Genetic Architecture of Southern Stem Canker Resistance in Elite Southern Soybean ( Glycine max [L.] Merr.) Germplasm

ABSTRACT

Southern stem canker (SSC), caused by the fungus Diaporthe aspalathi , is one of the major constraints to 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, the genetic architecture underlying resistance in elite southern soybean germplasm is poorly understood. Using an association panel of 927 advanced breeding lines from the University of Georgia Soybean Breeding Program, a genome‐wide association study (GWAS) identified two significant genomic regions corresponding to the major‐effect locus Rdm3 on chromosome (Chr) 14 (1,640,437 bp) and the minor‐effect locus Rdm2 on Chr 17 (12,871,988 bp). Haplotype analysis at the Rdm3 locus revealed that resistance is conferred by either Tracy‐M or PI 398469‐type resistance. In contrast, the Rdm2 locus exhibited a conditional effect, contributing to reduced SSC severity only in the presence of the Tracy‐M‐type Rdm3 haplotype. These results indicate that Rdm3 is the primary source of SSC resistance in this elite germplasm pool. Kompetitive Allele‐Specific PCR (KASP) markers targeting Rdm3 resistance types effectively distinguish resistance classes and can support marker‐assisted selection in soybean breeding.