Cataloging SCN resistance loci in North American public soybean breeding programs

Authors: MAHMOOD, ANSER - University Of Missouri; Bilyeu, Kristin; SKRABISOVA, MARIA - Palacky University; BIOVA, JANA - Palacky University; DE MEYER, ELIZABETH - University Of Missouri; MEINHARDT, CLINTON - University Of Missouri; USOVSKY, MARIOLA - University Of Missouri; Song, Qijian; LORENZ, AARON - University Of Minnesota; MITCHUM, MELISSA - University Of Georgia; SHANNON, GROVER - University Of Missouri; SCABOO, ANDREW - University Of Missouri

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/16/2023
Publication Date: 11/20/2023
Citation: Mahmood, A., Bilyeu, K.D., Skrabisova, M., Biova, J., De Meyer, E., Meinhardt, C., Usovsky, M., Song, Q., Lorenz, A., Mitchum, M., Shannon, G., Scaboo, A. 2023. Cataloging SCN resistance loci in North American public soybean breeding programs. Frontiers in Plant Science. 14. Article e1270546. https://doi.org/10.3389/fpls.2023.1270546.
DOI: https://doi.org/10.3389/fpls.2023.1270546

Interpretive Summary: In the United States, more soybean yield losses can be attributed to the soybean cyst nematode (SCN) than any other pest, and it is responsible for more than one billion dollars in losses each year. Soybean breeders have been addressing the SCN problem through incorporating genetic resistance from a small set of donor accessions and intensive phenotypic selection for resistance. Resistance to SCN is variable and the genetics are not thoroughly understood. The objective of this work was to utilize a large resource of soybean breeding program germplasm in an association analysis to uncover the full genetic architecture of SCN resistance and provide information to assist in identifying minor resistance genes. The results confirmed known sources of resistance to individual SCN populations, dissected the effect of minor loci in SCN resistance, and identified novel genetic combinations that effectively provided complete SCN resistance. The impact of this research is the knowledge to apply confirmed and new SCN resistance genes and loci to soybean breeding efforts to combat this important pest.

Technical Abstract: Soybean cyst nematode (SCN) is a destructive pathogen of soybeans responsible for annual yield loss exceeding $1.5 billion in the United States. Here, we conducted a series of genome-wide association studies (GWASs) to understand the genetic landscape of SCN resistance in the University of Missouri soybean breeding programs (Missouri panel), as well as germplasm and cultivars within the United States Department of Agriculture (USDA) Uniform Soybean Tests—Northern Region (NUST). For the Missouri panel, we evaluated the resistance of breeding lines to SCN populations HG 2.5.7 (Race 1), HG 1.2.5.7 (Race 2), HG 0 (Race 3), HG 2.5.7 (Race 5), and HG 1.3.6.7 (Race 14) and identified seven quantitative trait nucleotides (QTNs) associated with SCN resistance on chromosomes 2, 8, 11, 14, 17, and 18. Additionally, we evaluated breeding lines in the NUST panel for resistance to SCN populations HG 2.5.7 (Race 1) and HG 0 (Race 3), and we found three SCN resistance-associated QTNs on chromosomes 7 and 18. Through these analyses, we were able to decipher the impact of seven major genetic loci, including three novel loci, on resistance to several SCN populations and identified candidate genes within each locus. Further, we identified favorable allelic combinations for resistance to individual SCN HG types and provided a list of available germplasm for integration of these unique alleles into soybean breeding programs. Overall, this study offers valuable insight into the landscape of SCN resistance loci in U.S. public soybean breeding programs and provides a framework to develop new and improved soybean cultivars with diverse plant genetic modes of SCN resistance.