Seeding the Future

by Peter Kent

A bumper crop of genetic data will help boost yields and equip plants to cope with pests, diseases, and weather extremes.

Photo courtesy of CEFS, NC State University.

Murphy-Brown has a food problem. Raising about 17 million market hogs a year takes a lot of feed.

The North Carolina-based company, a subsidiary of Smithfield Foods Inc., is the largest hog producer in the world. Its hogs could eat all the corn grown on the Eastern Seaboard in a month and half. Company officials met with geneticist and plant breeder Stephen Kresovich to see how Clemson could help. Sorghum, in a word, is what Kresovich envisions—South Carolina farmers growing acres and acres of grain sorghum. Drought- and heat-tolerant, the hardy grass produces panicles—seed heads of grain—and can be genetically manipulated to optimize its yield for South Carolina’s growing conditions. Kresovich is one of many voices hailing this era as the “biological century.”

Decoding and reading life’s ultimate instruction book—DNA—genomics and bioinformatics have the potential to revolutionize ways we manage agriculture, practice medicine, cope with climate change, and develop innovative technologies based on natural design.

Last year, Kresovich evaluated two varieties of sorghum. One research plot had plants reaching fifteen feet tall. Across the way, sorghum grew three feet high.

“Manipulating four genes, we could change the genetic instructions for how tall the plants grow,” Kresovich says. “Tall plants put out a lot of leaves and stalks, which can be used as biofuel or silage—stover. The shorter variety puts more energy into growing panicles to produce grain that can be processed into palletized livestock feed. Sorghum is very versatile. It uses less fertilizer and other chemicals, and requires less water.”

A plant that can take the heat

Thought to have been first cultivated about 2000 BCE, sorghum is adapted to hot, dry conditions. In drought, the plant goes dormant and resumes growing when moisture returns.

In heat, the leaves wilt rolling up, making less surface area for evaporation. The waxy leaves and stalks also protect the plant from drying out.

Bred from its wild ancestors in Africa, sorghum (sorghum bicolor) made its way to America in the 1800s. Midwestern farmers who could not grow corn raised grain sorghum—called “milo”—as cattle fodder, while southern farmers found sweet sorghum, juicier and higher in sugar content, a homegrown substitute for white sugar. Many cultures worldwide use sorghum as a food crop, fuel, and building material.

Corn is a pig compared to sorghum, gobbling up costly nitrogen and pesticides, growing best under irrigation. Dryland corn is a gamble for growers, but corn prices make it worth the risk and the expense.

Corn is often a main ingredient in animal feeds. Cattle eat it, and so do pigs, poultry, and dairy cows, along with pen-raised catfish and salmon. Corn also feeds us, industrially shape-shifting from kernels to high fructose corn syrup and other less recognizable ingredients. It’s used as feedstock for chemical compounds and biofuels.

A commodity that much in demand can get costly and hard to come by. Price fluctuations and market competition are part of the problem. Add in the cost of Midwest corn and shipping it, and the unpredictability of crop yields because of the weather, and it’s easy to see why Murphy-Brown is interested. Sorghum could be regionally grown as a grain crop, a cost-effective alternative to corn.

What would Kresovich and Clemson have to do to make sorghum a menu item at the hog trough?

The to-do list involves genetics, plant breeding, ag economics, and precision-farming methods to grow sorghum—all areas that Clemson does well and is expanding.

In July 2013 Kresovich became director of Clemson’s Advanced Plant Technology initiative. He left the University of South Carolina, where he was vice president for research and graduate education.

“I missed the land-grant connection, doing research where you can follow its path from lab bench to research plot to farm field,” Kresovich says. Before USC, he had worked at another land-grant institution, as director of Cornell University’s Institute for Biotechnology and Life Science Technologies, in the Institute for Genomic Diversity. Kresovich got soil under his nails working on a master’s in agronomy at Texas A&M and a doctorate in crop science at Ohio State University.

The Advanced Plant Technology initiative—APT for short—is based at the Pee Dee Research and Education Center in Florence, South Carolina. The relationship Kresovich and Murphy Brown are creating exemplifies the mission of the initiative: Use basic science to leverage economic growth.

Kresovich thumb-taps his fingers as he lists what the program looks to accomplish—identify genes to improve foods and feeds, evaluate alternative crops to grow, find ways to use everything off the field, preserve wild plant varieties, and develop ways to grow crops to cope with climate changes—particularly heat, drought, salinity, and plant disease and pests on the move to more hospitable regions.

The mission dovetails with the state’s ambitious goal of increasing the South Carolina agribusiness economic impact from $34 billion annually to $50 billion, boosting the number of ag-related jobs from 200,000 to 290,000. The due date is 2020.

State legislators see APT as an investment in meeting the goal. During the past two years, they have approved $8 million to hire more researchers—plant breeders and scientists—and upgrade the Pee Dee Research and Education Center (REC). The $3 million used to renovate the building—which was built in the 1980s—will improve lab space and add equipment, but the biggest change will be amping up computer power via a digital pipeline to campus to handle the vast amounts of information in plant-genetics databases.

