said legal frameworks should be fit for a more than human future and developments such as genetic modification or engineering. This means covering everything from labradors to lab-grown brain tissue, rivers to robots.

We sometimes see ourselves as outside nature, that nature is something that we can manipulate, said OFlynn. But actually we are of nature, we are in nature, we are just another species. We happen to be at the top of the evolutionary tree in some ways, if you look at it in that linear kind of way, but actually the global ecosystem is much more powerful than we are. And I think thats beginning to come through in the way that we think about it.

An example of a right might be evolutionary development, where a species and individual is allowed to reach its full cognitive, emotional, social potential.

Such a right could apply to sows in intensive pig farming, calves taken away from their mothers and even pets, said OFlynn, adding: I say that as a dog lover. We do constrain their behaviour to suit us.

Developments in biotechnology also pose questions about the ethics of bringing back species from extinction or eradicating existing ones. Scientists are exploring reintroducing woolly mammoths and there has been discussion of wiping out mosquitoes, which carry malaria and other diseases.

The planet's most important stories. Get all the week's environment news - the good, the bad and the essential

We arent wise enough to manage all of these capabilities and to manage the ripple effects of decisions we make about our relationship with the living environment, said Schultz. Part of the issue is embedding some sort of framework for accountability and responsibility for the consequences of these things we do, and thats where law comes in.

The authors acknowledge potential resistance from very different traditions and beliefs in some western countries, compared with Ecuador and Bolivia, where rights to nature were granted under socialist governments and influenced by Indigenous beliefs (as was the 2019 ban on climbing Uluru in Australia).

Granting something that is culturally numinous rights just so you can preserve it gets us to a kind of valuation that, among other things, is a cultural shift away from the Judeo-Christian great chain of being dominion over nature, said Schultz. This is reconfiguring it to place us where we have always been and where we should be thinking of ourselves as belonging, as just a node in this greater web of life on the planet.

If that worldview can be enshrined in law, essentially granting personhood rights to the spirit of the river, the spirit of the trees or the spirit of the elephant, youre talking about enshrining a kind of neo-pantheism into 21st-century legal frameworks.

Visit link:
Give legal rights to animals, trees and rivers, say experts - The Guardian

Nuclear fusion reactions in the sun are the source of heat and light we receive on Earth. These reactions release a massive amount of cosmic radiation including x-rays and gamma rays and charged particles that can be harmful for any living organisms.

Life on Earth has been protected thanks to a magnetic field that forces charged particles to bounce from pole to pole as well as an atmosphere that filters harmful radiation.

ADVERTISEMENT

CONTINUE READING BELOW

During space travel, however, it is a different situation. To find out what happens in a cell when travelling in outer space, scientists are sending bakers yeast to the moon as part of NASAs Artemis 1 mission.

Cosmic radiation can damage cell DNA, significantly increasing human risk of neurodegenerative disorders and fatal diseases, like cancer. Because the International Space Station (ISS) is located in one of two of Earths Van Allen radiation belts which provides a safe zone astronauts are not exposed too much. Astronauts in the ISS experience microgravity, however, which is another stress that can dramatically change cell physiology.

As NASA is planning to send astronauts to the moon, and later on to Mars, these environmental stresses become more challenging.

The most common strategy to protect astronauts from the negative effects of cosmic rays is to physically shield them using state-of-the-art materials.

Several studies show that hibernators are more resistant to high doses of radiation, and some scholars have suggested the use of synthetic or induced torpor during space missions to protect astronauts.

ADVERTISEMENT

CONTINUE READING BELOW

Another way to protect life from cosmic rays is studying extremophiles organisms that can remarkably tolerate environmental stresses. Tardigrades, for instance, are micro-animals that have shown an astonishing resistance to a number of stresses, including harmful radiation. This unusual sturdiness stems from a class of proteins known as tardigrade-specific proteins.

Under the supervision of molecular biologist Corey Nislow, I use bakers yeast, Saccharomyces cerevisiae, to study cosmic DNA damage stress. We are participating in NASAs Artemis 1 mission, where our collection of yeast cells will travel to the moon and back in the Orion spacecraft for 42 days.

This collection contains about 6,000 bar-coded strains of yeast, where in each strain, one gene is deleted. When exposed to the environment in space, those strains would begin to lag if deletion of a specific gene affects cell growth and replication.

My primary project at Nislow lab is genetically engineering yeast cells to make them express tardigrade-specific proteins. We can then study how those proteins can alter the physiology of cells and their resistance to environmental stresses most importantly radiation with the hope that such information would come in handy when scientists try to engineer mammals with these proteins.

When the mission is completed and we receive our samples back, using the barcodes, the number of each strain could be counted to identify genes and gene pathways essential for surviving damage induced by cosmic radiation.

ADVERTISEMENT

CONTINUE READING BELOW

Yeast has long served as a model organism in DNA damage studies, which means there is solid background knowledge about the mechanisms in yeast that respond to DNA-damaging agents. Most of the yeast genes playing roles in DNA damage response have been well studied.

Despite the differences in genetic complexity between yeast and humans, the function of most genes involved in DNA replication and DNA damage response have remained so conserved between the two that we can obtain a great deal of information about human cells DNA damage response by studying yeast.

Furthermore, the simplicity of yeast cells compared to human cells (yeast has 6,000 genes while we have more than 20,000 genes) allows us to draw more solid conclusions.

And in yeast studies, it is possible to automate the whole process of feeding the cells and stopping their growth in an electronic apparatus the size of a shoe box, whereas culturing mammalian cells requires more room in the spacecraft and far more complex machinery.

Such studies are essential to understand how astronauts bodies can cope with long-term space missions, and to develop effective countermeasures. Once we identify the genes playing key roles in surviving cosmic radiation and microgravity, wed be able to look for drugs or treatments that could help boost the cells durability to withstand such stresses.

ADVERTISEMENT

CONTINUE READING BELOW

We could then test them in other models (such as mice) before actually applying them to astronauts. This knowledge might also be potentially useful for growing plants beyond Earth.

Hamid Kian Gaikani, PhD Candidate, Pharmaceutical Sciences, University of British Columbia

This article is republished from The Conversation under a Creative Commons license. Read the original article.

Also read | Why Chinas lukewarm support for Russia is likely to benefit Ukraine

Latest Stories

Continued here:
How yeast DNA may help protect astronauts from cosmic radiation in space - EastMojo

Most people have seen or at least know the premise of the Jurassic Park franchise. Man tries to bring back dinosaurs from the dead and ends up pushing the limits of science too far, with disastrous consequences. The movies serve as a lesson in caution and respecting natural life, portraying the dangers of not doing so through a very fictionalized scenario. Although we may be a long way from bringing back the dinosaurs, the technology used to genetically engineer the DNA of existing species is well-established and could potentially be used to bring extinct species back.

The process of reverse-engineering species involves taking the genetic material from a living species and using the genetic material of similar species in order to achieve a creature similar in genes and physical appearance to an extinct species. This is difficult to do for dinosaurs, as we do not have good enough documentation of their DNA sequences to create an accurate picture, and would instead have to guess by working backwards from reptiles or birds. However, just because Jurassic Park is further away than we might think doesnt mean this technology cannot be used to bring back more recently extinct species, such as certain rhinos, birds and tortoises.

In fact, in 2003, scientists attempted to use genetic engineering technology in order to bring back the extinct Pyrenean ibex, a type of goat. Although the attempt ultimately failed, it showed that scientists have the ability to bring back extinct species if they have access to the genetic material of that animal. With strides in gene-editing technology, it might not be necessary to have the full genetic sequence of a species in order to resurrect it.

CRISPR is a widely known DNA editing technique that involves taking short sequences of DNA and splicing them together to create a new DNA strand. In humans, this experimental technology has been largely used for editing out specific mutations to treat diseases on a genomic level. In extinct animals, it could be used to splice together DNA of existing animals to emulate an extinct animal for which scientists might not have the complete genetic information.

Even if this process has yet to be fully developed, as the possibility becomes more realistic it necessitates thinking through not only if it could happen, but if it should.

