Sex on the farm: How gene editing can revolutionize feeding the world

(Editor’s note: Change can be difficult, especially when it comes to adopting new ways of farming and producing food. But there are big innovations underway in labs and universities that analysts describe as "revolutionary," enabling the creation of new plants and animals in months rather than decades. For the next few weeks, Agri-Pulse will explore “The Breeding Edge” – a seven-part series on how these new precision methods for plant and animal breeding are set to transform global food production and the potential impact for agribusinesses, farmers and consumers around the world.)

The process of producing food, protecting the environment, and improving animal health is advancing at a seemingly breakneck pace.

These advancements are driven in part by new scientific discoveries, genetic research, data science, enhanced computational power, and the availability of new systems for precision breeding like CRISPR—an acronym for Clustered Regularly Interspaced Short Palindromic Repeats.

The outcomes possible with different types of precision breeding today might have seemed impossible just a few decades ago and these new opportunities have strong implications for both producers and consumers. Consider just a few of the possibilities:

• A new cassava plant, engineered to be resistant to brown streak disease, could make the difference between small farmers in Africa having a crop to eat and having no crop at all.
• New breeds of livestock and poultry could be engineered to no longer be susceptible to widespread disease outbreaks, like pigs resistant to Porcine Reproductive and Respiratory Syndrome Virus (PRRSv), which can cost hundreds of millions of dollars annually.
• Cover crops that naturally improve soil health can be developed to grow in more diverse climates, improving environmental sustainability, water quality and animal nutrition.
• Dairy cows can be bred without horns, removing the need for cows to endure the polling (horn removal) process.
• Fruits and vegetables could be engineered to resist browning, extending their consumer appeal and reducing food waste.

Indeed, the science is moving so rapidly that some are wondering if producers, as well as consumers, and regulators will ultimately be able to understand and embrace the changes.

As history demonstrates, new advancements in breeding have almost always been controversial – even though safety or environmental risks have not been proven.

“It is critically important that everyone in agriculture becomes rapidly conversant in this technology, as it already has been a game changer,” notes Kevin Folta, who chairs the Horticultural Sciences Department at the University of Florida in Gainesville. “If these technologies are delayed because of misunderstanding, we will lose many opportunities to bring improved varieties to the field and better fruits and vegetables to consumers.”

The long, long road to gene editing

Change has always occurred in plant and animal breeding, but by a long shot, agriculture’s genetic advances haven’t always been so brisk. Quite the opposite.

Even though the pace toward modern plant and animal breeding quickened remarkably in the 20th century, since the birth of farming about 8,000 BC, in what’s now Iran and Iraq, and in Central America not much later, most improvements in strains of crop and animal species have gradually evolved over hundreds of years.

Farmers, gardeners and others learned a wide range of husbandry skills over the centuries, says E. Charles Brummer, plant breeder at the University of California, Davis, and president of the Crop Science Society of America. “Cloning of grapes goes back hundreds of years,” for example, and manure has been used to enrich soils since the earliest agriculture; crop rotations have long been used, too, to improve soil and crop vigor, he points out.

K. Kris Hirst, of Iowa City, Iowa, an archaeologist who writes and speaks on early world agriculture, agrees that early farming R&D involved much more than selective breeding, and was “also a matter of the humans learning what the plants or animals need and finding a way to give it to them . . .”

Various water delivery systems, for example, were built thousands of years ago on several continents, she noted, “consisting of things like canal systems in Mesopotamia, rock terraces in Peru and Mexico, underground watering systems, such as the qanats that tapped groundwater in the Turpan Oasis of central Asia.”

But Hirst tells Agri-Pulse that selective breeding has been with agriculture from the beginning.

“Basically, you would collect the seeds from the best crops this year and replant them in the garden for next – picking the seeds from favored aspects and replanting them again, and not planting those without those preferred traits. Some early domestication changes had to do with moving the plant out of its normal habitat. So, the survivor plants were the ones that were best at adapting.”

In her writings, Hirst describes the start of farms and agriculture in the Near East and what’s called the New Stone Age: “The earliest structures made of stone were built in the Zagros Mountains, where people collected seeds from wild cereals and captured wild sheep.”

That period “saw the gradual intensification of the collecting of wild cereals, and by 8000 B.C., fully domesticated versions of einkorn (wild) wheat, barley and chickpeas. And sheep, goats, cattle, and pigs were in use within the hilly flanks of the Zagros Mountains, and spread outward from there over the next thousand years.”