Mapping the pathways with math

“Genetics today involves more mathematics than ever before,” Kresovich says. “It’s impossible to identify and follow the interactions of genes, modules, networks, proteins, amino acids, the bonds, and the pathways without using probabilities and algorithms.”

Revealing and putting the pieces together has created the -ics revolution—bioinformatics, genomics, proteomics, metablomics—a growing number of disciplines, involving computer science and mathematics, that explore and map how life works at the cellular and molecular levels.

In April 2003—just eleven years ago—the Human Genome Project was completed. A genome is an organism’s complete DNA, including all of its genes. A complete copy of the genome containing all the information needed to build and maintain that organism is kept in every cell with a nucleus. It took hundreds of scientists worldwide thirteen years at cost of roughly $3 billion to build the human genome with its three billion chemical base pairs and 22,000 or so genes.

But the cost and time required for producing a genome have been falling. “Now we are closing in on a ‘thousand-dollar genome sequence’ done by a technician in less than a day, using machines that cost less than one hundred thousand dollars,” Kresovich says.

Molecular mother lode

The steady decline in costs, time, and staff has spurred scientists to go DNA exploring. Hundreds of thousands of DNA sequences are stored in databases available to anyone with an Internet connection. The U.S. National Center for Biotechnology Information, and its sister groups in Europe and Japan, stockpile gene sequences in a database called GenBank. There are other databases as well.

Sorghum has about 30,000 genes. Why does a plant have 18,000 more genes than a human?

Plants are sessile—literally rooted in their environment, while humans and most other animals can move if conditions are bad. Plants need genes and gene networks that can send chemical signals to cope with conditions, turning on or off activities to survive. Every eventuality has to be preprogrammed—drought, insects, disease, temperature, salinity, nutrition, and soil quality.

The proliferation of genes offers plant geneticists a mother lode of molecular opportunities. Genes can be identified and manipulated to control activities. “This is the value of bioinformatics,” Kresovich says. “Computers and DNA-sequencing equipment have advanced so much in the past few years that we can now mine DNA to find the gold nuggets.”

Much of Kresovich’s research focuses on food and fuel characteristics in sorghum and sugar cane, both relatives of corn. These are C-4 plants, overachievers in photosynthesis, but to understand what a C-4 plant does we have to go back to the basics.

Carbon is the structural building block of the cells and organic chemicals. Carbon atoms are in the air and can be claimed one way—via photosynthesis. During photosynthesis, most plants extract three carbon atoms, so the plants are called C-3. C-4 plants have a distinct advantage, obtaining four carbon atoms in each photosynthesis exchange. That extra carbon atom boosts their efficiency. Their stomata open fewer times, which conserves another life-sustaining molecule: water. Each time a stoma opens, water vapor escapes. C-4 plants do better in dry, hot places.

Figuring out how to create plants that use C-4 photosynthesis would not only produce plants capable of more mass but also able to withstand heat and drought. “There’s long way to go from identifying the right genes to having something farmers could grow,” Kresovich says. “All the advances offer tremendous new avenues to explore, but the roads still lead to the research plots. That’s the proving ground for our ideas.”

It may be the proving ground, but it is also a bottleneck. Plant breeders must grow generation after generation of plants to get a desired trait to appear consistently—“pure lines” of seeds that growers can rely on.

It takes six generations to establish a pure line. Plant breeders can accelerate the process—fast crop breeding—getting a second season each year by sending the seeds to farms in warmer places. Kresovich sends seed to winter in Mexico.

“It still takes six to ten years to have something to sell,” Kresovich says, adding that the timeline is getting shorter because of better tools and techniques.

Research and breeding with sorghum are also being done with peanut, cotton, and soybean crops. Hired last year to work at the Pee Dee REC, Ben Fallen works with soybean and Shyam Tallury with peanuts, important crops in the state.

In 2012, South Carolina growers planted 380,000 acres in soybean, 340,000 acres of cotton, and 110,000 acres in peanuts, according to the USDA National Agricultural Statistics Service.

The work of Fallen and Tallury will help in the search for plant oils to replace hydrogenated oils with unhealthy trans fats, which are being phased out of foods.

The timing is right for the APT program. Last fall, China for the first time purchased U.S. grain sorghum. The reasons were economic: Chinese corn was expensive. Tariff quotas prevented more corn imports. U.S. sorghum was a good buy.

The U.S. Grains Council estimates that U.S. sorghum exports will double in one year, from 75 million bushels in 2012-2013 to 150 million bushels in 2013-2014. Much of this increase will result from higher demand from China, the council says.

China doesn’t have to be half a world a way to buy sorghum. Smithfield Foods Inc., parent company of hog producer Murphy-Brown Smithfield, made headlines last fall when it was purchased for $7 billion by Chinese food producer Shuanghui International.

Sorghum may well offer southern farmers far more than syrup for biscuits.

Stephen Kresovich is the Robert and Lois Coker Trustees Chair of Genetics and SmartState Chair of Genomics, Department of Genetics and Biochemistry, College of Agriculture, Forestry, and Life Sciences. Peter Kent is a news editor and writer in Clemson’s Public Affairs Activities.