Cotton Revolution: Unlocking New Cotton Varieties for a Sustainable Future

Since the first viral cotton disease was observed in Nigeria in 1912, quickly spreading from Africa to North America and Asia, we’ve known cotton is vulnerable. Over the decades, scientists and farmers have worked to protect the billion-dollar industry. With diverse applications spanning clothing, household essentials like bed sheets and towels, medical supplies, and even renewable biofuels, cotton remains an invaluable global crop.

New cotton diseases have appeared in recent decades, adding to the industry’s challenges. Climate change and limited resources compound these threats. Meanwhile, the global population continues to grow, further straining the supply chain for a plant that has been woven into our daily lives for the last 3,000 years. The result is rising prices to produce premium cotton.

Breeding new, disease-resistant, and affordable cotton varieties using traditional techniques to crossbreed plants with desired traits has been slow, sometimes taking more than a decade. However, genetic modification could significantly expedite this process, says Chris Saski, a plant geneticist with Clemson University, whose research explores the genetic architecture of cotton’s fiber-related traits.

“Right now, there are some major disease threats to cotton in the Cotton Belt. Sure, you can use classical breeding that requires extensive experimentation with crossing different plants to release a line with the right combination of traits to address those, but it can take up to a decade or more,” Saski said. “Our work could help shorten this timeline to just two breeding cycles, or about a year.”

The goal is to develop these premium cotton varieties with tailored characteristics achieved through precise genetic modifications using biotechnology and gene editing tools. New lines could be designed to produce cotton plants instilled with disease or drought-resistant properties or engineered to produce high yields—the possibilities are endless, says Saski.

“With genetic modification, we can design cotton that’s high quality and more resistant to pests and other threats while remaining affordable,” he said.

Perfecting the science of gene editing could revolutionize cotton production and lend knowledge to other essential crops; however, a fundamental problem stands in the way: delivering the gene-editing cassettes (small segments of DNA) and successfully regenerating modified plants from single cells. This genetic program of regeneration, called somatic embryogenesis, is written in the DNA of all crops but is silenced by various factors influencing it on Earth. To improve his system for genetic modification, Saski needs to turn these silenced genes on.

All life on Earth is subject to gravity, a critical factor in plant development. Gravity influences specific genetic signals and processes within plant cells that guide the development of plant shoots upward toward the sun and roots downward in the soil. But plant cells behave differently in space, where gravity is much weaker, potentially leading to a new understanding of the genetics underlying regeneration.

Scientists can revert plant cells into a stem cell-like form, similar to human stem cells. The cells can then be genetically modified and reprogrammed into a new plant. Studying the genetic architecture of plant stem cells in tissue culture, both on Earth and in microgravityThe condition of perceived weightlessness created when an object is in free fall, for example when an object is in orbital motion. Microgravity alters many observable phenomena within the physical and life sciences, allowing scientists to study things in ways not possible on Earth. The International Space Station provides access to a persistent microgravity environment., can help identify which genes need to be expressed during somatic regeneration—a key step in genetic modification.

Saski and colleagues proposed sending a plant tissue culture experiment to the International Space Station (ISSInternational Space Station) to explore whether microgravity can trigger plant stem cells to regenerate into whole plants from a single cell. The project was selected through the ISS National Lab Cotton Sustainability Challenge, which Target Corporation funded.

Results from this spaceflight research could help unlock the underlying molecular mechanisms of plant regeneration and remove a significant bottleneck in gene editing cotton and other crops on Earth. Saski envisions a future where gene editing becomes more accessible and efficient, addressing global food, fuel, and fiber supply challenges.

High-Flying Cotton

Saski’s method for precise genetic modification involves introducing foreign genes into a plant’s genome to produce desirable traits, such as pest resistance or improved yield. However, the success of genetic transformation often relies on the plant’s ability to regenerate transformed cells into whole plants. If regeneration is suppressed, it becomes challenging to achieve stable genetic modification, and the new plant fails to perform.

Scientists can potentially manipulate these processes to enhance regeneration efficiency by identifying the specific mechanisms suppressing the regeneration process, which Saski hoped to do in space.

He teamed up with Techshot, which has since been acquired by Redwire Corporation, to develop hardware for cultivating plant tissue cultures in microgravity. Saski said there were many challenges to overcome because experimenting with plant tissue cultures in space hadn’t been done since NASA’s Space Shuttle Program ended. These challenges mainly involved keeping contamination out of the hardware and simplifying the experiments.

“When students come to my lab to learn how to do tissue culture, the main concern is contamination, for example, having some sort of microbe or fungus contaminate your plates,” Saski said. “So, you can imagine our concern, sending our sterile tissue culture plates to the space station and having astronauts who are likely nontrained tissue culturists work on it.”

