Soybean stem canker resistance gene mapping and molecular marker development

Overview

Soybean stem canker (SSC), caused by Diaporthe phaseolorum var. meridionalis (Dpm), is a re-emerging disease that severely impacts soybean production. Genetic resistance is a key strategy for sustainable disease management, reducing yield losses and minimizing fungicide use. While four major dominant loci (Rdm1–Rdm4) were historically known to confer resistance to Dpm, only Rdm4 and Rdm5 have been mapped on linkage group A2 of the soybean genetic map. The genomic positions of Rdm1, Rdm2, and Rdm3 remain unknown, limiting the ability to pyramid multiple resistance genes for durable protection.

This research program aims to map Rdm1, Rdm2, and Rdm3 resistance loci, identify and validate molecular markers linked to them, and apply these markers in molecular-assisted breeding. The work builds on validated Rdm4–Rdm5 markers already used in marker-assisted selection and on existing soybean genotypes carrying pyramided resistance genes against multiple fungal pathogens, which are available as progenitors for breeding programs.

Technical specifications

• Mapping approach: Bulked Segregant Analysis using segregant populations developed for Rdm1–Rdm3, with local Dpm isolates for phenotypic characterization by progeny tests
• Marker development: Initial screening with molecular markers polymorphic between parental genotypes, followed by saturation of target genomic regions with additional markers to improve gene localization precision
• Prior validated assets: Molecular markers linked to Rdm4–Rdm5 on linkage group A2 (Gm 8), already validated in a germplasm bank and used in marker-assisted selection
• Pyramided genotypes available: Soybean lines carrying stacked combinations of resistance genes against Dpm, Cercospora sojina, and Fusarium sp., suitable as progenitors in breeding programs
• Resistance sources: Five known major dominant loci (Rdm1–Rdm5) conferring resistance to Dpm

Technology readiness level

The Rdm4–Rdm5 mapping and associated molecular markers are validated and currently used in marker-assisted selection within soybean breeding programs. Pyramided resistance genotypes combining Rdm4–Rdm5 with resistance to other fungal pathogens have already been developed and are available as breeding progenitors. Segregant populations for Rdm1, Rdm2, and Rdm3 have been obtained and are ready for phenotypic characterization and mapping. The next phase involves Bulked Segregant Analysis, marker saturation, and validation of new molecular markers for deployment in molecular-assisted breeding against soybean stem canker.