Diverse ways of applying genomics to solve challenges in modern agriculture

The HudsonAlpha Center for Plant Science and Sustainable Agriculture (Plant Center) applies genomics to plant research to create more sustainable farming practices, address the challenges of climate change, create plants that are resistant to pests and fungi, and much more. The Plant Center was formed to have our trusted experts and thought leaders in the field of plant genomics bring the most advanced techniques of genomic research to plants and agriculture. Our internationally recognized researchers, analysts, and informaticians can provide you with the support you need to plan and execute your plant and agricultural projects.

The Plant Center brings together the unique expertise of its five core members to create diverse ways to apply genomics to solve challenges in modern plant science and agriculture. We can identify problems in the field, discover genomic solutions by combining evolutionary and computational genomics, then apply functional genomics to transform and improve the plant or crop.

Genomic solutions to some of the world’s most pressing problems

It is predicted that by the year 2050 the world’s population will be 9.7 billion people, nearly 2 billion more than currently inhabit our planet. The world’s land and water resources are finite with population growth placing pressure on these valuable resources. Increasing heat and drought also threaten food security due to their negative impact on crop productivity.

In order to meet the increased need for food without depleting land and water resources, we need crops to produce more output on existing land with fewer inputs like water and fertilizers. So how do we increase the yield potential of crops without taking up more land mass? The answer might lie within the plants’ genomes.

Our Expertise

The five core members of the Plant Center each have unique expertise that combine together to create diverse ways of using genomics to solve challenges in modern plant science and agriculture.

Genome sequencing and analysis

Advanced technologies have given scientists both access to complex plant genomes and the ability to examine genetic differences across thousands of plant varieties. In addition, high-performance computing allows scientists to analyze and integrate these enormous amounts of data. With these new tools and extensive experience in plant genomics, members of the Plant Center are in a unique position to accelerate discoveries in crops and develop new scientific methods that will change the way we grow and use plants in agriculture.

Plant and crop improvement

With advances in technology, computational biology, and plant science, members of the Plant Center are able to identify key genes related to important crop traits such as increased yields, drought tolerance, or pest resistance. Together with expert partners such as land grant universities and farmers, the Plant Center can leverage these discoveries for practical use for plant and crop improvement.

Plant transformation and gene editing

In recent years, rapid advances have been made in the field of precision genome editing and plant biotechnology. These tools allow plant researchers to change a specific base in a gene or replace a gene with a better functioning one. Using traditional breeding to introduce important genetic variation takes many years. Members of the Plant Center can quickly create new, better adapted crop varieties by using these exciting new plant engineering tools.

Supporting biodiversity

Using the power of genomics and cutting-edge technology to harness new ideas, the Plant Center is identifying unique threats and finding innovative solutions to preserve plants and agriculture for tomorrow. For example, members of the Plant Center are using genome sequencing to help identify chestnut blight pathogen resistance genes in the American chestnut tree which was wiped out by blight in the early 1900s. The resistance gene could help breeders create more resilient American chestnut trees.


Biofuels, produced from renewable materials like plant matter, are promising alternatives to fossil fuel and have the potential to benefit the environment and decrease the cost of energy. By diversifying our fuel options, this research can help reduce the use of toxic chemicals as well as improve energy security. Members of the Plant Center study bioenergy crops like the perennial grasses Miscanthus and switchgrass. The group is working to understand the biology behind these crops in hopes to identify genes that will help increase their yields and improve their abilities to adapt to extreme environments such as poor soils and drought.

Educational Outreach

The Plant Center team, along with HudsonAlpha’s Educational Outreach team, aims to mentor and cross train young researchers at the high-school and collegiate level. The team hopes to help significantly increase the retention of young scientists in agriscience and broaden participation of minorities that are underrepresented in STEM fields, especially in agriscience.

Our Projects

By leveraging the expertise of our core members and their wide-reaching collaborative networks, we are able to participate in many impactful plant and agricultural projects.