While today’s farmers plant about 25,000 different strains of wheat worldwide, Hirst says, the earliest evidence of domesticated einkorn and emmer wheats has been found at the Syrian site of Abu Hureyra,” dated to 10,000-11,000 B.C. Evidence of the earliest rye is linked to “hunters and gatherers living in the Euphrates Valley of northern Syria” about 9,000-10,000 B.C.

Maize (corn) was domesticated as early as 7000 B.C. in Central America from a plant called teosinte, and cobs of domesticated maize identified in Guerrero, Mexico, were dated to before 4200 B.C. One theory has corn originating in Mexico’s highlands as a hybrid of diploid perennial teosinte and early-stage domesticated maize. In Peru alone, she says, specimens of 35 strains of maize from before Europeans’ arrival have been identified, including popcorns, flint varieties, and others for uses such as making chicha beer and textile dyes.

Corn was used in what is now the U.S. Southwest by about 1200 B.C. and, by the first century, the crop joined eastern North American natives’ other established foods such as pumpkin and sunflowers.

As with their crops, farmers around the world also selectively bred animals, adapting them to their needs for food and clothing and breeding them to flourish in new climates when, for example, they migrated to the Americas and Australia and brought cattle to those continents.

Hirst points out that farming migration in early agriculture was extremely slow. “People traveled much more slowly in the past – a person can travel about 12 miles in a day, and less than that if driving animals. So selective breeding was a very slow process” as groups “would move into drier climates or less ideal environments or respond to climate changes as they themselves ranged hither and yon. You would bring your goats with you and the ones that lived the longest or continued producing milk the longest would be, by definition, the ones that survived.”Initially, today’s hot- and cold-climate cattle breeds all began as aurochs (now extinct) in Europe and the Near East. Beginning about 10,000 years ago, they were domesticated and bred for mankind’s purposes across Europe and parts of southern Asia and northern Africa.

She said evidence for selective farm animal breeding in pre-history was apparently not, for example, focused on the biggest, toughest bulls or rams to protect the herd. Actually, she said, scholars believe most sought-after characteristics were those in animals that could adapt to living close to humans. “Domestication,” Hirst said, “is always associated with getting smaller, calmer, sweeter-tempered animals, who didn’t mind being milked and were disinclined to attack the humans or wander off.”

Cross breeding catches on in the 20^th century

Although Gregor Johann Mendel, a scientist and Augustinian abbot in Brno, Moravia (now in the Czech Republic), became hailed in the 20th century as the father of modern genetics, the long-delayed acceptance of his discoveries reflects the very slow pace of plant and animal breeding advances through most of human history.

He tested some 28,000 pea and other plants to learn about hybridization and demonstrate the dominant and recessive traits in evidence as a result of crossbreeding. He also experimented with breeding mice and bees. He was not alone. Other naturalists and farmers experimented with cross breeding plants in the late 19th Century as well, but the concept did not catch on.

So Mendel’s meetings with the Natural History Society in Brno in 1865 and his now-famous paper, Experiments on Plant Hybridization in 1866 were soon after ignored until the start of the next century, many years after his death.

However, in the early 20^th Century, other scientists, trying to better understand inherited traits, reproduced Mendel’s plant experiments and bought into his theories. In 1909, Nils Heribert-Nilsson, a Swedish botanist, demonstrated how results between crosses, or hybrids, yielded plants that outperformed either parent. That result was labeled “hybrid vigor” and became the spark for broad use of hybrid crop production.

Also, in 1917, American agronomist Donald Forsha Jones showed the benefits of employing the double-cross pollination method of hybrid seed production and helped usher in the first American hybrid corn seed in the 1920s.

Meanwhile, English naturalist Charles Darwin, who researched and wrote concurrently with Mendel, posted his Origin of Species in 1859 and Natural Selection in 1875, broadly influencing scientific thought on genetics as well. The findings of Mendel and Darwin were at the center of genetics and evolutionary biology by the mid-20th century.

Through the decades since, the magic of hybridization, back-breeding to isolate and infuse a desired trait, and other cross breeding has enhanced farm production along with crop and livestock health. But of course, there were other factors.

