Allele variation at the Rdm3 locus conferring resistance to soybean southern stem canker

Crockett and PI 398469 carry distinct resistance alleles at the Rdm3 locus for soybean southern stem canker, supported by progeny analysis, sequence variation, candidate gene expression profiling, and allele transmission patterns. Genetic resistance to southern stem canker (SSC) in soybean is predominantly conditioned by the Rdm3 locus on chromosome (Chr) 14. Resistance at this locus has been identified in 'Crockett' and PI 398469; however, the allelic relationship between these lines remains unresolved. This study aimed to determine whether SSC resistance in Crockett and PI 398469 is governed by the same or distinct alleles at the Rdm3 locus. Progeny analysis of a Crockett × PI 398469 recombinant inbred line (RIL) population identified recombinant lines with weaker resistance and broader phenotypic variation than either parent, indicating that recombination at the Rdm3 locus disrupted favorable allele combinations and generated unexpected SSC resistance phenotypes. Consistent with this, sequence analysis of two priority candidate genes, Glyma.14G023500 and Glyma.14G022600, revealed variation associated with resistance between Crockett and PI 398469, as well as among resistant and susceptible RILs. Expression profiling of these candidate genes further demonstrated genotype-dependent temporal patterns, suggesting distinct regulatory mechanisms underlying resistance conferred by Rdm3 alleles from Crockett and PI 398469. In addition, the resistance alleles differed in their transmission behavior, with segregation distortion and underrepresentation of the Crockett allele observed across breeding populations and germplasm pools. Pedigree analysis further indicated an atypical origin of the Crockett Rdm3 allele. These results demonstrate that Crockett and PI 398469 carry functionally distinct resistance alleles at Rdm3, confirming allelic variation at a major SSC resistance locus and providing insight into the effective deployment of Rdm3 resistance in soybean breeding.