Bringing back extinct species, especially those from as far back as the Jurassic period, could have disastrous environmental effects. A study found that reintroducing extinct species to the ecosystem could overall decrease biodiversity, rather than increase, especially if the government or private institutions start allocating more resources towards the revived species rather than our existing life. Bringing back extinct species also means bringing back their sources of food. It means making sure that they are able to withstand different global temperatures, pathogens and predators of today. Without all this, they would have to be kept under close watch in enclosures, requiring even more resources.

The cost of the resources that these revived species would need to survive is expensive, and not just in monetary terms. Currently, species are going extinct 100 to 1,000 times faster than anticipated, meaning that at least 2,000 species go extinct each year (and that number might be a severe underestimate). Instead of focusing efforts on trying to bring back each of these, it would be much more efficient and effective to simply focus on spending money, time and energy on finding ways to reduce the rate at which human activity is killing life on Earth.

Investigating more sustainable sources of energy, developing consumption policies for individuals and corporations and trying to limit our global pollution would all be much more likely to sustain or at least slow down the destruction of our current biodiversity. When we can limit the destruction of biodiversity, then the whole planet will benefit, from improving water and air quality to mitigating food shortages and resource depletion.

The concept of genetic engineering is not inherently bad. It could be used to bring back recently extinct species, i.e., ones that are more adapted to the current environment, without negatively affecting our biodiversity. It could be used to treat life-threatening heritable disorders. But when put into the larger context of our planet and the current climate crisis, it seems to be a waste of resources and time. There are many other ways to improve our planets health without looking to the past, if only we look to preserve the future instead.

Continue reading here:
Life finds a way, but should it? The ethics of genetic engineering - The Trinitonian

Against the backdrop of the cost-of-living crisis it is argued that the UK could bolster food security, combat climate change and lower food prices by relaxing the rules on and around genetic engineering. By designing more resistant crops which are less reliant on fertiliser and are more nutritious, progress could be made. On the other hand, this may be a short-sighted approach to deregulation and taking the risk could result in disastrous consequences.

The Genetic Technology (Precision Breeding) Bill 2022

The arguments are surfacing as The Genetic Technology (Precision Breeding) Bill (GT (PB) Bill) which is currently in the House of Commons at the report stage (allowing the House to consider further amendments) heading for its 3rd reading. Much of the debate centres around the understanding of the technology.

Genetically Modified Organisms (GMOs) are organisms in which the genetic material (DNA or RNA) has been altered in a way that does not occur naturally, and the modification can be replicated and/or transferred to other cells or organisms. This typically involves the removal of DNA, manipulation outside the cell and reinsertion into the same or other organism. Gene editing (GE) is arguably different as rather than inserting new DNA it edits the organisms own DNA - which could happen over time, but this essentially speeds up the natural process. Both plants and animals can be genetically manipulated.

Regulation (EC) No 1829/2003 provides the general framework for regulating genetically modified (GM) food in the EU with a centralised procedure for applications to place GM food on the EU market. It focusses on the traceability and labelling of GMO and the traceability of food and feed products to ensure a high level of protection of human life and health. GM foods can only be placed on the market after scientific risk assessment of the risks to human health and the environment.

The EU implemented these regulations back in 2001 which heavily restricted the use of GMOs and it has maintained that conservative position since. To continue not to allow GMOs is at odds with other countries, such as Australia, Japan and the US. As the technology developed several member states (including the UK) felt that a more relaxed approach to genetic editing would be beneficial. However, in 2018 the European Court of Justice in, Confederation Paysanne v Premier Minister (C-528/16) decided that there was no real distinction with gene editing (also described as Precision breeding) and they were to be treated as GMOs within the meaning of the GMO Release Directive 2001.

Nevertheless, in the UK in 2019 the then prime minister famously declared that he would liberate the U.K.s extraordinary bio science sector from anti-genetic modification rules. Consequently, since leaving the EU the UK has been working on moving away from the EUs stricter definition of a GMO as evidenced by the GT (PB) Bill.

The Bill defines precision bred to be, if any, or every feature of its genome results from the application of modern biotechnology and every feature of its genome could have resulted from either traditional processes or natural transformation.[1]

It is argued that this removes unnecessary barriers to innovation inherited from the EU to allow the development and marketing of precision bred plants and animals, which will drive economic growth and position the UK as a leading country in which to invest in agri-food research and innovation.

The main elements of the Genetic Technology (Precision Breeding) Bill are:

Creating a new, simpler regulatory regime for precision bred plants and animals that have genetic changes that could have arisen through traditional breeding or natural processes. No changes are proposed to the regulation of animals until animal welfare is safeguarded.

Introducing two notification systems for research and marketing purposes where breeders and researchers will need to notify Department for Environment, food and Rural Affairs (Defra) of precision bred organisms. The information collected on precision bred organisms will be published on a public register.

Establishing a new science-based authorisation process for food and feed products developed using precision bred organisms.

This is the result of an All-Party Parliamentary Group which called for amendments to be made in 2020 to the, at the time, forthcoming Agriculture Bill 2019-21 (now the Agriculture Act 2020) to allow precision breeding in the UK.

The amendments would require changes to the UK Environmental Protection Act 1990, including changing the use of the EU definition of a GMO which would allow UK scientists, farmers and both plant and animal breeders access to gene editing technologies that other countries outside the EU have.

The focus in the UK is to allow traditional breeding methods to alleviate some of the effects such as extreme weather, food shortages, the cost-of-living crisis and to encourage pest-resistance.

The Genetically Modified Organisms (Deliberate Release) (Amendment) (England) Regulations 2022

On 11th April 2022, the Genetically Modified Organisms (Deliberate Release) (Amendment) (England) Regulations 2022 implemented an alignment of GE with the regulation of plants using traditional breeding methods. The Regulations removed the need to submit a risk assessment and seek consent from the Secretary of State before releasing certain GE plants for non-marketing purposes. They apply to England only.

This will allow for the release and marketing of gene edited products under certain circumstances that has so far been prohibited by the EU. It will allow UK scientists to develop plant varieties and animals with beneficial traits that could also occur through traditional breeding and natural processes, while providing safeguards in both marketing and authorisations via regulation.

Taking a Risk?

Another consequence of leaving the EU is that the Food Standards authority (FSA) is now responsible for authorising Novel foods applications in the UK. The FSA points to this need for authorisation as a further check and balance on any risks that may arise from a divergence from EU regulation.

Although it is argued that the Bill may have been drafted a little hastily, any food developed using new technology is subject to the scientific scrutiny of a Novel foods application. If there is a risk of unintended consequences from GE (it is argued that there is a risk of unidentified and untested mutations resulting from gene editing) the role of regulatory authorities such as DEFRA and the FSA is to ensure that no unintended product gains approval.

The debate is becoming increasingly focussed as the cost-of-living crises deepens.

Co-Authored by Laura Hipwell, Trainee Solicitor at CMS.

See the original post:
To modify or not to modify? Genetic Modification and Gene Editing - A divergence by the UK - Lexology

Gene therapy has a history of presenting possibilities that stay out of reach for a long time. The tantalizing idea of using exogenous good DNA to replace defective DNA was suggested by Stanfield Rogers in 1970. Then, in 1972, the idea was elaborated upon by Theodore Friedmann and Richard Roblin, who wrote that viruses could be tweaked to contain human genes and allowed to infect patients. Once copied into patients cells, the genes could start to function, compensating for defective and disease-causing genes.1

Despite these conceptual advances, clinical progress was slow. Indeed, there were dead ends and reversals. In 1971, Rogers deployed a naturally occurring virus in an attempt to treat an arginase deficiency. And in 1980, Martin J. Cline tried to treat b-thalassemia by using an ex vivo procedure in which bone marrow cells were transfected with a recombinant human globin gene and then reintroduced to patients. Both these efforts were, at best, inconclusive.

Finally, a partial and temporary gene therapy success was reported in 1990. Scientists led by William French Anderson used an ex vivo procedure to treat a four-year-old girl suffering adenosine deaminasedeficient severe combined immunodeficiency disease. They infected the patients own white blood cells with a virus that had been engineered to carry a gene encoding a functional variant of the adenosine deaminase gene. For two years, transfusions were administered that incorporated transfected white blood cells. The transfusions didnt bring about a cure, but they did help reduce the patients symptoms.

