HudsonAlpha Leader in Plant Genomics and Sustainable Agriculture Research

Modern agriculture produces the food, fiber and fuel that sustain our lives. While consumers expect plant production to keep pace with an increasing human population, farmers and foresters face many serious challenges from an increasing scarcity of resources. 

Using new tools and HudsonAlpha’s extensive experience in plant genomics, HudsonAlpha researchers 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, forestry and other plant applications. To date, approximately half of all of the plant sequenced in the public domain have been completed by HudsonAlpha Institute for Biotechnology scientists. 

A Global Leader

The HudsonAlpha Institute for Biotechnology’s Genome Sequencing Center (HAGSC) is a global leader in generating de novo (original) whole genome sequencing, assembly and analysis. The HAGSC specializes in applying genomic techniques to understand how plants function in response to environmental factors like water, temperature, fertilizer and harmful pests. 

The center, led by faculty researchers Jeremy Schmutz and Jane Grimwood, PhD, has been part of the development of half of all of the plant reference genomes in the public domain. Reference genomes are important as a baseline to study and understand organisms. By comparing the similarities and differences, researchers can discover the functions of particular genes and identify which ones are important. The HAGSC has generated reference genomes for crops like the American chestnut, cotton, sorghum, pecan, peanut, eucalyptus and more. Visit Shareable Science to learn more about how the reference genomes for plants are created.

“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.”

Finding Answers in the Genome

One of the key challenges facing modern agricultural is crop sustainability. Resources are limited and in time they could be exhausted. By studying the genome and function of the plants, researchers can provide key information for improvement of perennial crops and increase farmers choices for crop diversity, decreasing the dependence on a limited number of crop plants for human use. 

Through sustainable crop research, farmers may be able to reduce inputs for water and fertilizer allowing for drought tolerance and decrease runoff. Plant genomics offers solutions to some of today’s key challenges in understanding plant biological processes and how they use and recycle resources.

In addition, the genome holds answers for increased understanding and implementation of pest resistance. By studying and understanding plant disease immunity and the plant response to attack from pests, it is easier to select plant varieties that are resistant to these pests.

A Sweet Reward

People around the world consumed nearly 7.7 million tons of chocolate last year. Unfortunately, the cacao crop that supports chocolate production is facing serious environmental threats. To combat this danger, HudsonAlpha scientists from the Genome Service Center, with funding from Mars Wrigley, have recently completed and released a new reference genome for Theobroma cacao, the tree that produces cacao beans. The improved reference genome will help researchers and farmers develop healthier, more productive cacao crops. To read the full story, click here.

Crop Potential in Bioenergy 

Kankshita Swaminathan, PhD

HudsonAlpha scientists, in collaboration with plant geneticists from the University of Illinois, are studying miscanthus, a type of grass sometimes cultivated as silvergrass in ornamental gardens. The research is focused on the agricultural applications of miscanthus as a source of biofuel. 

Researchers are also field testing already developed hybrids that show promise for both cold tolerance and high yields. HudsonAlpha’s work is focused on targeted traits such as plant height or stem thickness to identify better biofuel options.

“We’re excited about the possibilities of this project to identify plants that are better adapted to their environment and have higher yields than the current crops in the biofuel supply chain,” said Kankshita Swaminathan, PhD, a faculty investigator at HudsonAlpha. 

Supporting Plant Science and Sustainable Agriculture

As the global population grows, overall demand of resources will also increase. HudsonAlpha is a leader in plant genomics and working to find solutions to these challenging problems. Recently, the Institute hosted the CROPS conference which convenes leading researchers applying genomic based techniques to crop improvement and plant molecular breeding experts, along with traditional breeders who are interested in applying these techniques within their crops of interest to find solutions to feed and fuel the world. 

With more resources and funding, HudsonAlpha’s plant science programs can continue to make investments in our future. To make a gift and support our work in sustainable agriculture, visit