Old fashioned selective breeding, along with fertilization, pest control, soil health enhancement, and other techniques have enhanced crop production, just as livestock breeding successes have been augmented by improved animal nutrition, disease prevention and husbandry skills.

Nonetheless, breeding has led to success across virtually all of the farm sector: veggies with enhanced flavors; apples, citrus and other fruit that are sweeter and with longer shelf lives; even popcorn that pops better.

Corn breeders plunged into hybrids in the 1930s, producing double-crosses to maximize advantageous traits, and seed companies began aggressive selling of their hybrid seed to Midwest farmers. The U.S. average corn yield soared from 20 bushels an acre in 1930 to 90-100 bushels in the 1970s and to more than 170 bushels in recent years. And even higher averages seem likely. The top yield in the 2017 National Corn Growers Association’s annual yield contest topped 542 bushels per acre in the no-till/strip-till irrigated category.

Meanwhile, since 1950, the U.S. average yield for wheat has climbed from 16 bushels per acre to about 50 in recent years; soybeans, from 21 bushels to 50.

The accelerated growth rates of meat animals speak especially to selective breeding and rearing success. In the early days of the commercial poultry industry, each chicken required approximately 16 pounds of feed to achieve a four-pound weight. Today, that amount of feed has been reduced by more than half – less than seven pounds of feed – to grow the same size bird, all without the use of growth hormones or steroids, according to the National Chicken Council.

Fryer-sized chickens used by restaurants reach 4-pound slaughter weight at 35 or fewer days of age, about twice as fast as in the 1960s. Meanwhile, tom turkeys for the holidays are now raised to the typical 14 to 16 pounds in nine to 10 weeks, versus the four months or more required, for example, in the 1980s.

America builds an R&D infrastructure

The road to modern science-infused farming in the United States wasn’t built in a vacuum. America started laying the foundation for publicly-funded agricultural research and advancement with the Morrill Act of 1862, by which Congress granted tracts of land to states at 30,000 acres per member in Congress. The land was to be sold to start and maintain colleges “where the leading object shall be . . . to teach such branches of learning as are related to agriculture and the mechanic arts . . .” The act resulted in the birth of the national land grant universities. The Second Morrill Act of 1890 extended similar support to Southern states to open similar institutions to accommodate black students.

National support for agricultural R&D came with the Hatch Act of 1887, which provided money for the state land-grant colleges to set up agricultural experiment stations and disseminate information from the stations. Later, the Smith-Lever Act of 1914 established a system of cooperative extension services, linked to the land-grant colleges, to help people learn about and implement new farming practices and livestock discoveries, advances in home economics and to support 4-H clubs and other outreach to farms and rural communities.

The Green Revolution goes global

Cross-breeding of corn was not the only yield-building game in town. Especially with countries in South and Southeast Asia facing severe and chronic food shortages and starvation in the 1950s, governments and plant breeders joined in the 1960s in aggressive rice and wheat breeding of hybrid and selective strains, plus improving farming practices to boost crop yields and feed more people.

In 1960, the Philippines government joined with the Ford and Rockefeller foundations and established a rice breeding collaboration called the International Rice Research Institute (IRRI). Its first rice release, IR8, called “miracle rice,” allowed the Philippines to more than double its average rice yield in about two decades.

The IR8 variety led to other varieties of rice adapted to flourish in other countries in the region, including Indonesia, Cambodia, Malaysia, Vietnam and Myanmar (then, Burma). A new dwarf variety, IR36, was planted in India, and, when fertilized, it out-yielded other traditional rice by a factor of ten by 1968.

Norman Borlaug, the American agronomist (shown at right)  who became known as the father of the Green Revolution, was working with the Rockefeller Foundation to improve wheat varieties in the 1940s in Mexico, which was succeeding in its own wheat improvement program. He went to India in 1961 at the government’s request and began improving wheat to relieve hunger there, importing seed developed by breeders with the International Maize and Wheat Improvement Center.

Building on the global collaborative efforts to improve field crops in developing countries, the Ford Foundation, World Bank and others began in 1970 to set up a network of agricultural research centers under permanent direction. The result was the Consultative Group on International Agricultural Research (CGIAR), which is also supported by the United Nations Food and Agriculture Organization and others. CGIAR operates several research centers.