Then, in 1999, the field suffered a major setback when an 18-year-old patient with a metabolic disorder died after suffering an immune overreaction to an adenovirus designed to restore a missing liver enzyme. And a few years later, several patients with immunodeficiencies developed leukemias after receiving gene therapy, as the viruses caused insertions into cancer-related genome sites. The U.S. Food and Drug Administration (FDA) reacted swiftly, putting many gene trials on hold.2 The development of gene therapy stalled.

In subsequent years, however, researchers learned from these setbacks. For instance, safer viral vectors were identified, such as adeno-associated viruses (AAVs). The genes they deliver typically remain in the cell cytoplasm and are expressed there, rather than being integrated into human cells genomes, making them less likely than some earlier vectors to trigger cancer.

Since 2017, the FDA has approved several gene therapies for disorders caused by defects in single genes, including Luxturna for retinal dystrophy, Zolgensma for young children with spinal muscular atrophy, and Zynteglo for certain patients with b-thalassemia. The agency has also green-lighted several cell-based gene therapies which alter patients cells and reinfuse them into patients. For example, approvals have been granted to several therapies that use modified T cells, specifically, chimeric antigen receptor (CAR) T cells. They have proven effective in treating certain blood cancers.

Meanwhile, hundreds more gene therapy trials are underway. To get a sense of what these trials tell us about the current status and near-term future of gene therapy, GEN spoke with representatives of companies at various stages of clinical development. They took the opportunity to expand on the results they shared at the 25th Annual Meeting of the American Society of Gene and Cell Therapy (ASGCT), which was held last May in Washington, DC. They emphasized that for many diseaseshereditary monogenic disorders, complex diseases, and even cancersingle-dose gene therapies held disease-modifying potential.

The New York Citybased Lexeo Therapeutics has been developing a treatment for Friedreichs ataxia (FA), a rare condition that is currently incurable. Its caused by a mutation in the frataxin gene FXN which leads to progressive degeneration of the nervous system. Rather than targeting the diseases neurological pathology, which is tricky as the viruses fail to transduce efficiently and specifically in affected brain areas, Lexeo tackles the oft-fatal cardiac disease associated with FA, said Jay Barth, MD, Lexeos executive vice president and chief medical officer.

Lexeos therapeutic, LX2006, employs an AAV thats effective at infecting cardiac cells, introducing the FXN gene, increasing frataxin levels, and thereby restoring mitochondrial function. According to data presented at the ASGCT conference, mouse models of FA that received a single intravenous dose of LX2006 had improved heart function, general mobility, and survival compared with untreated rodents, even after they developed fairly advanced cardiac disease, Barth noted.3

Lexeo is planning a Phase I/II trial to assess safety of the therapy in 10 FA patients with cardiomyopathy. One of the goals is to identify the maximum safest dose for LX2006.4 Investigators are taking a cautious approach, Barth said, as overexpression of frataxin has been associated with safety issues.

The first study cohorts will receive the lowest dose thats shown efficacy in mice, and the dose will be incrementally increased in subsequent groups. Frataxin levels will be monitored through heart tissue biopsies. Patients will be followed for one year, and then for an additional four years as the FDA requires. In Barths view, the study could help find some way to prolong the lives of these patients beyond what the disease would give them.

While many gene therapy companies focus on restoring lost functions to normal cells, the Australia-based immuno-oncology company Imugene is employing the method to help kill cancer cells. In 2019, the company acquired an oncolytic virus called CF33, a chimeric vaccinia that infects and selectively replicates in malignant solid tumor cells.5

Imugene scientists have tinkered with CF33 in various ways that are already being tested in patients with specific cancer types. But according to Leslie Chong, the companys chief executive officer and managing director, the crown jewel of Imugene is a version of CF33 that contains a gene encoding the CD19 protein.

This surface protein is expressed on B cells and is the target of several CAR T-cell therapies. Using CF33 to induce uniform expression of CD19 across tumor cells could make CAR T-cell therapy work against solid tumors, which has proven a challenge as the tumors often express a heterogeneous mix of cell surface antigens. But with CF33, Chong explained, We line all your solid tumor [cells] with the CD19-directed targets, such that when you add a CD19-targeted therapy, you then obliterate the solid tumor where it hasnt had markers before.

In 2020, scientists at the City of Hope National Medical Center published data in support of this approach.6 Specifically, the scientists used mouse models of various cancer types to study the effects of administering the CD19-carrying CF33 virus followed by CD19-directed CAR T-cell therapy. Mice that received the antigen-matched therapy survived significantly longer than mice that received only mock T cells or CD19-CAR T cells.

Imugene looks forward to identifying indications that may benefit the most from this onCARlytics approach. The company is also planning a human trial. In our initial in-clinic study, we will be focused on certain indications, Chong noted. However, I think the application could be huge.

The North Carolinabased gene therapy company Asklepios BioPharmaceutical (AskBio) is also pursuing a target that falls outside the usual paradigm of monogenic disorders: congestive heart failure (CHF), a chronic and progressive condition in which the heart cannot pump blood sufficiently. Theres a high unmet medical need to develop additional medicines to reduce mortality and improve quality of life for the patients, said Canwen Jiang, MD, PhD, AskBios chief development officer and chief medical officer.

AskBios approach to tackling this complex disease has been to deliver a gene encoding the phosphatase-1 inhibitor-1, a key protein in regulating cardiac contractions. Introducing the gene via an AAV thats engineered to target cardiac cells could improve heart function as well as reverse and prevent the detrimental remodeling of cardiac muscle that occurs in CHF, Jiang said. The therapy, NAN-101, is delivered via a one-time injection into the hearts coronary arteries.

After collecting robust preclinical data, AskBio launched a Phase I study in 2019, enrolling eight individuals with Class III CHF. According to preliminary results presented at the ASGCT meeting, investigators observed efficient transduction of NAN-101 in heart cells of one trial participant from whom a tissue biopsy could be obtained.7 A cohort consisting of three patients who had completed their 12-month follow-up appeared to tolerate the treatment well and saw consistent improvements in heart function.8

If successful, such studies will not only motivate AskBio to expand into broader CHF indications, but also bolster the idea that gene therapy is useful beyond monogenic disorders. It would be a confidence-building example for the industry, for the academic community, as well as for the regulatory agencies, Jiang said.

One of the companies at the Phase III stage is Sarepta Therapeutics, a Cambridge, MAbased biotech firm specializing in rare diseases such as Duchenne muscular dystrophy (DMD), a monogenic disease that causes progressive muscle deterioration.

The gene therapy SRP9001 is based on an AAV virus subtype with an affinity for reaching muscle cells. It contains a gene encoding a form of the dystrophin protein, which is lacking in DMD patients tissues, coupled with a promoter that causes selective expression in skeletal and cardiac muscle cells, explained Jake Elkins, MD, Sareptas senior vice president of research and development and chief medical officer.

In a pilot study that tracked four DMD patients aged four to seven, data was collected four to five years after SRP9001 was taken. The treatment was well tolerated, and patients showed a 7-point improvement on a 17-step mobility scale (the North Star Ambulatory Assessment), despite being at an age where theyd typically experience rapid deterioration of mobility.9 A randomized Phase II study of 41 pediatric participants has so far bolstered these observations at one year of follow up, Elkins noted.10

Currently, Sarepta is closely tracking 120 boys with DMD aged four to seven in a Phase III study. The first half of patients are receiving gene therapy in the first year, during which the second half will receive a placebo until being rolled onto gene therapy after one year. At one year, were able to document clinically meaningful effects of the therapy, Elkins said. We view it as a confirmatory study of our early findings, but [it] will really expand our knowledge base of how this treatment works across the range of ambulatory patients with DMD.

Ultragenyx Pharmaceutical, a California-based rare disease-focused company, has also reached the Phase III stage with DTX401, which tackles glycogen storage disease type IA (GSDIa). This condition is caused by a genetic deficiency of the enzyme glucose-6-phosphatase, which breaks down glycogen reserves into glucose during fasting periods. GSDIa causes low blood sugar and accumulation of glycogen in the liver and kidneys, and patients need to regularly take cornstarch to maintain normal blood sugar levels, explained Eric Crombez, MD, Ultragenyxs chief medical officer for gene therapy and inborn errors of metabolism.

