Genetic loci resistant to soybean southern stem canker in Tracy-M and its progeny

Southern stem canker (SSC), caused by Diaporthe aspalathi, is a major soybean disease causing yield losses of up to 80%. Genetic resistance is the most effective and sustainable strategy for managing SSC. "Tracy-M" is a cultivar with broad resistance to D. aspalathi isolates; however genomic location of the resistance is unknown. To determine the genetic basis of SSC resistance in Tracy-M and its derived progeny, two Tracy-M-derived lines, D85-10404 and D85-10412, were each crossed with a common susceptible parent, G81-2057, to develop recombinant inbred line (RIL) populations. Quantitative Trait Locus (QTL) sequencing (QTL-seq) and composite interval mapping (CIM) identified a common major QTL on chromosome (Chr) 2 in both lines corresponding to Rdm1 locus defined from a previous genetic study. Additionally, second QTL located on Chr 17 (Rdm2 locus) was only detected in the D85-10412-derived RIL population. To validate Tracy-M-derived resistance, an F2:3 population from G00-3213 × Tracy-M was developed. Bulked segregant analysis (BSA) and CIM identified a major QTL on Chr 14, overlapping the previously reported Rdm3 locus in "Crockett" and PI 398469, while Rdm1 was not detected, suggesting genetic background effects. Kompetitive allele-specific PCR (KASP) markers were developed to facilitate selection of Rdm1, Rdm2, and Rdm3 resistance alleles in soybean breeding programs.