Crop breeding

Why is it important to increase genetic diversity in crops, especially in soybean?

Most of us have a favorite variety of apple. ‘HoneyCrisp’ is my new favorite because, as the name implies, the taste is super sweet, and the bite is crunchy. For apple pies, I prefer the more tart Granny Smith. It stands up to baking better.

I also have other favorite varieties from the garden – Silver Queen for corn on the cob, German Johnson tomatoes for sandwiches, Candor peaches and Charleston Gray watermelons for eating on hot summer afternoons. They are so good! Varieties really do make a difference.

So, how do we get new varieties? Behind the scenes, plant breeders develop new varieties every day. Just as one might breed a new variety of dog, such as the cockapoo, these scientists breed new plant varieties in labs, greenhouses, and test fields.

One reason to breed new varieties is to create our ‘farmers market’ favorites. But breeders also create an array of new varieties in non-garden crops as diverse as soybean, pine trees, and lawn grasses. New varieties may taste sweeter if they are fruits or vegetables. Or they may be more nutritious, resist pests, and perhaps just grow better. But they are born and bred for one purpose – to increase food security and to make us healthier and happier with our food choices.

What does genetic diversity have to do with variety development? The answer is that the genetic basis for new varieties is found in old varieties. Food crops have pedigrees just like people. We all come from somewhere, ancestrally speaking!

soybeans with different heights in a field, demonstrating genetic diversity
In order to increase efficiencies in growing soybean, genetic diversity was decreased in this crop. A new plan from the USDA-ARS, known as the 301 Plan, has the goal to restore diversity to applied soybean breeding programs. Credit: Tommy Carter

It turns out that we have lots of old varieties that farmers have developed for millennia. Long before Darwin and Mendel, farmers domesticated wild plants and continued improving them by selecting out desirable types (landraces) as they popped up. They did so each growing season as people and crops slowly spread across regions and continents.

During this long process, ancient farmers selected out thousands of new landraces. These ancient landraces created collectively a wealth of genetic diversity in our crop plants that is preserved today. In fact, old varieties are reservoirs for hundreds of important genes and alleles now used by modern plant breeders in variety development. 

Although our large collections of farmer-selected millennia-old landraces are diverse, the relatively small group of modern varieties derived from them are much less so. Modern honing of new varieties to increase yields and farming efficiencies has led to fewer types of varieties planted and harvested.

This loss of diversity in our current fields and gardens has real consequences. Modern varieties are often too uniform genetically speaking for good agricultural health. That’s because many new varieties are too closely related – like cousins or siblings. This uniformity makes them less useful as breeding stock in current breeding efforts because they have lost useful genes which are still present in the landraces.

Soybean provides a good example regarding the insufficient diversity in modern varieties. Farmers domesticated soybean perhaps five thousand years ago in central China. These seeds spread through most of Asia via caravans with population migration. Adapting soybean to local conditions as soybean spread slowly over Asia, ancient farmers selected out more than 10,000 diverse varieties from domestication to the present. Many of these are now preserved by the U.S. Department of Agriculture and China in seed banks

pile of green soybeans
Fresh green soybeans. Credit: Canva

Although the thousands of old Asian soybean landraces are genetically diverse, modern U.S varieties are not. In the process of developing modern soybean varieties for U.S. farmers, the first generations of U.S. soybean breeders (~1930-1990) essentially ignored genetic diversity. They instead focused on adapting soybean for mechanical farming. Hundreds of new varieties were released to U.S. farmers in a successful endeavor to improve productivity, but these varieties were not very diverse, genetically speaking.

Today, U.S. soybean breeding programs are widely recognized as limited by insufficient genetic diversity. Breeding progress slowed, and the reasons are twofold:

  1. The first is that only seventeen ancestors (among thousands available) account for 86% of the collective parentage in modern U.S. soybean. Seventeen is a small number when one considers that eighty million acres of soy are grown in the United States.
  2. The second reason is that the diversity in this initial narrow genetic base has been reduced further as a victim of its own successful breeding. That is, early modern varieties by their popular nature dominated 20th century breeding programs. Genetic bottlenecks resulted which severely constricted following soybean breeding to the present. This effect is known as genetic drift.

Two landmark soybean USDA cultivars, Lee and Forrest, in the southern US offer prime examples of this problem. They were released in the 1950s and 70s. Their superior agronomics and popularity on the farm led to their heavy use as parental stocks for breeding during the following decades.

The result was a new generation of progeny (soybean “children”) that were highly related not only to the landmark varieties Lee and Forrest, but to each other as well. Although they performed well in the field, these “brother and sister” soybeans were not good mating stock for producing new varieties. The term inbreeding is often used to describe this effect in animal breeding, and the term applies here as well.

many different types of soybeans in a field
Today, U.S. soybean breeding programs are widely recognized as limited by insufficient genetic diversity. But, a plan called 301 Plan will improve diversity. Credit: Tommy Carter

Short-term gains made in developing Lee and Forrest, thus, came at the expense of long-term progress. Diversity, the basis for new progress, was lost. But a new plan from the USDA-ARS, known as the 301 Plan, has the goal to restore diversity to applied breeding programs. Science in the 301 Plan results in new, unique breeding lines which have diverse pedigrees and genetics.

A new release of soybean “USDA-N6004” is part of that effort.* Breeders created USDA-N6004 soybean by hybridizing of USDA cultivar “NC-Roy” and Japanese cultivar “Blue Side.” Blue Side is a vegetable (edamame) soybean that comes from outside the U.S.’s genetic base. Japanese germplasm generally is not well represented as parental stock in U.S. breeding. Thus, Japan appears to be a rich untapped source of diverse genes for future U.S. soybean breeding.

The story of this new soybean provides a good case study that illustrates why genetic diversity is important in developing new varieties. Old landrace varieties provide the diversity that makes new varieties possible.

Moving forward with the 301 Plan will increase the diversity of our soybean crops. This should lead to new soybean varieties that are less closely related, more productive and more resistant to disease and changing weather. USDA and other agricultural research teams are fixing the problem of insufficient genetic diversity by going back to landrace varieties developed by ancient farmers and using them as parental stock. The USDA maintains well over 100,000 stocks and landraces for use in breeding.

Answered by Tommy Carter, retired USDA

*When new varieties of plants are certified by the USDA, they receive an official registration number. Some breeders then choose to name their variety with a more common name, such as “Lee” and “Forrest” soybean mentioned in this blog.

About us: This blog is sponsored and written by members of the American Society of Agronomy and Crop Science Society of America. Our members are researchers and trained, certified, professionals in the areas of growing our world’s food supply while protecting our environment. We work at universities, government research facilities, and private businesses across the United States and the world.

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