DTX401 is based on a liver-targeting AAV designed to restore glucose-6-phosphatase expression in patients hepatocytes. According to results presented at the ASGCT meeting, a Phase I/II study of DTX401 reported only mild adverse events in adult GSDIa patients.11 And all 12 participants were able to reduce their daily cornstarch intake by around 70% over three years. When interviewed at 52 weeks, most of the patients reported having more energy and better mental clarity.

If the transgene wasnt working, they would be having a lot of problems, Crombez asserted. [We can see that] they dont, [which] shows that weve established the normal breakdown of glycogen to produce glucose.

Motivated by these results, the company launched a Phase III study in 50 patients to compare the efficacy of DTX401 to that of a saline infusion. Primary endpointsincluding patients ability to taper cornstarch usewill be assessed after 48 weeks, but investigators hope to follow patients for as long as possible.

As the liver has high cell turnover, and the therapy doesnt integrate into the genome, the transgene will eventually be lost, Crombez said. Thats why he doesnt describe gene therapy as a cure in the strictest sense. However, he emphasizes that even if you need [another] dose 20 years down the road, [youve still] treated it for a very long period of time.

References1. Friedmann T, Roblin R. Gene Therapy for Human Genetic Disease? Proposals for genetic manipulation in humans raise difficult scientific and ethical problems. Science 1972; 175(4025): 9499552. Pollack A. FDA halts 27 gene therapy trials after illness. New York Times. Published January 15, 2003.3. Zuluaga CM, Gertz M, Yost-Bido M, et al. Identification of the Therapeutically Beneficial Intravenous Dose of AAVrh.10hFXN to Treat the Cardiac Manifestations of Friederichss Ataxia. Paper presented at: 25th Annual Meeting of the American Society of Gene and Cell Therapy; May 1619, 2022; Washington, DC.4. Lexeo Therapeutics. LEXEO Therapeutics Announces FDA Clearance of Investigational New Drug Application for LX2006, an AAV-Based Gene Therapy Candidate for Friedreichs Ataxia Cardiomyopathy. Published February 16, 2022.5. Imugene. Today we enhanced our portfolio with a compelling oncolytic virus technology. Published July 15, 2019.6. Park AK, Fong Y, Yang SK, et al. Effective combination immunotherapy using oncolytic viruses to deliver CAR targets to solid tumors. Sci. Transl. Med. 2020; 12(559): eaaz1863.7. Tretiakova AP, Ozkan T, Sethna F, et al. Rationally designed cardiotropic AAV capsid demonstrates 30-fold higher efficiency in human vs. porcine heart. Paper presented at: 25th Annual Meeting of the American Society of Gene and Cell Therapy (ASGCT), Washington, D.C., May 16-19, 20228. Henry T, Chung ES, Egnaczyk GF, et al. A first in-human phase 1 clinical gene therapy trial for the treatment of heart failure using a novel re-engineered adeno-associated vector. Presented at: 25th Annual Meeting of the American Society of Gene and Cell Therapy; May 1619, 2022; Washington, DC.9. Sarepta Therapeutics. Sarepta Therapeutics Investigational Gene Therapy SRP-9001 for Duchenne Muscular Dystrophy Demonstrates Significant Functional Improvements Across Multiple Studies. Published July 6, 2022.10. Sarepta Therapeutics. Sarepta Therapeutics SRP-9001 Shows Sustained Functional Improvements in Multiple Studies of Patients with Duchenne. Published October 11, 2021.11. Ultragenyx Pharmaceutical. Ultragenyx Announces Positive Longer-Term Durability Data from Two Phase 1/2 Gene Therapy Studies at American Society of Gene & Cell Therapy (ASGCT) 2022 Annual Meeting. Published May 19, 2022.

Continue reading here:
Gene Therapy Hits Its Stride in the Clinic - Genetic Engineering & Biotechnology News

GWAS identifies genetic variations associated with agronomic traits in foxtail millet

A total of 827 foxtail millet cultivars collected from China were sequenced and genotyped using common single-nucleotide polymorphisms (SNPs) based on a ~423Mb Setaria italica cv. Zhanggu reference genome (v.2.3)27. In total, 161,562 SNPs were detected after stringent steps of quality control, including population stratification and pedigree filtering, individual- and site-level call-rate filtering, and minor allele frequency (MAF) filtering. The SNPs were evenly distributed along chromosomes and the genetic distance for linkage disequilibrium (LD) decay to its half maximum was 9kb (Supplementary Fig.1A, B). Phylogenetic analysis based on the genetic SNPs revealed three main groups in the tested foxtail millet cultivars (Supplementary Fig.1C).

In addition, we planted these 827 foxtail millet cultivars for a field trial in Yangling, China, and measured their agronomic traits (Supplementary Data1). Twelve agronomic traits were used for further analysis, including six growth traits and six yield traits. The growth traits were mainly composed of top second leaf length (TSLL), top second leaf width (TSLW), main stem height (MSH), main stem width (MSW), panicle diameter of the main stem (MSPD) and fringe neck length (FNL) while the yield traits were represented by panicle length of the main stem (MSPL), per plant grain weight (PGW), main stem panicle weight (MSPW), hundred kernel weight (HKW), spikelet number of the main stem (MSSN) and grain number per spike (SGN). Genotypephenotype analysis showed that all 11 traits were significantly heritable except the trait HKW (H2=0.006, P=0.15). Growth traits exhibited higher heritability than yield traits, for example, MSPD showed the highest heritability (H2=0.46, the broad sense heritability) while PGW showed the lowest heritability (H2=0.16) (Supplementary Fig.2). GWAS on phenotypes was performed to identify the SNPs associated with the growth and yield traits. In total, 86 significant SNP loci and 91 associations for 10 traits (except MSPW and TSLW) were identified under suggestive P-value thresholds (P<2.01e5), some of which were for multiple traits (Fig.1, Supplementary Data2). Among these, 15, 16, 11, 10 and 16 significant SNPs co-located on chromosomes 2, 4, 6,7 and 9, respectively. The candidate genes located around the significant signal were analyzed for known molecular functions (Supplementary Data3). Firstly, several candidate genes responsible for growth and development regulation were observed such as ATG8C, ERF1B, PRR37 and Cyclin-like F-box. For example, the peak SNP signal si7:30050703 of MSW, located within the genic region of a homolog of ATG8C (autophagy-related protein 8C, Fig.1B), which functions in the early development of xylem and phloem tissues28. Additionally, SNP si2:6562955 was associated with MSW and near ERF1 (ethylene-responsive transcription factor) (Fig.1B and Supplementary Data3). ERF1 is implicated in cambium proliferation29, which might influence main stem width. Interestingly, the candidate gene PRR37 near the peak SNP si2:49328133 of the MSPL (Fig.1D), suppressed heading and showed shorter panicle length than its mutant in rice30, which might directly regulate the panicle length of foxtail millet. Besides, the peak SNP si2:6646016 of PGW was located within the genic region of Cyclin-like F-box (Fig.1C), which controls many crucial processes such as embryogenesis, hormonal responses, seedling development, floral organogenesis, senescence, and pathogen resistance31,32.

Manhattan plots showing the genome-wide associations between host genetic SNPs and A panicle diameter of the main stem (MSPD), B main stem width (MSW), C per plant grain weight (PGW) and D panicle length of the main stem (MSPL). The dotted line corresponds to a significance threshold of 2.01e5. Genes with significant SNPs are marked in red; genes near the significant SNPs are marked in green. NADKs: NAD+ kinase; PP2C:Phosphoinositide phospholipase C 2; WAT1:WAT1-related protein; ERF1: ethylene-responsive transcription factor 1; ATG8C:autophagy-related protein 8C; PRR37: two-component response regulator-like PRR37.

