June

Checkoff Researchers Find New Possibilities with Soybean Genome

The complete soybean genome has been likened to a map for soybean researchers. But it’s turning out to be a treasure trove of possibilities for not only researchers, but also for breeders and, eventually, U.S. soybean farmers.

The U.S. Department of Energy Joint Genome Institute (DOE JGI) released the draft of the complete soybean genome in early 2009. Sequencing tools developed by research funded by the United Soybean Board (USB) and the soybean checkoff proved to be instrumental in assisting researchers in mapping the genome.

A genome serves as the hereditary information of an organism. This has often been likened to a map to a soybean’s characteristics and holds information, for example, about the genes responsible for developing roots, leaves and stems. This map also includes information on the genes that control functions such as yield and protein and oil content, just to name a few.

Ever since it has been released, U.S. soybean researchers have used a variety of techniques to glean even more information from the genome such as telling one variety from another. By delving further into it, researchers continue to learn more about what genes control various characteristics of the soybean and the location of these genes.

It’s not surprising that improving U.S. soybean yield is the first thing on many of these researchers’ minds.

“The USB production committee has done a good job supporting research to increase yields for farmers, in order to improve their opportunity for profit,” explains Jason Bean, soybean farmer from Holcomb, Mo., and chair of USB’s production research program. “The research that led to the mapping of the soybean genome is among the most significant the checkoff has supported, in terms of its potential effect on U.S. soybean farmers’ profitability.”

Sequencing tools developed thanks in part to checkoff-funded research helped researchers complete the soybean genome map. Soybean researchers are now using this map to find more precise ways of breeding plants.

Finding the differences

Using the genome map, U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS) scientist Perry Cregan, Ph.D., has found genetic markers that define the genetic variability that distinguishes one type of soybean from another. He’s now using these many thousands of genetic markers to compare 19,000 soybean landraces and varieties found in the USDA germplasm collection to determine its genetic diversity. By reviewing some of the 1 billion data points among these landraces and varieties, Cregan explains that previous research shows 86 percent of soybean genes can be traced back to 17 different landraces. Through comparing different varieties and the forms of genes that have been most often selected over 70 years of soybean breeding, Cregan hopes to help breeders develop approach to combine the genes into improved soybean varieties.

“The major thing is trying to get data on the germplasm collection so we can have a resource for the whole community to use when someone needs to know what’s present at positions on the genome,” adds Cregan.

Cregan and his team have given attention to some trickier soybean characteristics, such as protein and oil. He notes that as soybean production in the United States has moved farther north, this could continue to be a concern for the U.S. soybean industry. However, increasing soybean yields by using the genome is the first priority.

“The potential is fabulous – there just seems to be all kinds of genetic improvements that could occur,” adds Cregan. “It requires that we continue to define and use the genetic variability present in the soybean genome.”

Organization and expression

When the soybean checkoff helped release the genome, all of the pieces were there, but it was continued research funded by the checkoff that helped to organize the chromosomes into the correct order. But researchers haven’t dug into the genes to see which ones are actually being expressed in the plant.

At Iowa State University, USDA-ARS researcher Randy Shoemaker, Ph.D., has been looking at the transcripts of the soybean genome, which are the message products of the genes that the soybean genome expresses. All of these transcripts can be put together into a transcriptome, which basically serves as a library of all the expressed genes in that variety.

“We’ve published an atlas of transcriptome maps for roots, leaves, stems, pods at the different stages of development in the soybean plant,” explains Shoemaker. “Now we’re looking for specific expressions for traits such as high and low yields. We’re also comparing soybeans to look for iron and other nutrient deficiencies and more efficient plants.”

Shoemaker finds the important genes by comparing two transcriptomes of different soybeans and looking for differences. He adds that it’s these differences that show which genes are important.

The researchers have experience in all areas of soybean genetics, and Shoemaker says that the interdisciplinary aspect of the team is necessary in order to work on improving the entire soybean.

Brian Diers at the University of Illinois appreciates the soybean checkoff’s continued support of research on the soybean genome. He admits it’s a big project but adds that the researchers are motivated by their determination to improve yields for U.S. soybean farmers.

Location, location, location

Brian Diers, Ph.D., professor of soybean breeding and genetics at the University of Illinois, studies the locations of genes that control yield soybeans. He’s also looking into whether the yield-increasing genes found in exotic varieties can be bred into current varieties to improve their own yields.

“In collaboration with several other researchers, we’ve developed 5,600 soybean experimental lines using 40 different crosses of soybean varieties or experimental lines, and we plan to map genes controlling yield using data across all these different populations,” explains Diers. “Because of the large size of the study when the data from all of these populations are combined, we should be able to obtain very accurate measurements of the effects of all of these different genes that control yield, as well as very precise location of these genes.”

Diers hopes to gain a better understanding of the location of yield genes in soybeans. This should help breeders reduce both the guesswork associated with determining which varieties to cross in breeding programs and the uncertainty that is commonplace in many soybean-breeding efforts today.

“After we complete this study, we will hopefully provide breeders tools that they can deploy in their own programs,” adds Diers. “Using this information, we hope they’ll make faster progress in improving the yields of varieties.”

Duplication

With more than 45,000 genes, it’s easy to imagine there are a few duplicate genes in the soybean genome. But those duplicates prove to be important to consider as well.

“We look at how the genes are expressed and how they control plant development, especially the duplicates,” explains Scott Jackson, soybean researcher at Purdue University. “When a gene is present in more than one copy, it’s important to understand what to do with both copies of genes to effectively engineer the plant.”

Looking at duplicate genes across the entire genome, all 45,000 genes, hasn’t been done in this genome before. But these duplicates are an important part of genetic engineering. When duplicate genes are present, the engineered changes sometimes don’t affect them. Jackson’s team has been focusing on improving yield and composition.

“A large number of genes can be effective in improving the soybean,” Jackson adds.

Increasing U.S. soybean yield is just one improvement that could result from the genome and continued production research. Better pest and disease control, excessive moisture and drought tolerance, stable protein and oil content, and plant efficiencies are just a few others researchers are looking forward to seeing made.

Improving U.S. Soybean Varieties

Diers notes that the common goal of increasing U.S. soybean yield has brought together researchers from across the soybean community to work on this massive project. The researchers have experience in all areas of soybean genetics, and Shoemaker says that the interdisciplinary aspect of the team is necessary in order to work on improving the entire soybean.

“Farmers have invested a large amount of checkoff money in DNA sequencing and genetic mapping, and we hope that, through this project, we can use these investments to improve yields,” adds Diers.

But the possibilities in using the soybean genome to improve soybeans don’t end at yield or with any of these projects. Just like the mapping of the genome itself, these findings represent stepping-stones to improving U.S. soybeans and the potential for profit for all U.S. soybean farmers.

“The potential is fabulous – there just seems to be all kinds of things that could occur,” adds Cregan. “It does require that we have the soybean genome.”