Breeders pry into the cell nucleus

The path toward breeders’ genome manipulation required access to and knowledge of the millions of genes on chromosomes, which lie in the cell nucleus. That access began with British researchers like Rosalind Franklin, who, with an assistant, began producing the first high-resolution photos of deoxyribonucleic acid (DNA) fibers in 1951.

Using such imagery, in 1953 molecular biologists James Watson and Francis Crick were able to describe chromosomes’ double helix, the twisted-ladder structure of DNA. That discovery became the sort of first-grade graduation into modern molecular biology, which is focused on how genes control the chemical processes of an organism’s growth and bodily functions.

Biochemist Frederick Sanger, another British scientist, and colleagues pioneered what became known as the “Sanger Method” of mapping the base pairs of genes, which are the letters of an organism’s genetic code. His method was the original one for sequencing DNA and, in 1977, he published the sequence of a virus genome of over 5,000 base pairs.

The Sanger Method became the usual one for mapping an organism’s genome. In recent decades, with the expanding knowledge of DNA and massive capacity of computers to store and communicate such data, researchers have moved ahead, compiling entire genomes of plants and animals. Sequencing of the 3 billion base pairs of the human genome, a 13-year international collaborative project, was completed in 2003.

Since 1995, scientists have sequenced the genomes of dozens of plants, including the major commercial crops. Sequencing the genomes of farm animals began with that for a chicken in 2004, and those for a cow (in 2009), and pig (2012) have since been published. Sequencing allows scientists to find specific genes on the chromosomes and learn how each gene works together with an organism’s other genes to create its phenotype, which is its appearance and how it grows, functions, and responds to changes, and other characteristics.

At the same time, genetic engineering techniques were evolving to allow for the introduction of new traits as well as greater control over traits than previous methods such as selective breeding and mutation breeding, which is the process of exposing seeds to chemicals or radiation to generate mutants with desirable traits that can then be bred with other cultivars.

The first genetically modified plant was produced in 1983, using an antibiotic-resistant tobacco plant. In 1988, the Food and Drug Administration approved the first application of genetically modified organisms in food production. In the early 1990s, recombinant chymosin – an enzyme with a role in digestion in some animals -- was approved for use in several countries.

The first genetically modified food approved for release was the Flavr Savr tomato in 1994. This tomato was developed by Calgene to have a longer shelf life.

A year earlier, China had introduced virus-resistant tobacco, becoming the first country to commercialize a transgenic crop. Transgenics refers to processes that impose a gene or genes from an unrelated species into a plant or animal species nucleus.

The first pesticide-producing crop, Bacillus thuringiensis (Bt) potato, was approved in the U.S. in 1995. That same year saw the approval for marketing of other GM crops, including canola with modified oil composition, Bt maize, cotton resistant to the herbicide bromoxynil, Bt cotton, glyphosate-tolerant soybeans, virus-resistant squash, and another delayed ripening tomato. Golden rice was created in 2000, the first time scientists had genetically modified food to increase its nutrient value.

The full genomes of a rainbow trout and salmon were also sequenced a few years ago, and researchers used such access to tweak the genes of Altantic salmon, inserting a gene from another fish, called the ocean pout. The change allows the salmon to grow and gain weight twice as fast as conventional varieties.

Two years ago, after more than 25 years of research, the U.S. Food and Drug Administration approved that fish, Aquadvantage, as the first genetically engineered food animal it has ruled as safe to eat. But Alaska lawmakers worked to stop the sale of the product in the U.S. and it's currently for sale only in Canada.

The new piece in the breeder’s pipeline

Many genetics laboratories and crop and animal breeders are knee-deep in new gene editing processes.

Gene editing takes an approach to genetic alteration that is fundamentally new and different from the kinds of transgenic modifications – popularly known as GMOs -- that researchers have pursued with varying success for two decades. Instead, they’ve found quick, inexpensive ways to edit the proteins within plant and animal chromosomes and with precise and predictable results.

Gene editing is akin to cutting and pasting text within a document, explained Jennifer Doudna, professor of molecular and cell biology and chemistry at the University of California, Berkeley, at a recent conference on gene editing on that campus.

In the 25 years of her cell biology and biochemistry career, she has “never seen science moving at the pace it is moving right now,” and she sees GE as generating much of the stampede.

Brummer, the plant breeder from UC, Davis, says most breeders and agricultural professionals he knows, after decades of persistent popular suspicion and opposition to transgenic crops, see gene editing as potentially less objectionable.