The team worked with Techshot to design several small, round Petri dishes with growth media and samples of stems from a cotton plant grown on Earth. “The cut stems respond to hormones in the media that initiate cellular de-differentiation into stem cells,” Saski says. On the ISS, the Petri dishes were put into a plant habitat the size of a large microwave that provided controlled light, temperature, and humidity levels for growing the cells.

The flight hardware was adorned with Clemson stickers, symbolizing the university’s contribution to cutting-edge space research. In 2021, the experiment was launched to the space station onboard SpaceX’s 24^th Commercial Resupply Services (CRS) mission.

The experiment took place over about 90 days, “and long story short, there was no contamination, the astronauts did an amazing job, and the experiment was a success,” says Saski. “We do believe that we were able to visualize some interesting morphological changes in the stem cells because of the lack of gravity.”

Now, co-principal investigator Jeremy Schmutz, a geneticist at HudsonAlpha Institute for Biotechnology, and his team are analyzing the space-flown cotton samples. As analysis continues over the next few months, data from the space cotton should begin flooding in.

Based on preliminary results, Saski expects the space experiments will reveal key genes involved in regeneration and how the genes are regulated. The research team can translate this information into a system that enables regeneration in virtually any cotton line that does not currently regenerate, which is typical of most cotton lines, Saski said.

With this ability, researchers can edit commercially grown elite cotton lines with genetic traits tailored for growing in specific environments.

“So, when we need to engineer drought resistance or resistance to a pathogen, we can use our new system from this project to directly modify an elite line, saving decades,” he said.

Over the past few years, Saski’s research team has also performed many experiments back on Earth related to the ISS National Lab-sponsored project. For example, Sonika Kumar, a senior scientist in the department of plant and environmental sciences under Saski’s direction, has identified several key morphogenic genes that facilitate the rapid generation of genetically engineered Coker 312, an upland cotton line with traditionally poor agronomic and fiber traits compared with commercial lines.

She developed a system that makes Coker 312 regeneration faster and more efficient and allows her to manipulate plant traits, including drought and disease resilience. This initial research led to new findings related to plant regeneration for upland cotton, which were published in the National Institute of Health journal Plants (Basel). Importantly, the outcomes allow Kumar to establish regeneration systems for direct gene editing of commercially available lines. Saski says these findings have already significantly improved his gene editing system, and the team is excited to see what more is revealed in the space-flown cotton.

“It was fascinating to watch the callus, or stem samples, float in microgravity during subculturing by the astronauts,” says Kumar. “I enjoyed configuring plant tissue compatible with flight hardware and developing protocols for the astronauts to conduct our experiment and to capture high-resolution image data. Now, we’ve completed all our space and ground experiments and are working with the genomic data to advance our project to the next stages.”

The team plans to use what they’ve learned to regenerate elite lines of cotton, such as Pima cotton, more efficiently and rapidly—saving time and money.

Space Solutions for Earth’s Cotton

Saski’s project was partly funded by Cotton Incorporated, a national program for upland cotton, the most widely planted species of cotton. The program supports hundreds of research projects to improve profitability for both growers and retailers. Don Jones, director of breeding, genetics, and biotechnology at Cotton Incorporated, says that upland cotton falls behind much larger acreage crops such as corn and soybean when it comes to investment devoted to crop improvement. Not only are there fewer research investments, but cotton is also further hindered by its basic biology: poor somatic embryogenesis.

“This, in turn, has slowed gene editing techniques such as CRISPR Cas9 in cotton,” says Jones. “Dr. Saski’s space station project aims to significantly improve embryogenesis, allowing for greater deployment of the latest gene editing techniques to increase yield and sustainably improve fiber quality.”

Already, agricultural companies have approached Saski about licensing his technology, but the benefits continue beyond that. Gene banks that store plant diversity in various forms, like seeds, living plants, or cells, could benefit from Saski’s work. If researchers understand genetic programs well enough to store and regenerate cells, we could streamline how we maintain plant diversity on Earth and explore options for space colonization and deep space exploration, Saski says.

“Imagine storing plant species as single cells, providing astronauts with a diverse array of plants for research or even sustenance during long-duration space missions,” he said.

Saski’s primary focus, though, is growing more crops with less land and water to feed a growing population amidst climate change. As he moves closer to removing the plant regeneration barrier, Saski has become interested in understanding and engineering genetics from weeds into crops, an idea that could help meet the needs of 10 billion people on Earth by 2050.

“What resilient traits can we translate from indigenous weeds that might help our crops grow more plentiful and resistant to threats?” he said. “We’re trying to develop pathways to do that, which would significantly benefit people worldwide.”