Bulked segregant analysis using the goldengate assay to locate the Rpp3 locus that confers resistance to soybean rust in soybean

Few resistance loci to soybean rust (SBR), caused by Phakopsora pachyrhizi Syd., have been genetically mapped and linked to molecular markers that can be used for marker assisted selection. New technologies are available for single nucleotide polymorphism (SNP) genotyping that can be used to rapidly map traits controlled by single loci such as resistance to SBR. Our objective was to demonstrate that the high-throughput SNP genotyping method known as the GoldenGate assay can be used to perform bulked segregant analysis (BSA) to find candidate regions to facilitate efficient mapping of a dominant resistant locus to SBR designated Rpp3. We used a 1536 SNP GoldenGate assay to perform BSA followed by simple sequence repeat (SSR) mapping in an F₂ population segregating for SBR resistance conditioned by Rpp3. A 13-cM region on linkage group C2 was the only candidate region identified with BSA. Subsequent F ₂ mapping placed Rpp3 between SSR markers BARC-Satt460 and BARC-Sat-263 on linkage group C2 which is the same region identified by BSA. These results suggest that the GoldenGate assay was successful at implementing BSA, making it a powerful tool to quickly map qualitative traits since the Golden-Gate assay is capable of screening 1536 SNPs on 192 DNA samples in three days.