Secondly, numerous drought stress-responsive (PP2C, ARR12, NPF1.2, NPF4.6, WDR26, Plastocyanin-like protein, CPK2a, PIP5K1) and tolerant genes (APX, DTX12, bHLH3, Thioredoxin fold domain containing protein, SAPK9, Ca2+-transporting ATPase, InsP3, E3 ubiquitin-protein ligase, MIEL1) whose expression are frequently upregulated and contribute to drought resistance in drought-stressed seedlings, were found to be associated with the growth and yield traits (Supplementary Data3). For example, the SNP si2:49320133 that was associated with MSPD was located within the genetic region of PP2C (phosphatidylinositol-specific phospholipase C) (Fig.1A, Supplementary Data3), a stress and ABA-responsive gene that is involved in many physiological responses, including salt, drought and osmotic stress, carbon fixation in C4 plants, and inducible plant responses to pathogen33,34. In addition, NPF1.2 (protein NRT1/ PTR FAMILY 1.2) near the peak SNP (si4:27590764) of MSPD, which functioned as an ABA importer, is important for the regulation of stomatal aperture in inflorescence stems of Arabidopsis35. Another candidate gene SAPK9 (serine/threonine-protein kinase SAPK9) near the significant SNP (si3:44029863) of PGW improves drought tolerance and grain yield in rice by modulating cellular osmotic potential, stomatal closure and stress-responsive gene expression36 (Supplementary Data3).

Thirdly, a great number of plant immune responsive genes and pathogen defense genes were also found to be associated with traits, mainly including RPP13, RGA2, RPS2, LRR-RLKs, EF-Tu SYP22, NOG1, BBE, NB-ARC, and WAK2. Finally, several candidate genes responsible for nutrient uptakes such as iron transporter (IRT1, IRT2) and phosphate transporter (PT) were also observed (Supplementary Data3). Most of the candidate genes related to the significant SNPs were mainly involved in abiotic and biotic stress responses, implying that the host genotype and environment interaction might co-contribute to plant adaption and modulate the traits of foxtail millet.

To explore the contributions of genetic variations to plant performance, linear regression models were used to calculate the role of host genotypes on key growth (TSLW, MSPD, MSW)- and yield (MSPW, PGW, MSPL)-related traits of the 827 different foxtail millet cultivars. Considering no SNPs associations with phenotypes TSLW and MSPW under suggestive thresholds, we extended the candidate SNPs (adjusted P<1.0e4) as inputs of the linear regression models34,35 (Supplementary Data4). After performing thirty rounds of five-fold cross-validation, the genetic SNP markers in predicting model could explain an average of 32.82%, 28.55%, 47.27%, 15.02%, 38.89% and 64.60% of the variances in TSLW, MSPD, MSW, MSPW, PGW and MSPL in the testing data, respectively (Supplementary Fig.3).

Root associated microbiota are thought to promote resistance to pathogens and tolerance to specific environmental constraints, and also contribute to plant performance37,38. Firstly, linear regression models were performed to calculate the effect of the rhizoplane microbiota on growth- and yield-related traits of the 827 different foxtail millet cultivars. The 1004 rhizoplane operational taxonomic units (OTUs) with a 70% occurrence in all samples (here defined as common OTUs), covering an average of 61.30% of total abundances were used as the input data as these OTUs commonly exist in the root zone of foxtail millet cultivars. The common sub-community (1004 common OTUs) showed higher evenness and correlations with the growth traits than the whole microbial community (Kruskal-Wallis test (one-way analysis), Pevenness=2.58e30, Supplementary Fig.4AC). The average variation degree (AVD) index from the common sub-community, 0.5 and 0.3 sub-community (OTUs with 50 and 30% occurrence), were calculated to assess the microbiota stability. The common sub-community had a lower AVD value than the other two sub-communities, indicating that it has a more stable microbiota (Supplementary Fig.4D). In the common sub-communities, the moderate OTUs (covered 83.67% of OTU numbers) were abundant, followed by abundant OTUs (12.85%) and rare OTUs (3.48%) (Supplementary Table1). The network analysis was used to disentangle the ecological role and co-occurrence patterns of 1004 OTUs in the common sub-community. Abundant OTUs (ATs) had significantly higher values of the degree, closeness, betweenness centrality and hub scores than both rare (RTs) and moderate OTUs (MTs) in the network (Kruskal-Wallis test (one-way) with P<0.001, Supplementary Fig.4E), indicating their important roles in sustaining the stability of the microbial community. Thus, the candidate OTUs that were significantly correlated with the traits (adjusted P<0.05) were selected from the common sub-community and used as the input of the predicting models (Supplementary Data5). A five-fold cross-validation approach was repeated thirty times for each trait to reduce the noise in the estimated model performance. The candidate OTU markers in the OTU-predicting models explained an average of 32.47%, 17.43%, 56.06%, 30.36%, 35.17% and 12.61% of the variances in TSLW, MSPD, MSW, MSPW, PGW and MSPL in the testing data, respectively (Supplementary Fig.3).

To explore the contributions of genetic variations and environmental microbiota to plant performance, we used linear mixed models to calculate the role of host genotypes and rhizoplane microbiota on the aforementioned growth and yield traits. We used the candidate SNPs (adjusted P<1.0e4) as inputs of the linear regression models39,40 to predict phenotypic variations (Supplementary Data4). Then the candidate OTUs markers from the above models were also added to the linear regression model (Supplementary Data5). After performing thirty rounds of five-fold cross-validation, the genetic SNP and OTU markers in predicting model could explain an average of 46.50%, 59.08%, 65.69%, 38.45%, 43.04% and 44.31% of the variances in TSLW, MSPD, MSW, MSPW, PGW and MSPL in the testing data, respectively (Supplementary Fig.3). The correlation coefficients only using genotype as variables were obviously higher than that only using root microbiota as variables in several agronomic traits such as MSW and MSPL.However, in the trait MSPD and MSPW, the contribution of root microbiota to phenotypic plasticity was higher when root microbiota variables were used instead of genotype variables alone, indicating a different contribution of host genotype and root microbiota to phenotypic plasticity. The combination of host genotype and root microbiota significantly promoted the explanation of variations in all six traits than genotype and root microbiota alone (Wilcox rank test, P<0.001) except for the trait MSPL (Supplementary Fig.3). Consistently, the panicle length has been proven to be directly impacted by gene PRR3725, similar to our observed data. The predictive models with the best prediction accuracy for the phenotypes using the SNP and OTU variables were retained, which explained 53.42%, 63.73%, 70.54%, 50.16%, 55.88%, and 54.82% variations for TSLW, MSPD, MSW, MSPW, PGW and MSPL trait, respectively, resulting in a final set of 257 marker OTUs (Fig.2AF, Supplementary Data5). Network analysis of 257 marker OTUs showed that the abundant marker OTUs (AMTs) had a significantly higher value of the degree, closeness and betweenness centrality than both rare (RMTs) and moderate marker OTUs (MMTs), indicating the abundant marker OTUs have more important roles in community structure (Kruskal-Wallis test (one-way) with P<0.05, Supplementary Fig.5 and Supplementary Table1).

AF The variation of growth (TSLW, MSW, MSPD) and yield (MSPW, PGW, MSPL) traits explained by the genetic SNPs and microbial OTUs combined. Each panel shows observed values on the x-axis and model-predicted values on the y axis, with a fitted linear regression. Specifically, the predicted value of TSLW, MSW, MSPD, MSPW, PGW, and MSPL is calculated based on 136, 100, 117, 126, 110 and 106 samples in the testing dataset, respectively. The dark trend line illustrates the predicted effect in the linear model (LM). The gray shading around the line represents a confidence interval of 0.95. TSLW, top second leaf width; MSW, main stem width; MSPD, panicle diameter of the main stem; MSPW, main stem panicle weight; PGW, per plant grain weight; MSPL, panicle length of the main stem.

Among the 257 marker OTUs identified by MWAS, 145 and 128 marker OTUs were significantly correlated with growth and yield traits, respectively (Supplementary Data5). Taxonomic profiling of these marker OTUs revealed 86 genera distributed across 15 phyla. The top five abundant phyla were Proteobacteria (with 68 OTUs), Actinobacteria (54 OTUs), Bacteroidetes (36 OTUs), Acidobacteria (35 OTUs), and Firmicutes (33 OTUs) (Fig.3A). In particular,17 marker OTUs were shared by growth and yield traits. Unexpectedly, no marker OTU or genus was shared by all six traits (Supplementary Fig.6), suggesting that the microbial markers may function in different development stages or different processes of foxtail millet.

