Genetic architecture of southern stem canker resistance in elite southern soybean germplasm

Authors: WIDYAWAN, HABIB - University Of Georgia; BUCK, JAMES - University Of Georgia; Song, Qijian; ZENGLU, LI - University Of Georgia

Submitted to: Plant Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2026
Publication Date: 8/12/2026
Citation: Widyawan, H., Buck, J.W., Song, Q., Zenglu, L. 2026. Genetic architecture of southern stem canker resistance in elite southern soybean germplasm. Plant Breeding. 1-12. https://doi.org/10.1111/pbr.70120.
DOI: https://doi.org/10.1111/pbr.70120

Interpretive Summary: Southern stem canker is a highly destructive disease capable of causing soybean plant death and severe yield losses, particularly in the southern United States and South America. Although certain soybean varieties naturally possess resistance to this pathogen, breeders have yet to fully identify which specific genes confer this protection within modern soybean breeding lines. This study aimed to identify the genes responsible for conferring resistance by analyzing 927 advanced soybean breeding lines developed at the University of Georgia. Researchers from the University of Georgia and the USDA-ARS in Beltsville, Maryland, evaluated the resistance of these lines by artificially inoculating them in a greenhouse with the fungus that causes Southern stem canker and subsequently assessing the severity of their disease symptoms. Concurrently, they analyzed the DNA of each line to identify genetic markers closely associated with this resistance. The results of the analysis revealed that a single gene, designated "Rdm3," serves as the primary source of resistance within the elite soybean germplasm currently utilized in the U. S. Southern region. The researchers also detected a second associated genomic region located on a different chromosome; however, this region contributes only marginally to overall resistance. These findings indicate that modern soybean resistance to Southern stem canker relies heavily on the Rdm3 gene—a fact that underscores the necessity of introducing more diverse sources of resistance to enhance the crop's long-term protection. Furthermore, this study developed a DNA marker that enables the rapid identification of resistant plants, thereby providing breeders with an efficient tool to facilitate the more precise and effective selection of resistant soybean lines.

Technical Abstract: Southern stem canker (SSC), caused by the fungus Diaporthe aspalathi, poses a major challenge for soybean [Glycine max (L.) Merr.] production in the southern United States and South America. Genetic resistance is the most effective strategy for managing SSC. However, genetic architecture underlying resistance in the elite southern soybean germplasm remains poorly understood. Using an association panel of 927 advanced breeding lines developed by University of Georgia Soybean Breeding Program, a genome-wide association study (GWAS) identified a significant region on chromosome 14 associated with SSC resistance. The peak that was tagged by the SNP marker Gm14_1613564 overlapped with the Rdm3 locus previously reported from ‘Crockett’, PI 398469, and ‘Tracy-M’, suggesting that Rdm3 locus is the major source of SSC resistance in this elite germplasm pool. Evaluation of the Rdm3 haplotypes within the association panel revealed high frequencies of the Rdm3_Tracy-M and Rdm3_PI 398469 haplotypes. KASP markers defining the Rdm3 haplotypes can effectively differentiate soybean lines based on their SSC resistance and Rdm3 haplotype identity. They can be used for marker-assisted selection in soybean breeding.