He says they are “hopeful that regulatory concerns would be minimized and we could move forward. There are certainly a lot of positive things you could do with CRISPR.”

He points out that, though CRISPR may spell less regulation, the breeder still must know well the gene or genes to be removed or changed, and what the results should be, in order to succeed.

So, Brummer advises, “the availability of CRISPR doesn’t so much speed up, but adds variability to genetics in the breeding program. You still have to go through the field testing, make sure that the yields are high, and produce the seed for farmers. So, there are still a number of years, in any event, you’ll have to go through to get a new variety.”

“Whether it’s trans-genes, genetic markers, or other technology,” he said, “these are all tools that are added to an existing plant breeding pipeline. And that pipeline is sort of our new cultivar delivery process. Maybe you can accelerate parts of it, or you can bypass parts of it, but, by and large, you still have that same pipeline . . . and all that stuff has to, in some sense, happen.”

Advances in breeding almost always start out as controversial. Note that a century ago, some prominent scientists continued to condemn Mendel’s 19th century findings as fraudulent, charging that his results were fudged to conform to the numbers he anticipated in his pea experiments.

And even now, some strains of transgenic corn and soybeans have still not been approved in some foreign markets – despite years of solid performance in the U.S. So gaining acceptance by U.S and foreign governments for new gene-edited products is an ongoing challenge for all involved.

But failure to explore these new breeding technique should not be an option, says Illinois pork producer Thomas Titus.

“It would be irresponsible not to continue to research and explore the possibilities with these new precision breeding tools” both for farm animals and humans, Titus said. “Think of the opportunities this holds for human health and the ability to eliminate certain diseases.”

A rising tide of farm production challenges

Breeders don’t rest. Their fight to keep farm plants and animals healthy and productive is nearly always a catch-up game or rear-guard action. So, crop and livestock breeders can never secure enough tools, and are always looking for new ones to counter the latest threat from pests or disease or to boost production to help producers remain efficient and keep up with competition.

But while much of crop and livestock breeding means playing defense, the demand side of world agriculture is not sitting still either. Human population is climbing toward 9 billion by mid-century and folks have an increasing appetite for more diverse and nutritious foods.

Besides the prospect of more and more people to feed, the world’s breeders are trying to find farmers new answers as they continue facing an array of ever-mounting production challenges:

• More crops and livestock on fewer acres: Available arable crop and pasture is declining as urban areas expand and industries take over farmland, so crop yields have to rise, and animals produce more meat, milk and such from available forage and feed.
• More crops with less later: Fresh water available to farms is declining as urban and industrial uses claim more water and aquifers are drawn down to keep food production going, and as climate change leaves some farming regions with less water. The means selecting less-thirsty types of crops and breeding more drought resistant varieties.
• Liming expansion of croplands to preserve forests and other wild areas.
• Improving plants’ nutritional quality: More nutrition per calorie makes the best use of resources.
• Helping crops to adapt: Breeders need to help them adjust to rising temperatures and increasingly volatile weather.
• Conserving plant and animal genetic diversity: The broader our genetic diversity, the more resilient our crops can be against the next disease or natural disaster.

Limiting expansion of croplands to preserve forests and other wild areas.Improving plants’ nutritional quality: More nutrition per calorie makes the best use of resources. Helping crops to adapt: Breeders need to help them adjust to rising temperatures and increasingly volatile weather.Conserving plant and animal genetic diversity: The broader our genetic diversity, the more resilient our crops can be against the next disease or natural disaster.

Hirst, meanwhile, isn’t in the life sciences arena, but has a view about GE, the new laboratory magic entering the ancient plant and animal breeding pipeline.

“I’m all for developing new versions of our plants that may be better able to survive in the climate changes that are already in progress. We desperately need more plants that are adapted to drier and less stable climatic situations as soon as possible – shorter growing seasons, less dependency on irrigated water, stronger resistance to drought.”

She adds a suggestion: “What about ways to clean extra nutrients out of the dead zones such as the one [in the Gulf of Mexico]? You could develop plants to do that.”

But she advises caution, too.

“I am not for lowering regulatory bars” to the new GE products, she says, adding that she wants to see protection of biodiversity at the forefront when approval of gene editing products are considered. “Biodiversity is a must have; not a nice to have, especially now, when we don’t have a good grasp on what the future will bring,” she says.