Team cracks soybean pest’s puzzling genome

(Credit: Wikimedia Commons)

Researchers have sequenced the genome of the soybean cyst nematode.

The discovery paves the way for better management practices to combat the pest.

Soybean cyst nematodes are parasitic roundworms that infect the roots of soybeans and can devastate yields in infected fields. Nematode populations build up in fields and stay for years, meaning infested acres become a perennial management concern for farmers.

Crop breeders have studied genes in soybeans that can boost their resistance to the nematodes. Sequencing the nematode genome fills important gaps in scientists’ understanding of these pests that had remained stubbornly blank for years, says Thomas Baum, professor and chair of plant pathology and microbiology at Iowa State University and senior author of the paper in BMC Genomics.

“Researchers look at resistance on the soybean side of the equation, but it’s been difficult getting comprehensive work done on the biology and virulence of the pest because a workable genome had not been available,” Baum says. “Our work is a giant step in enabling novel research.”

Repetitive genes

The genetics of the soybean cyst nematode present challenges that kept scientists from assembling the full genome for years. The research team sequenced the genome first by sequencing smaller portions and then piecing those portions together into the full genome.

About a third of the nematode’s 29,769 genes are repetitive, meaning many of the genes come in multiple copies, says lead author Rick Masonbrink, an associate scientist in the Office of Biotechnology. The repetitive DNA greatly complicated the sequencing and assembly process, he says.

Coauthor Andrew Severin, manager of the Iowa State Genome Informatics Facility, likens it to a jigsaw puzzle of a blue sky in which all the pieces are identical in shape and color, making it difficult to figure out how all those repetitive pieces fit together.

A method called long-read sequencing technology made it possible to assemble a high-quality genome.

Offense and defense

Now, the fully assembled genome could lead to the development of better pest management strategies, and will help scientists compare different nematode populations at the gene level.

When the nematodes infect a soybean plant, they battle with the soybean’s natural defenses. The genome can help plant breeders understand how the nematodes manage to override the soybean’s defenses.

“This helps us to understand the basic pathology of the worm,” Baum says. “Now we can see both sides of the arms race, both the offense and defense.”

The researchers made their findings available in an open online database for other scientists to access.

The North Central Soybean Research Program and the National Science Foundation I/UCRC Center for Arthropod Management Technologies funded the work.

Additional coauthors are from Iowa State; Agriculture and Agri-Food Canada; the Joint Genome Institute in Walnut Creek, California; the Worcester Polytechnic Institute; the University of Missouri; the University of Cambridge; and the University of Illinois.

Source: Iowa State University