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HudsonAlpha On Team Awarded 5-year, $68M Biofuels Grant

Several research groups at HudsonAlpha Institute for Biotechnology are passionate about producing crops that can be used as fuel to create clean and sustainable energy for our planet.

And now, with the help of a newly awarded Department of Energy grant, they can move one step closer to this goal.

The grant is part of a DOE project that will provide $68 million in funding over five years for basic research aimed at making more productive and resilient crops that can be used to produce fuel, called biofuel. Material from these crops, referred to as biomass, can be harvested and converted into liquid biofuels for use in transportation, or as energy for heat and electricity. Biofuel represents an important alternative to fossil fuels because it is a renewable, sustainable, and carbon-neutral source.

Faculty Investigator Jeremy Schmutz of HudsonAlpha is on a team of researchers from across the United States working for more than a decade to genetically characterize and improve the biomass production of switchgrass. The collaborative research team is led by Dr. Thomas Juenger of the University of Texas. Dr. Kankshita Swaminathan of HudsonAlpha brings her team’s expertise in plant gene editing to the project.

One of the most exciting aspects of our project is the diverse research perspectives on the team – a group that includes ecologists, evolutionary biologists, genomic and data scientists, microbial ecologists, physiologists and plant breeders,” Juenger said. “The broad perspectives provided by the team have been critical for developing creative solutions to improving switchgrass.”

Switchgrass grows in much of North America and is commonly used for livestock feed and erosion control. Switchgrass is a promising biofuel candidate because its deep roots that allow it to access nutrients easily from a variety of soils, and it has a higher tolerance for extreme water conditions, such as drought or prolonged periods of rain.

There are several varieties of switchgrass based upon the climate and their environment. For example, the southern lowland switchgrasses are tall and thick-stemmed, while the northern upland switchgrasses are short and thin-stemmed.

For biofuel production, tall and hearty switchgrass is desirable to produce the most biomass per plant. The research groups aim to produce a variety of switchgrass that is high-producing like the southern plants but has cold tolerance like the northern plants.

By breeding switchgrass that can thrive across different climates, the research group hopes to create a biofuel crop that is not only sustainable and clean but can also be grown on lands that are not traditionally useful for growing food. The ability of a biofuel crop to grow on otherwise uninhabitable land is important in the quest to increase biofuel crop production without jeopardizing commercial farming.

Planting switchgrass in common gardens at 10 sites across the United States allows the research group to study how genetics and the environment interact. This helps the researchers determine the genes or genetic changes responsible for desirable switchgrass traits. Such traits include high biomass production, cold tolerance, sustainability, and a high success rate of plant establishment from seeds.

“We hope to be able to solve long standing issues with switchgrass crop improvement by applying our large-scale genomic efforts,” Schmutz said. “Improved switchgrass varieties will bring greater cold tolerance and increased yield for biofuel feedstocks for this highly sustainable perennial crop.”

The group will identify genes that confer these key traits in switchgrass and use Swaminathan’s expertise in targeted editing and plant breeding to make varieties of switchgrass that will produce the most biomass yet will survive in colder climates.

“Over the last decade, this team has used the latest technology in genomics to explore the effect of genetics and environment in switchgrass and have identified genes that likely influence many desirable traits,” said Swaminathan. “It is a really exciting time to test these hypotheses using recent advances in plant biotechnology and genome editing.

“This will allow us to explore the precise function of genes of interest and help inform directed breeding for more resilient, high yielding plants.”

 

 

HudsonAlpha Study Reveals Similarities Between Wild, Domesticated Cotton

Plant genomics researchers at HudsonAlpha Institute for Biotechnology announce the surprising results of a cotton sequencing study led by Dr. Jane Grimwood and Jeremy Schmutz, who co-direct the HudsonAlpha Genome Sequencing Center. The goal of the project was to identify differences among wild and domesticated cotton that could be used to bring back traits like disease or drought resistance. The results, however, surprised the researchers and led them to unexpected conclusions, as described in their paper in Nature Genetics.