A Phylogenetic tree of the 257 microbial markers associated with agronomic traits of foxtail millet. The outer circle represents the phylum level. The beta estimates of the microbial OTUs to growth and yield traits are plotted in the inner circles, respectively. The arrows indicate the strains tested in planta (B, C), including strains responded to six positive marker OTUs: Acid550 to Acidovorax OTU_46, Baci299 to Bacillaceae OTU_22228, Kita594 to Kitasatospora OTU_8, Baci154 to Bacillus OTU_19414, Baci312 to Bacillus OTU_25704, Baci429 to Bacillales OTU_381, and strains responded to four negative marker OTUs: Shin228 to Shinella OTU_37, Baci81 to Bacillus OTU_54, Baci173 to Bacillaceae OTU_19835 and Baci554 to Bacillaceae OTU_28133. The strains predicted to affect growth traits are validated by plate (B) and sterilized soil (C). Significance is determined within each pair of treatment and control via one-tailed t-test and the P-values are adjusted by Benjamini-Hochberg (BH) method. n=41, 40, 38, 34, 43, 43, 44, 32, 21, 34 and 27 (from left to right) biological replicates in plate experiment. From Kita594 to Baci554, adjusted P(plant height)=8.68e07, 1.02e09, 0.07, 0.001, 0.49, 0.29, 0.03, 0.40, 0.001, 5.39e06, adjusted P(root length)=0.012, 0.10, 0.40, 0.18, 0.01, 0.11, 1.14e06, 0.02, 1.20e09, 5.68e12. n=20, 32, 31, 40, 23, 20 and 23 (from left to right) biological replicates in sterilized soil experiment. From Kita594 to Baci554, adjusted P(plant height)=1.6e07, 0.003, 0.018, 0.011, 0.98, 0.06, adjusted P(root length)=0.046, 4.4e04, 8.43e05, 0.016, 0.058, 0.15. *, ** and *** represented the adjusted P<0.05, 0.01 and 0.001, respectively. The box depicts the interquartile range (IQR) between the 25th and 75th percentiles, respectively and the line within the box represents the median. The whiskers extend 1.5 times the IQR from the top and bottom of the box, respectively.

To validate the predicted effects of these microbial markers on foxtail millet growth, we isolated a range of taxonomically different bacterial strains from root microbiota of the foxtail millet varieties grown in the field. A total of 644 bacterial strains were collected, and 257 bacterial isolates with complete 16S rRNA gene sequences were retained, representing four bacterial phyla and 25 genera (Supplementary Data6).

A cultured strain was considered a representative OTU if its 16S rRNA gene had 97% similarity with the rhizoplane microbiota OTU (Supplementary Data6). Representative cultivated strains of six positive marker OTUs (Acid550 to Acidovorax OTU_46, Baci299 to Bacillaceae OTU_22228, Kita594 to Kitasatospora OTU_8, Baci154 to Bacillus OTU_19414, Baci312 to Bacillus OTU_25704 and Baci429 to Bacillales OTU_381) and four negative marker OTUs (Shin228 to Shinella OTU_37, Baci81 to Bacillus OTU_54, Baci173 to Bacillaceae OTU_19835 and Baci554 to Bacillaceae OTU_28133) with top beta estimation in the regression model were selected for the validation experiments (Fig.3A and Supplementary Fig.7). We co-cultivated these 10 biomarker strains with foxtail millet Huagu12 (a bred cultivar of foxtail millet (Setaria italica) at Shenzhen, China) for 7-days in sterilized plates, and observed altered root lengths and plant heights compared with the control (Fig.3B and Supplementary Fig.7A). The positive biomarker strains representing OTUs with top beta estimation showed significant growth-promoting abilities. Specifically, positive biomarker strain Kita594 (Kitasatospora OTU_8) promoted both root and stem growth, whereas Baci299 (Bacillus OTU_22228) and Acid550 (Acidovorax OTU_46) only promoted shoot growth compared to the control (one-tailed t-test with adjusted P<0.05, Fig.3B and Supplementary Fig.7A). The negative marker strain Baci173 (Bacillaceae OTU_19835) and Baci554 (Bacillaceae OTU_28133) suppressed the shoot and root growth of Huagu12 (one-tailed t-test with adjusted P<0.05, Fig.3B and Supplementary Fig.7A). While the negative marker strains Shin228 (Shinella OTU 37) and Baci81 (Bacillus OTU 54) exhibited growth-promoting effects, they may only function in special root microbial flora in collaboration with other strains or be mistakenly identified as representative strains due to high 16S rDNA sequence similarities with negative marker OTU 37 and 54.

Next, we validated the effects of four positive marker strains (Kita594, Baci299, Baci154 and Acid550) and two negative marker strains (Baci173 and Baci554) with good promoting or suppressing performances on plant growth in plate experiment by watering millet seedlings grown in sterilized soil with these bacterial suspensions separately. Consistently, the seedlings watered with suspensions of the promoting bacterial strains Kita594, Baci299, Baci154 and Acid550 showed significantly increased plant height and root length compared with the control, whereas the seedlings watered with suspensions of the suppressing bacteria Baci173 showed shorter roots (one-tailed t-test with adjusted P<0.05, Fig.3C and Supplementary Fig.7B). These results validated the plant growth promoting (PGP) traits of marker microbes in foxtail millet.

To shed light on how bacterium regulates the growth of foxtail millet, we analyzed the transcriptomes of seedlings colonized for 14 days with the growth-promoting strains Baci299, Acid550, Kita594 or with the growth-suppressing strain Baci173. The differentially expressed genes from biomarker strain-inoculated versus non-inoculated samples were enriched in different pathways (Fishers exact test, q<0.05, Fig.4A). For example, the differentially expressed genes caused by growth-promoting strains were mainly enriched in the pathways such as Phenylalanine, tyrosine and tryptophan biosynthesis (ko00400), Biosynthesis of amino acids (ko01230), Phenylalanine metabolism (ko00360), Carbon fixation in photosynthetic organisms (ko00710), Photosynthesis-antenna proteins (ko00196), Photosynthesis (ko00195), MAPK signaling pathway-plant (ko04016), Plant-pathogen interaction (ko04626), Diterpenoid biosynthesis (ko00904), Monoterpenoid biosynthesis (ko00902), alphaLinolenic acid metabolism (ko00592) and Selenocompound metabolism(ko00450), while the differentially expressed genes caused by suppressing strain were mainly involved in the pathways such as Arginine and proline metabolism (ko00330) and Valine, leucine and isoleucine degradation (ko00280) (Fig.4A).

A KEGG enrichment analysis of differentially expressed genes in Baci173-, Baci299-, Acid550-, Kita594- inoculated seedlings. The differentially expressed genes represent the genes that were significantly upregulated or downregulated in seedlings inoculated with marker strain compared with control. Circle size represents the number of genes within the pathway and color represents the significance of the pathway. B Venn diagram showing the overlap of the significantly upregulated genes under different inoculations. C Transcript abundance of genes that were induced only in Baci173-, Baci299-, Acid550- and Kita594-inoculated seedlings, respectively.

Interestingly, the growth-promoting strains displayed strain-specific induction of genes involved in nutrient transformation, pathogen defense, anti-abiotic stresses and growth-promoting processes (Fig.4B, C, Supplementary Data7). For instance, the ammonia producing gene (K01455_fomamidase) and terpenoids synthase (K15803, germacrene D) were highly induced by strain 299; ethylene synthase (K05933, aminocyclopropanecarboxylate oxidase) and plant immunity responsive genes (K18834, WRKY1; K20538, MPK8; K00430, peroxidase; K13422, MYC2; and K04079, HSP90A) were abundantly induced by strain 550, and photosynthesis-related genes (K02692, psaD, K01092, IMPA; and K08916, LHCB5), anti-oxidant gene (K00434, Lascorbate peroxidase) and pterostilbene biosynthesis gene (K16040, ROMT) were highly induced by strain 594 (Fig.4C). Intriguingly, the expansin gene that mediates cell wall loosening and increased root and shoot growth in rice41, was induced by all of the growth-promoting strains.

