Crop Genetics & Breeding

The Nebraska Food for Health Center (NFHC) works to bring together agriculture and health science through microbiome research. The crops that all of us eat every day have the capacity to synthesize a diverse array of molecules and metabolites that influence the human gut microbiome when we consume food made from these crops. While large scale commercial breeding programs often evaluate new crop varieties primarily on yield and stress tolerance, the NFHC genetics program is enabling plant breeders at the University of Nebraska to understand how different crop varieties have different impacts on the human gut microbiome and human health. Our long-term goal is to develop new, higher value crop varieties that promote and sustain healthy human gut microbiomes.

Crop flow chart

Why does this matter?

Microbiomes are composed of microbes including bacteria, fungi, and viruses. Most environments have microbiomes, from the surface of plant roots to your keyboard or skin. The largest, most complex and most important microbiome in your own body is found in your large intestine (your gut). Your gut microbiome essentially functions as another organ by 1) teaching the immune system what organisms are beneficial or harmful, and 2) digesting parts of the food you eat and producing new metabolites that are beneficial for other parts of your body. 

The types of bacteria, fungi, and viruses found in a gut microbiome can vary a lot from one person to another. Some species are helpful, others are harmful, and in other cases, groups of bacteria can work together in positive or negative ways depending on the overall makeup of the microbial community in a particular person’s gut. Our bodies function best with diverse and healthy microbiomes abundant in beneficial species. Your gut microbiome feeds on fiber and other things in the food you eat that your body can’t digest on its own, including metabolites found in crops such as corn, wheat, beans, etc.  Different metabolites from different foods promote the growth of different sets of bacteria. NFHC’s technology and infrastructure allow our plant breeders and geneticists to measure how new crop varieties will change the microbiomes of different people and ultimately develop crop lines that promote the growth of beneficial gut microbes. The impact of this new trajectory for agriculture will be new approaches for preventing and treating diseases, new products (crop lines, food products, probiotics, prebiotics, and synbiotics), and ultimately a new sector of the economy. Furthermore, this idea and methodology can be applied globally, both to diseases and crops.  It can also be adapted to treat animals and livestock.  The microbiome is specific to an individual which puts us on the path to personalized nutrition. The science holds the potential for a future where we could stop or prevent a disease in genetically susceptible individuals by proactively incorporating a newly discovered crop line, food product, or synbiotic.


What are we working on?

Corn (also called Maize)

In the United States, we call this crop corn. In much of the rest of the world, they call it maize. Whatever you call it, corn is one of the three crops, along with wheat and rice, that produce half of all the calories human beings eat around the globe. Corn also makes a big impact on the Nebraska economy, with our annual crop worth more than $10 billion dollars (2021 estimate). The vast majority of that corn is sold as “Number 2 Yellow Corn” a standardized product that ends up in everything from cornflakes to bourbon, gets fed to cattle, and processed into corn syrup. But corn is actually an extraordinarily diverse crop. The three major kinds of corn that humans eat are dent corn, popcorn, and sweet corn. The Nebraska Food for Health Center has researchers working on all three.


With support from a major food processing company, Prof. David Holding developed new varieties of popcorn that have different and more easily digestible proteins. In a recent Nebraska Food for Health Center study, Dr. Holding’s new popcorn varieties were shown to promote the growth of butyrate-producing bacteria. Increases in butyrate production by the human gut microbiome are, in turn, associated with improvements in human health outcomes.

Did you know? Depending on the year, Nebraska ranks first or second for the state that grows the most popcorn.

Read the full article from Frontiers in Microbiology 

FAQ on Quality Protein Popcorn 

Press Releases


Beans were domesticated in the Americas more than 10,000 years ago. In many countries they are a critical staple food, providing a healthy source of protein in low meat diets. Beans also contain large amounts of complex fibers that can be an important source of food for human gut microbiomes.

Did you know? The different beans you see at the grocery store (“Navy”, “Pinto”, “Black”, ”Kidney”, and so on) are all the same species, and breeders can make crosses between them. 

The University of Nebraska’s bean breeding program is run by Prof. Carlos Urrea who works at the University of Nebraska’s Research Center in Scottsbluff, more than six hours from NFHC headquarters in Lincoln. There he develops new varieties of beans for Nebraska farmers. Nebraska is the #1 producer of Great Northern beans in the United States and the #2 producer of Pinto Beans.

One of the populations of beans that Prof. Urrea works with is called the Middle American Diversity Panel (MADP), a set of 308 types of beans developed by bean breeders working at Universities and private companies across the United States and Canada. NFHC scientists have been able to use the AIMs system to understand the unique impact of each different bean variety on the different bacteria that make up the human gut microbiome. Doing this can both help to identify the beans that do the most to promote health, and also to identify genes in the bean genome that control the differences in how the beans feed gut microbiomes.




A Recombinant Inbred Line (RIL) panel of 429 lines was grown at the NIC greenhouse/phenotyping facility and seed from each line was screened for effects on a single human microbiome.  Genetic analysis of the human gut microbiome phenotypes led to the discovery of 8 different regions in the sorghum genome where genetic variation in the RILs has major effects on the gut microbiome.

Sorghum is a close relative of corn that was originally domesticated in Africa. It grows with less water and less fertilizer and plays a key role in African and Indian recipes. In the USA, sorghum is found growing from Nebraska to Texas where farmers prize its ability to grow on land with less water and nutrients than are required to grow corn. The Nebraska Food for Health Center is studying hundreds of types of sorghum from around the globe and their individual effects on the human gut microbiome, using seed grown right here in Lincoln, Nebraska.

At NFHC, we have already found that changes in the regulation of only a small handful of genes in sorghum are sufficient to dramatically alter how the human gut microbiome responds to sorghum. Some of those genes are the same ones that were targeted by selection in Africa, part of a fascinating story of how selection has shaped not only the genetics of sorghum, but the human genome itself.

Read the full article in Nature Communications 

Press Releases[%e2%80%a6]ut-microbiome/article_6ed689a8-4347-11ed-9331-f7969dba611d.html

Did you know? Forty years ago, Nebraska Food Scientists developed “Captain Milo” breakfast cereal in an effort to get Americans to eat more of this healthy grain. 


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