Major USDA grant supports pioneering agricultural genome to phenome collaboration led by Iowa State University

Sep 30, 2022

AMES, Iowa (AgPR)— The U.S. Department of Agriculture’s National Institute of Food and Agriculture announced today it is awarding more than $1.8 million to support the work of the Agricultural Genome to Phenome Initiative (AG2PI) being led by Iowa State University in collaboration with the University of Nebraska-Lincoln and University of Idaho.

The goal of AG2PI is to help advance multidisciplinary crop and livestock research by addressing genome to phenome challenges, developing solutions for research infrastructure needs and sharing solutions across kingdoms. It aims to foster collaborations of crop and livestock scientists with colleagues in diverse areas, including data science, statistics, engineering and social sciences, to improve the long-term efficiency and resilience of U.S. agriculture.

Researchers working from genomics to phenomics explore how genomes (organisms’ complete set of DNA) influence the expression of observable, phenotypic traits.

The primary focus of the new grant will be to provide competitive funding for projects that will implement a vision for research the AG2PI has been developing with community input over the past two years.

“The pioneering work supported by this initiative is beginning to provide scientists and breeders with the tools needed to adapt agricultural systems to improve their profitability and make them more sustainable and resilient to climate change,” said Distinguished Professor Patrick Schnable, project director for the transdisciplinary, multi-institutional grant, the Iowa Corn Promotion Board Endowed Chair in Genetics and director of the Plant Sciences Institute at Iowa State.

The new grant is the third and largest award made through USDA NIFA’s AG2PI national initiative launched two years ago as part of the 2018 Farm Bill. The first, three-year USDA award was geared toward building a cross-kingdom community of researchers. The second award focused on expanding a small seed grant program to recruit involvement and innovation of researchers across the country. So far, the AG2PI seed grants have supported 27 research projects at levels ranging from $15,000–$100,000. This third award would further expand the grant program with larger, “coconut”-level (big seed) grants of up to $250,000, aimed at generating greater interest and impact.

“Achieving sustainable genetic improvement in agricultural species is a `wicked problem,’ meaning that a solution requires diverse and creative teams of scholars, producers and stakeholders,” said Jennifer Clarke, lead researcher directing the project seed grants and director of the Quantitative Life Science Initiative at the University of Nebraska-Lincoln. “This award will make it feasible for such teams to invest more deeply to tackle related problems for the benefit of both agriculture and society.”

Nurturing researchers getting established in their careers has been one of the program’s goals: Of 142 seed grant team members and collaborators, about one-third consider themselves to be in the early stages of their professional career.

Since its inception, the national AG2PI team has sponsored or co-sponsored an ambitious set of virtual field days, workshops and mini-conferences. Products from the initiative also include a set of white papers about related research, opportunities, gaps and challenges. In early September 2022, AG2PI co-hosted a hybrid conference with USDA-NIFA in Ames to bring together researchers and other experts from diverse institutions to visualize the future of agricultural genomes to phenomes work. Recordings from these events can be accessed for free on the initiative’s website, https://www.ag2pi.org.

Although all USDA funds remain in the US, researchers from more than 155 countries have participated in the project’s field days and workshops. “We are connecting with researchers around the world,” Schnable said. “While the AG2PI program is focused on increasing profitability, sustainability and resilience here in the United States, agriculture is a global endeavor, and science benefits when collaboration comes from everywhere.”

Other leaders on the new grant include: Professor Christopher K. Tuggle and Distinguished Professor Jack C.M. Dekkers, animal science, Iowa State University; and Associate Professor Brenda M. Murdoch, animal, veterinary and food sciences, the University of Idaho. A stakeholders committee that involves nearly 20 industry organizations is chaired by Iowa State alumnus David Ertl (’82 MS, ’84 PhD plant breeding), technology commercialization manager for the Iowa Corn Growers Association.

“This genome to phenome research will have far-reaching effects,” Ertl said. “It will allow breeders to create improved varieties faster, allow farmers to produce more resilient crops and livestock, and give consumers more choices for sustainably produced food.”

This work is supported by the Agricultural Genome to Phenome Initiative, grant number 2022-70412-38454, project accession number 1029371, from the USDA National Institute of Food and Agriculture.

Source : Ag News Center

Video: Turning Plant Defense Into a Management Strategy

Turning Plant Defense Into a Management Strategy

Understanding how a plant responds to stress is one thing.

Using that knowledge to make better management decisions is another.

Systemic acquired resistance, or SAR, is the plant's more direct defense response. When stress or infection occurs, the plant begins signaling throughout its system and preparing defensive compounds.

But if we know that response exists, can we help prepare the plant before the stress arrives?

The answer starts with understanding what triggers the response and what the plant needs to carry it out.

The Trigger and the Fuel

Salicylic acid plays an important role in triggering the SAR pathway.

Think of it as turning the truck on.

The engine may be running, but it still needs fuel to do the work.

In this case, manganese plays an important role in supporting the enzyme systems involved in the plant's defensive response.

This makes manganese status an important part of the conversation. Whether a producer is using tissue testing, sap analysis, or simply scouting for visible deficiency symptoms, the goal is to make sure the plant has adequate manganese available.

Manganese is required in relatively small amounts, but that does not make its role small.

If the plant receives a signal to defend itself but lacks the nutrition needed to support that response, it may struggle to carry out the process efficiently.

The trigger matters.

The fuel matters too.

Prepare Before the Stress Arrives

The best time to think about stress management is before the plant is overwhelmed.

Once a crop is already struggling, management can quickly turn into a game of catch-up.

This is similar to nitrogen management. Once a plant becomes severely deficient, correcting the problem does not necessarily erase the time and yield potential already lost.

Plant defense can work the same way.

Low-rate, targeted approaches designed to support the SAR pathway may fit best ahead of an expected stress event rather than after significant damage has already occurred.

That requires producers to think about predictable stress.

We may not know exactly what the weather will do tomorrow, but we generally know summer heat is coming. We know certain field conditions increase disease pressure. We know a herbicide application can temporarily stress a crop as the plant processes the chemistry.

Even a properly timed and labeled herbicide application can create a temporary response in the plant.

That does not mean the herbicide is bad.

Weeds can create significantly more yield loss than the temporary stress caused by controlling them.

The question is not whether we should eliminate every stressor.

The question is whether we can better prepare the plant to manage necessary and predictable stress.

Not All Stress Is Bad

Stress is a normal part of plant growth.

A perfectly stress-free environment does not exist in the field.

In fact, some stress is necessary for normal plant development. A plant responds to wind, temperature, moisture, sunlight, and countless other environmental signals throughout the season.

The environment is stress.

The plant's job is to manage it.

Problems begin when the stress load becomes greater than the plant's ability to respond.

Extreme heat, drought, high salt concentrations, disease pressure, and even certain management practices can add to that load.

This is where understanding SAR becomes useful.

Instead of waiting until the plant is visibly struggling, producers can begin identifying periods when stress is likely and make management decisions around those windows.

ISR Starts With the Soil

While SAR is a more direct defense response, induced systemic resistance, or ISR, brings the conversation back to soil health.

The longevity of a farm is closely connected to the health of its soil.

Carbon plays a major role because it supports biological life within the soil. Bacteria, fungi, and other organisms interact with plant roots and influence how the plant grows, accesses nutrients, and prepares for stress.

This is why soil health cannot be reduced to one product or one application.

It is a system.

Keeping living plants in the field longer can support biological activity. Cover crops may fit some operations. Better water management can improve soil conditions.