Similarly, 39 genes were significantly induced only by the growth-suppressing strain Baci173, including auxin synthetase (K01426, amidase; K00128, aldehyde dehydrogenases ALDH), auxin-responsive protein IAA (K14484, auxin-responsive protein), L-glutamine synthetase (K01915) and branched-chain amino acid synthetase (BCAT, K00826) (Fig.4B, C, Supplementary Data7), which all have well-documented roles in inhibiting root growth42,43,44. Thus, the plant growth mechanisms mediated by microorganisms were strain-dependent.

To explore the relationship between the host genotype and rhizoplane microbial composition, Mantels test was used to evaluate the correlation between host phylogenetic distances and rhizoplane microbiota distance, exhibiting a significant Mantels correlations (r=0.06, P=0.0003, 9999 permutations). Subsequently, to investigate host genotype-dependent variation in the foxtail millet rhizoplane microbiota, the heritable microbes were identified based on a common rhizoplane OTUs data set, which covered 17 phylum and 52 orders. Using an SNP-based approach, the heritability for individual OTU was calculated. 281 OTUs with H2 (the broad sense heritability) more than 0.15 were defined as highly heritable and the others as lowly heritable (Supplementary Data8). Bacillales and Gp4 orders enriched greater numbers of highly heritable OTUs when compared with the lowly heritable fraction (Fishers exact test, q<0.05, Supplementary Fig.8A), implying that these bacterial orders were more easily impacted by host genotypes of foxtail millet. To explore whether there are similarities in heritable microbes across Poaceae family, we compared the top 100 most heritable OTUs from foxtail millet, sorghum45 and maize datasets46,47. After removing the order with a total number of OTUs less than 4, seven bacterial orders such as Bacillales, Actinomycetales, Burkholderiales, Rhizobiales, Myxococcales, Sphingobacteriales and Xanthomonadales were identified, which shared and covered more than half of the most heritable OTUs from foxtail millet, sorghum, and maize datasets, respectively (Supplementary Fig.8B, C). These results hence indicated that the microorganisms in these bacterial orders were more sensitive to genetic variations across both sorghum, maize and foxtail millet.

To further assess the association of host genetic variations and root microbial abundance, we ran mGWAS on 1004 common rhizoplane OTUs of foxtail millet. We identified significant associations of 2108 SNP loci with 838 microbial OTUs (here called SNPs-associated OTUs) at the genome-wide suggestive significance threshold of P<2.01e5 (Supplementary Data9). To identify how the host genetic variations drove abundance variations of the specific microbial taxonomies, especially the bacterial orders that were more sensitive to genetic variations, the SNP-associated genes for each order were enriched into pathways (Supplementary Fig.9). However, only four bacterial orders associated genes were significantly enriched into different pathways. Taking Bacillales for example, the associated genes were mainly enriched in the monoterpenoid biosynthesis pathway (Fishers exact test, q=0.05, Supplementary Fig.9). The GP4 associated genes were significantly enriched in producing D-galacturonic acid (Fishers exact test, q=0.08, Supplementary Fig.9). GP4 from Acidobacteria phylum, which has been reported with the capability of utilizing galacturonic acid, a characteristic component of the cell wall in higher plant48, might be recruited to rhizoplane by plant-secreted galacturonic acid. The genes associated with plant pathogen-containing order Xanthomonadales were significantly enriched into the pathway such as peroxisome and MAPK signaling pathway (Fishers exact test, q=0.01 and 0.04, Supplementary Fig.9), which are involved in disease and abiotic resistance49,50. These results provide key insights into how the host genetic mechanism drive plant-associated microbiota.

In addition, significant SNP loci located in the generic region were also deeply analyzed (Fig.5, Supplementary Data9). For example, the peak SNP signal si7:13687399 located in the genic region of bHLH35 was associated with 39 common OTUs from different microbial taxonomies such as Acidobacteria (28), Proteobacteria (8) and Bacteroidetes (3). bHLH35 proteins are transcription factors induced by effector-triggered immunity (ETI), and also involved in tolerance to abiotic stresses51. The SNP si1:32157654 located in the generic region of WAK2 (wall-associated receptor kinase 2) was associated with 30 common OTUs, including Acidobacteria (21), Bacteroidetes (4), Proteobacteria (4) and Actinobacteria (1). The WAK2 protein bound to pectin, is required for cell expansion and is induced by a variety of environmental stimuli, including pathogens and wounding52. Similarly, the 50 common OTUs were found to be associated with FLS2 (si7:2994337, Supplementary Data9), a flagellin sensor that perceives conserved microbial-associated molecular patterns (MAMPs) in the extracellular environment53. Clostridia OTU_19207 and Nocardioides OTU_26357 associated si8:20598566 located within the gene of NPF1.2 (Fig.5 and Supplementary Data9), which is involved in ABA importing and nitrate utilization, regulates plant development and influences the root microbiota14,35,54. An NPF1.2 homologue in loci si1:20064466 was significantly associated with Bacillaceae OTU_28839. Collectively, host genes related to plant immunity (RPM1, RGA2, HSL1, CRKs, LRR-RLKs), metabolites (Flavonoids, Diterpenes, amyA, alpha-N-arabinofuranosidase, beta-glucuronosyltransferase), nutrient uptake (Acid phosphatase, Mg2+ transporter, H+-transporting ATPase), plant hormone signal transduction (BRI1, DELLA protein, EFR3, PI-PLC, SDR, ARR1) and others (E3 ubiquitin protein ligase) are perhaps common host genetic factors with function to modulate root microbial composition assembly (Fig.5 and Supplementary Data9).

Manhattan plots show the significant SNPs for microbial abundance. SNPs located in gene coding regions are labeled with numbers. Details of the associations between the host genes and microbial species are given in the table below. All of these associations of SNP loci and microbial OTUs were significantly lesser than 2.01e5.

Plants primarily influence their microbiomes through targeted interactions with key taxonomic groups or diffuse interactions with entire communities55. To further investigate the mode of host-microbe interactions, the hub microbial taxa and non-hub microbial taxa and their associated genes were identified. Firstly, we defined hub taxa as OTU with high values of degree (>400) and closeness centrality (>0.5) in the network as described in a previous study56, resulting in 102 hub OTUs. We identified that 90 hub OTUs and 748 non-hub OTUs had significant associations with the host genetic SNP loci (Supplementary Fig.10A, Supplementary Data9), indicating host plant might interact with these hub microbes and diffusely interact with these non-hub microbes. We aggregated these SNP-associated hub OTUs (90 hub OTUs) and non-hub OTUs (748 OTUs) into 12 and 36 microbial orders, respectively. Comparative analysis showed that one order GP7 was only composed of SNP-associated hub OTUs, and 25 orders such as Sphingobacteriales, Bacillales, Ohtaekwangia, Sphingomonadales and Acidimicrobiales were only composed of SNP-associated non-hub OTUs, and 11 orders were composed of both SNP-associated hub and non-hub OTUs (Supplementary Fig.10B). These data indicated that the foxtail millet employed two modes to structure the rhizoplane microbiota: targeted interaction with several hub microbes and diffused interaction with most of the microbes. To decipher the potential mechanism of the interaction between plant and microbe, the candidate host genes around the SNP loci associated with the hub and non-hub OTUs were extracted separately. The networks showed that the host immune genes FLS2 and transcription factor bHLH35 are widely associated with the hub and non-hub taxa (Supplementary Fig.11A, B). However, the host plant still employed different genes to interact with different taxa (Supplementary Fig.11C), suggesting a taxa-dependent regulation model.

