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Research Highlights
Equipping Soybeans for the 'Arms Race' Against Diseases

Phytophthora isolates defeating the Rps1K resistance gene in a soybean field. Photo: Anne Dorrance, Ohio State University

By Laura Temple

Common diseases steal an estimated 420 million bushels of soybean yield annually across the U.S., according to university research. Two soil-borne pathogens, Phytophthora sojae and Pythium species, contribute to that yield loss. Phytophthora sojae causes Phytophthora root and stem rots, and it is considered the second most common pest after soybean cyst nematode. Pythium species, which cause damping-off and root rot, comprise another critical group of soybean diseases with increasing prevalence in soybean-producing regions.

“Host resistance, bred into soybean varieties, is the most practical, economical and environmentally friendly way to manage diseases like Phytophthora and Pythium,” explains Dr. Saghai Maroof, a professor and researcher in the School of Plant and Environmental Sciences at Virginia Tech. “However, as we have developed soybeans with resistance to these diseases, the pathogen populations have changed, developing the ability to defeat those resistance genes. This creates an ongoing ‘arms race’ between soybeans and pathogens.”

To help soybeans maintain resistance to these ever-changing, costly diseases, the Virginia Soybean Board and the United Soybean Board are providing checkoff funding for research to develop disease-resistant soybeans. Maroof is part of an interdisciplinary team collaborating with multiple universities working to identify novel genetic resistance to Phytophthora and Pythium.

“More than 20 Phytophthora resistance genes have been developed and bred into current soybean varieties,” Maroof says. “But some of these genes no longer work effectively. The goal of this research is to develop germplasm with novel genetic resistance that public and industry soybean breeders can incorporate into new soybean varieties, providing farmers with effective disease resistance in their fields.”

He acknowledges that this needs to be an ongoing process as Phytophthora and Pythium develop new variants in soybeans, much like the coronavirus does in humans.

Identifying Novel Resistance to Phytophthora

To identify and develop new germplasm with resistance to Phytophthora sojae (Rps), Maroof and the team are taking two genetic approaches. With both efforts, they are identifying genes within the 20 soybean chromosomes that confer resistance to Phytophthora variants, or isolates, that can defeat currently available Rps genes.

First, the team conducted a genome-wide association analysis. They requested more than 1,800 unique soybean plant lines, or plant introductions, from the comprehensive USDA germplasm collection.

“Prior United Soybean Board investment to fingerprint soybean plant introductions in this collection facilitates this approach,” Maroof says. “DNA marker data already exist for this germplasm.”

Seeds from the 1,800 lines were inoculated with current Phytophthora isolates. The resulting disease reaction data were analyzed for resistance, combined with the existing DNA marker data, and subjected to association analysis.

“The team identified 75 novel trait loci that confer resistance to Phytophthora infections,” he reports. “And, we know the DNA markers associated with them, allowing breeders to accelerate incorporation of these resistance genes into soybean lines.”

Then the team selected five lines with strong Phytophthora resistance for an inheritance study. The resistant lines were crossed with the susceptible Williams, a soybean variety commonly used for research purposes, with a fully sequenced version.

From these five genetic crosses, they screened 1,500 soybean lines and collected Phytophthora disease reaction data similar to the genome-wide association analysis. Because these were new lines, they collected DNA data to construct chromosomal maps and identify new resistance genes and their associated DNA markers.

“This work showed that four of the 20 soybean chromosomes offer novel resistance,” Maroof says. “We identified Phytophthora resistance genes on chromosomes 3, 7, 13 and 18.”

Adding New Pythium Resistance

Ideally, soybean farmers need varieties with resistance to multiple diseases.

Seedling damping off from Pythium. Photo: Marty Chilvers, Michigan State University

The team screened the 150 most Phytophthora-resistant lines for resistance to several prevalent Pythium species. They report that 58 of those lines were also resistant to at least one Pythium species. Eight lines showed resistance to two Pythium species.

“We have identified genes on soybean chromosome 6 that provides resistance to two species of Pythium, and genes on chromosome 8 conferring resistance to three species,” he explains. “In addition, we identified eight minor-effect genes on different chromosomes that offer some additional resistance to Pythium.”

The results of this work and the germplasm from those lines will be made available to soybean breeders to accelerate development of soybeans with better resistance to both diseases.

“Improved germplasm from this study should facilitate development of superior soybean cultivars for domestic and export markets,” Maroof says. “This genetic material adds to the foundation to protect soybean yield and improve profitability of U.S. soybean producers.”

This project was funded by the soybean checkoff. To find research related to this research highlight or to see other checkoff research projects, please visit the National Soybean Checkoff Research Database.