Dr. Jane Grimwood

“The importance of this study is that it helps us understand more about cotton fiber development,” said Grimwood, who is a faculty investigator at HudsonAlpha. “But perhaps more importantly, it reinforces the surprising concept that wild and domesticated cotton is remarkably similar, leading us to the conclusion that we will need to work on other approaches to generate diversity for cotton species.”

For the study, the group sequenced and pieced together the complete genomes of five different species of cotton – both wild and domesticated – for comparison. Their genomic analysis showed that two ancestral diploid cotton genomes came together to form what is basically the modern tetraploid cotton between 1 and 1.6 million years ago.

“When we compared the wild cotton plants to domesticated cotton, we expected to see that the wild traits had been lost,” said Schmutz, a faculty investigator at HudsonAlpha. “What you typically see with these crops is that all the selection has gone into improving production, potentially at the cost of losing beneficial genetic material from the wild species.”

What they found, however, surprised them.

The wild and domesticated genomes, it turns out, were incredibly similar.

Jeremy Schmutz

“There’s less diversity between what are supposed to be different species of cotton than between two humans or even within different cells in a single human body,” Schmutz said.

This lack of diversity means that researchers won’t be able to as easily reach back into the wild cotton gene pool to introduce lost traits such disease resistance back into cultivated cotton plants.

“We can’t only rely on the gene pool to make changes to cotton as a crop because those wild genes don’t exist. The only real way forward is really going to be targeted genome editing,” Schmutz said.

Even though the group was surprised to find so much similarity among the cotton genomes, they did find some useful variation. Wild cotton, for instance, has some more genetic disease resistance triggers than cultivated cotton varieties, which tend to be more vulnerable.

“This is the basis from which we can start to compare what else we can do with existing cotton diversity,” Grimwood said. “Breeders have selected for ‘improved’ strains of cotton based on how the plants perform in the field, but they don’t necessarily have a full understanding of the changes they are making on the genetic side. With this new information, they can really look at what their selections are doing on a genetic level.”

Even though the project results were unexpected, the entire team is confident that the newly assembled cotton genomes will lead to direct benefits for cotton producers and the cotton industry.

Don Jones, the director of Agricultural Research at the nonprofit Cotton Inc., said these reference grade assemblies are significant advancements for improving the sustainability of cotton production.

“The results described in this Nature Genetics publication will facilitate deeper understanding of cotton biology and lead to higher yield and improved fiber while reducing input costs. Growers, the textile industry, and consumers will derive benefit from this high impact science for years to come,” Jones said.

This work is supported by grants from the National Science Foundation, U.S. Department of Agriculture and Cotton Inc.

In addition to the HudsonAlpha team, the publication included researchers from 12 other institutions: the University of Texas; Nanjing (China) Agricultural University; Texas A&M University the U.S. Department of Agriculture in Raleigh, N.C., and Stoneville, Miss.; Zhejiang A&F University in Lin’an, China; Clemson University; Iowa State University; the U.S. Department of Energy Joint Genome Institute in Walnut Creek, Calif.; Mississippi State University; Alcorn State University; and Cotton Inc. in Cary, N.C.

HudsonAlpha Brings Power of Genomics to Capitol Hill

WASHINGTON – Along with research, education is a key element of the HudsonAlpha Institute for Biotechnology’s mission.

So, officials with the Huntsville-based center went on a mission to Capitol Hill last month and presented “Genomics in Agriculture 101: Exploring the Basics” in the Rayburn House Office Building. It was the third time HudsonAlpha held a “Genomics 101” session for lawmakers and their staff.

Members of Congress, their staff and House and Senate Committee staff members engaged with Jeremy Schmutz, faculty investigator and co-director of the HudsonAlpha Genome Sequencing Center; Dr. Kankshita Swaminathan, faculty investigator; and Dr. Neil Lamb, vice president for Educational Outreach, during the briefing.

The purpose for “Genomics in Agriculture 101” was to provide a forum for leaders in plant genomics to interact with the leaders who drive national policy, impacting agriculture for the United States and beyond.