To determine if the genotype-dependent rhizoplane microbiota influence agronomic traits in foxtail millet, we compared the 838 SNP-associated OTUs (mGWAS identified) with the 257 marker OTUs (MWAS identified). We discovered that 219 of the SNP-associated OTUs overlapped with the marker OTUs in our data sets, covering 85.2% of 257 marker OTUs. (Supplementary Fig.12A, 219 out of 257=85.2%). 682 SNP loci were significantly associated with 219 marker OTUs (here called marker OTU-associated SNPs). However, for the 682 marker OTU-associated SNPs, only 4 overlapped with the 45 non-redundant marker SNPs (GWAS identified) that were associated with the aforementioned agronomic traits of foxtail millet (Supplementary Fig.12B). Most of the genetic variations that were associated with marker OTUs were not directly associated with agronomic phenotypes. These genetic variations might affect agronomic phenotypes indirectly, only in the presence of environmental factors such as marker microbes. Moreover, the Mantel test also showed that SNP-associated marker OTUs had higher correlations with the growth trait (MSPD and MSW) than non SNP-associated marker OTUs, while having no difference in correlations with trait TSLW, MSPW, PGW and MSPL (Supplementary Table2). It means that the genotype-dependent marker OTUs might explain more variances in plant growth traits.

To decipher host plant genetic mechanisms for marker microbe selection, KEGG pathway enrichment analysis revealed that the genes within or nearby the significant SNP loci were enriched in pathways related to plant-pathogen interaction (ko04626), MAPK signaling (ko04016), Steroid biosynthesis (ko00100) and so on (Supplementary Data10). Specifically, the genes enriched in plant-pathogen interactions included microbial pattern-recognition receptors (PRRs), disease-resistant genes RPM1 and RPS2, an activator of pathogenesis-related genes PTI1 and PTI6, key regulators of plant immune responses CALM and transcription factor WRKY25. These results suggest that the plant defense genes may also underpin the microbial ecology in the root habitat in addition to protecting from pathogens.

Among the 219 SNP-associated marker OTUs, 77 were highly heritable (Fig.6A). The association between host genetic variation, the abundance of specific marker microbes and phenotypes, especially for 77 genomic heritable marker OTUs were closely examined (Fig.6A, Supplementary Data8). Remarkably, plant defense-related genes and transcription factors, such as the plant immune receptor FLS2 (si7:2994337), transcription factor bHLH35 (si7:13687399) and WAK2 (si:2:5642650) had a dominant impact on the marker OTUs from the phylum of Acidobacteria (Fig.6A). In contrast, genes involved in nutrient uptake, metabolites and abiotic stress response, such as magnesium transporter (si7:19232862), triterpene synthase (si:7:11346839, achilleol B synthase), BGLU12 (si:3:4780643, Beta-glucosidase 12) and RXW8 (si:3:39749463, CSC1-like protein RXW8), mainly associated with marker OTUs from Actinobacteria, Bacteroidetes and Proteobacteria, which mostly contribute positively to the growth and yield traits of foxtail millet (Fig.6A). Other genes involved in plant growth and development processes, such as SUZ12 (Polycomb protein SUZ12) and WAT1 (WAT1-related protein), impacted the marker OTUs from Firmicutes (Bacillaceae OTU_19835) and Proteobacteria (Xanthomonadaceae OTU_10146) respectively, but these marker OTUs have opposite effects on the growth of foxtail millet (Fig.6A). Additionally, we observed strong associations between the positive marker Acidovorax OTU_46 and EREBP-like factor (si7:27291504, dehydration-responsive element-binding protein 1B-like), and between positive marker Kitasatospora OTU_8 and FaQR (si2:36177507, 2-methylene-furan-3-one reductase) (Fig.6A). To explore the host genetic mechanisms that might drive the associations of the plant host gene and rhizoplane microbiota, we examined the specific expression pattern of candidate genes from the RNA-seq datasets obtained from the sterilized soil experiments. Obviously, the genes FaQR, vWA (von Willebrand factor, type A), SUZ12 and EREBP-like factor (ethylene response element binding protein) exhibited significant variation after being inoculated with strain Kita594 (Kitasatospora OTU_8), Baci299 (Bacillaceae OTU_22228), Baci173 (Bacillaceae OTU_19835) and Acid550 (Acidovorax OTU_46) compare to control, respectively (Supplementary Fig.13), implying that the candidate host genes likely interacted with specific bacterial strains.

A Venn diagram displaying the overlaps among 838 SNP associated OTUs, 257 marker OTUs and 281 highly heritable OTUs. B A network of associations between the candidate genes and marker microbial OTUs. Edges between the marker OTUs and host genes were colored according to the correlation coefficients. The pink color represents the positive correlations while the green color represents the negative correlations. The circle represents the OTUs colored according to the phylum taxonomy information, the triangle represents the genes colored according to the function module information, the square represents the growth traits colored in green and the yield traits are shown in yellow. Plant height (C) and root length (D) of seedlings of FaQR reference cultivars (C494 and C1631) and allele cultivars (C571 and C1119) grown axenically (no bacteria, control) or with growth-promoting Kita594. n=22, 26, 36, 37, 50, 46, 45 and 41(from left to right) biological replicates. Plant height (F) and root length (G) of seedlings of SUZ12 reference cultivar (C946 and C306) and allele cultivar (C1296 and C1021) grown axenically (no bacteria, control) or with growth-suppressing Baci173. n=39, 32, 46, 40, 50, 24, 45 and 31 (from left to right) biological replicates. The deviation of promoting and suppressing effect of marker strain Kita594 (E) and Bci173 (H) were calculated separately. n=26, 37, 46, 41, 26, 37, 46 and 41 (from left to right) biological replicates for the treatment with marker strain Kita594 (E). n=32, 40, 24, 31, 32, 40, 24 and 31 (from left to right) biological replicates for the treatment with marker strain Bci173 (H). Different letters in C to H indicate statistical significance (adjusted P<0.05) among the treatments according to one-way ANOVA and LSD test at the 5% level. In C, df=7, F=19.73, adjusted P<2.0e16; in D, df=7, F=13.76, adjusted P=2.09e-15; in E, df=3, F=2.10, adjusted P=0.102; df=3, F=18.29, adjusted P=4.04e10; In F, df=7, F=18.11, adjusted P<2.0e16; in G df=7, F=14.83, adjusted P<2.0e16; in H, df=3, F=19.57, adjusted P=2.0e10; df=3, F=6.751, adjusted P=2.90e4. The box edges depict the 75th and 25th percentiles, respectively and the line within the box represents the median. The whiskers extend 1.5 times the IQR from the top and bottom of the box, respectively.

Finally, based on cultivars with different genotypes, the influence of functional SNPs on marker OTU abundance was thoroughly examined. The abundance of marker OTUs shifted among the different genotypes at the most strongly associated SNPs (Supplementary Fig.14). We hypothesize that host gene-regulated promotion/suppression microbes could establish genotype-dependent microbe-mediated growth phenotypes. To test this hypothesis, we germinated the FaQR and SUZ12 reference and allele foxtail millet cultivars on sterile plates inoculated with a growth-promoting or suppressing strain that corresponds to each cultivar: the growth-promoting strain Kita594 to FaQR reference (C494 and C1631) and allele (C1119 and C571) genotype cultivars, the growth-suppressing strain Baci173 to SUZ12 reference (C946 and C306) and allele (C1021 and C1296) genotype cultivars. Intriguingly, we found that strain Kita594 had a statistically significantly shoot-promoting effect only on the allele cultivars, but not on reference cultivars (Fig.6CE, adjusted P<0.05 by ANOVA-LSD), supporting that plant-growth promoting rhizobacteria support genotype-dependent cooperation with the plant. We observed strong root growth inhibition in seedlings inoculated with the growth-suppressing strain Baci173 (Fig.6FH, adjusted P<0.05 by ANOVA-LSD), and a more significant suppressing effect on root length was observed in the allele cultivars (C1296 and C1021) compared to the reference cultivars (C946 and C306). Significant effects of the interaction between the genotype and strain Kita594 and strain Baci173 on the shoot and root length were also detected by PERMANOVA, respectively (genotypes*Kita594: R2=13.048, P<0.001; genotypes*Baci173: R2=0.07, P<0.001, Supplementary Table3). Together, these results suggest that host genetic variation might impact the interactions between marker strains and host plants, finally affecting the plant phenotypes.

The rest is here:
GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet - Nature.com