Crops for a diverse Alabama agricultural economy

All five Plant Center core members, along with collaborators from Auburn University’s departments of Crop, Soil and Environmental Sciences and Entomology and Plant Pathology, and Alabama A&M’s Winfred Thomas Agricultural Research Station, are working together to develop better agriculture seed varieties to produce healthier and more productive crops. The goal of the project is to use the power of genomics and plant breeding to introduce new, improved agricultural crops in Alabama.

Creating more nitrogen efficient sorghum

Nitrogen plays an important role in the health and growth of plants. Without nitrogen, plants are unable to produce the chlorophyll that makes it possible for them to photosynthesize, the process where plants use energy from the sun to break down water and carbon dioxide to form sugars. Plant Center members Kankshita Swaminathan, PhD, and Jeremy Schmutz, along with collaborators from the University of Nebraska-Lincoln and Alabama A&M University were awarded an NSF grant for their research efforts into understanding nitrogen uptake mechanisms in sorghum, while also increasing workforce diversity in agricultural research.

Creating low aflatoxin peanuts

Plant Center member Josh Clevenger, PhD, and a team at Mars, Incorporated aim to tackle two related problems in peanuts, aflatoxins and drought tolerance. Aflatoxins are a group of toxins that can contaminate agricultural crops like peanuts, tree nuts, maize, and grains. In humans, the toxins can lead to liver cancer and severe damage to the liver. Clevenger and his team are using genomics and computational tools to identify genetic markers that confer drought tolerance during late growing season stress.

Investigating duckweed’s promise as a biomass crop

Duckweed has several characteristics, such as its fast growth rate and short doubling time, that make it a promising candidate as a biomass crop, for both fuel and feed production. Plant Center member Alex Harkess, PhD, along with many other collaborators, are constructing a species tree that describes relationships between all 37 duckweed species. This will help the team understand how traits like rapid reproduction have evolved and changed over time, as well as the genes that might influence those traits.

Towards more sustainable switchgrass

The Department of Energy (DOE) designated switchgrass a promising candidate for biofuel, renewable fuel that is produced from the biomass of plants. Plant Center members Jane Grimwood, PhD, Jeremy Schmutz, and Kankshita Swaminathan, PhD, are part of a multinational team of researchers that have been studying the genome of switchgrass for over a decade. Their goal is to create plants that can survive across a range of environments while still producing a large amount of biomass that can be turned into biofuel.

Our Team

The Center for Plant Science and Sustainable Agriculture is home to five core members and their labs that apply their genomics expertise to solve modern agricultural problems.

Jane Grimwood, PhD


Jeremy Schmutz


Kankshita Swamanthaian, PhD


Josh Clevenger, PhD


Alex Harkess, PhD


Genome Sequencing Center

HudsonAlpha Genome Sequencing Center (GSC) provides researchers with high-quality genome sequencing, assembly and analysis for plants, fungi, archaea and algae species with the infrastructure and expertise to exceed your project needs. The GSC also leverages ever-advancing sequencing technologies to generate high-quality, non-clinical human genome sequences and assemblies. The experts at the HudsonAlpha Genomic Sequencing Center can help with your large or small sequencing projects, whether they are de novo sequencing or resequencing projects.

Khufu Data

Khufu is a data analysis platform that uses bulk sequence analysis to accurately map traits to genes. Scientists and breeders can use Khufu to quickly and accurately identify selection markers and quantitative trait loci (QTL) to rapidly introduce beneficial traits such as disease, drought or pest resistance into cultivated agricultural crops.

Collaborate with us

HudsonAlpha aims to leverage the synergy between discovery, education, medicine, and economic development in genomic sciences to improve the human condition around the globe. The Center for Plant Science and Sustainable Agriculture is just one of the ways we are trying to reach our goal of improving life. To join forces with us at HudsonAlpha, contact us to see how we can collaborate together. To see a few of the other areas where we are collaborating with others, go to: hudsonalpha.org/agriculture/.