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Identifying genes to improve soybeans


November 30, 1999
By Heather Hager


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Soybean geneticists are creating a toolbox of plant materials that they hope will facilitate soybean breeding for specific characteristics down the road. “It’s a pretty exciting project because soybean only became a major crop in North America within the past 50 years, and it’s really come a long way in that time,” says Dr. Wayne Parrott, University of Georgia professor and crop geneticist. “It’s a crop that is showing that it’s lending itself to an ever wider range of uses.” He is referring to the ability to make soybean varieties that produce specific oils or proteins, for example, for various applications. Parrott is the project’s lead investigator. 

The goal of the project is to identify which genes control which soybean traits. The soybean genome has been sequenced, meaning that the order of the individual DNA components is known. However, the function of most of the genes remains a mystery, says Parrott. To find out what roles various genes have in the soybean plant’s functions, the researchers create a random mutation in the plant’s DNA and then grow the plant to see how it has changed, for example, in stature or seed protein content. They then analyze the plant’s DNA to find where in the genome the change occurred. Finding the altered gene allows them to identify it as having a function in that particular plant trait. Geneticists and soybean breeders then know which genes to work with when developing new soybean varieties that have specific traits.

The project is a massive undertaking by an extensive list of collaborators, including four principal investigators: Parrott, Dr. Gary Stacey from the University of Missouri, Dr. Tom Clemente from the University of Nebraska at Lincoln, and Dr. Carroll Vance from the University of Minnesota and United States Department of Agriculture Agricultural Research Service. It began in 2009 and is funded by a three-year, $2.5-million grant from the US National Science Foundation. 

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Linking traits with their genes
The group is using two methods to generate mutations in soybean DNA: jumping genes and irradiation. Parrott, Stacey, and Clemente work with jumping genes. The process begins by inserting a jumping gene from maize, tobacco, or rice into a single, isolated soybean cell in the lab, and then growing the cell into a soybean plant using special culture methods. As the plant grows, the jumping gene randomly inserts itself into one of the soybean genes, disrupting the function of that gene. This can affect the appearance or performance of the plant and its subsequent offspring. The researchers examine the plant for changes and then find the location of the jumping gene. The soybean gene that contains the jumping gene is interpreted as being linked to that specific plant trait.

Similarly, Vance and Stacey are using irradiation to alter gene function. They irradiate soybean seeds at certain doses that cause mutations by damaging the DNA. They then plant the seeds and examine the resulting plants for altered appearance or performance. Plant tissue samples are taken for DNA analysis in which the altered DNA is compared with the unaltered soybean genome to identify the affected genes. The seed is saved for future use. “A tremendous asset is that the soybean genome has been sequenced, so we will be able to lay our DNA sequence right on top for comparison,” says Vance. This allows them to locate the
altered genes. 

The DNA analysis might sound fairly quick and simple, but in reality, it is very expensive and time consuming, Vance explains. Even though the technology has advanced to a point “that was hardly imaginable when I was in graduate school,” he says, with an estimated 45,000 genes in the soybean genome and only a small portion of genes already identified, it would take decades to identify the function of every gene. So the researchers can analyze only some of the plants they produce. 

Some of the remaining irradiated soybean lines will be available for use by others who want to search for mutations. “We’re going to have a publicly accessible website that will have photographs of all the mutants, and hopefully we’ll have an idea of where some of the mutations lie in the genome,” says Vance.

In summer 2009, Vance and post-doctoral researcher Yung-Tsi Bolon had about 15,000 soybean plants growing in the field, each one examined, catalogued and harvested individually. They have found differences in height, leafiness, plant shape, leaf shape, flower colour, seed coat colour, hairiness of the stems and leaves, seed carbohydrate content, and seed oil content. And as yet, they have not even begun to look at root characteristics or responses to stresses such as drought.  With the help of several other collaborators, they will identify the genes for some of the traits. They had another 15,000 or so plants in the field again in 2010. In addition, Parrott and post-doctoral researcher Nathan Hancock had the first plants derived from jumping genes in the field in 2010.

The potential applications of this work are numerous and varied. “In addition to understanding which genes control which traits, we’ll hopefully come up with some traits that are good for soybean growers such as oil, yield, protein or some other aspect of quality,” says Vance.

The DNA analyses will also allow the development of genetic markers, which soybean breeders can use to locate the specific genes in varieties that are appropriate for specific growing regions.