“Enormous progress has been made in plant genomics in just a few short years. We have gone from generating a single reference genome for a single plant, to generating hundreds of reference plant genomes and detailed diversity of crop collections,” said Schmutz. “These advances are providing solutions to the many agricultural challenges faced by the farming community every day.

“Genomics 101 provided decision makers on national policy an opportunity to learn more about the reach and impact of genomics in agriculture.”

Some of the topics discussed at the briefing involved the power and utility of the information gained through genomics, specifically regarding improvement of crop yields; acceleration of breeding cycles; resistance to diseases and pests; reaction and resulting changes based as a result of drought or floods. Additionally, the group from HudsonAlpha stressed the importance of collaboration within the field of plant genomics.

HudsonAlpha Scientists Help Secure the Future of Chocolate with Improved Cacao Reference Genome

People around the world consumed nearly 7.7 million tons of chocolate in the last year, but the cacao crop that supports the production of these sweets is under significant environmental threat.

Millions of cacao farmers in West Africa, Southeast Asia and Latin America feel the pressures of ever-increasing consumption, a changing climate and devastating fungal infections. In 2017, The New York Times said there is “a battle to save the world’s favorite treat.”

Scientists at the HudsonAlpha Institute for Biotechnology with funding from Mars Wrigley Confectionery have created the newest weapon in that battle — an improved reference genome to help researchers and farmers develop healthier, more productive cacao crops.

Sweets Under Siege

The production of one of the world’s favorite delicacies relies on a particularly delicate plant. Cacao can only be grown within 20 degrees of the equator, and global studies suggest that the effects of climate change will shrink the farmland currently suitable for production even further. Increasing temperature and decreasing humidity in the areas that currently produce cacao will mean the crop must be grown at higher elevations.

Cacao also proves particularly vulnerable to fungi and diseases. It suffers from a number of menacingly named blights, including frosty pod rot, witches’ broom, black pod and cacao swollen-shoot virus. One fear is that if any of these blights spread from its native region, it could sweep through global crops, devastating worldwide production.

The Newest Weapon in the War to Save Cacao

HudsonAlpha scientists have completed and released an updated reference genome for the tree that produces cacao beans. Researchers generated this resource using advanced long-read sequencers to produce an updated reference genome than the first version, which was completed in 2010. 

A reference genome identifies parts of the genome to be carried through to the next generation of plants, such as genes that promote drought tolerance, increase yield or improve disease resistance. Then, researchers can sequence each generation of selectively bred plants to quickly find which ones carry the desirable traits.

This most recent effort was was led by HudsonAlpha faculty investigators Dr. Jane Grimwood and Jeremy Schmutz.

“As our technology improves, we’re able to produce more detailed, versatile reference genomes, which are critical for the kind of rapid crop improvement you want to see with cacao,” Schmutz said.

Farmers have used selective breeding to improve crops for centuries. The process works by crossbreeding two plants, hoping to combine desirable traits and make hardier plants. Then, the offspring with those traits are bred again. This selective breeding process takes time though, because each crop must mature. A cacao tree, for example, takes about five years to start generating fruit.

A Better “Chocolate Tree”

Cacao trees, like many modern crops, do not show much genetic diversity. Most of the cacao trees worldwide come from a handful of clones selected in the 1940s. Because the trees are so closely related, they have similar genetic weaknesses. If a disease reaches a group of cacao trees that doesn’t carry any genetic resistance to that disease, it can destroy the entire crop. 

“Having so little genetic diversity leaves the cacao tree vulnerable,” said Grimwood. “However, it also means that genes can be exchanged between trees, which gives researchers and farmers an opportunity.”

Using this new reference genome, researchers will be able to guide crossbreeding and hybridization efforts more quickly. That means traits such as drought tolerance can be bred into a population faster and disease resistances can be introduced more efficiently.

The “chocolate tree” remains under threat, but now scientists and farmers alike have a more complete tool kit to produce more robust cacao crops.