Discovery and deployment of soybean rust (Phakopsora pachyrhizi) resistance (Rpp) genes
King, Zachary Raymond
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Soybean rust (SBR), caused by the fungal pathogen Phakopsora pachyrhizi is an economic threat to soybean production, especially in the Americas. Host plant resistance is important for SBR management. PI 567068A possesses a resistance gene on chromosome 18 near the Rpp6 locus of PI 567102B, determined by bulked segregant analysis (BSA). Linkage mapping placed Rpp6 between 5,916,005 to 5,961,229 bp and the resistance gene from PI 567068A between 5,961,229 to 6,122,387 bp (Wm82.a1). PI 567068A reacted differentially to two international P. pachyrhizi isolates when compared with PI 567102B. Both PI 567068A and PI 567102B carry the same haplotype designated as Rpp6/Rpp[PI567068A]. The result indicated that PI 567068A possesses a novel allele that is either at the Rpp6 locus or at a new locus. Four near-isogenic lines (NILs) of G00-3213 were developed by backcrossing rust resistance genes Rpp1, Rpp2, Rpp3, or Rpp4 into an elite, maturity group VII soybean line, G00-3213 and were designated as G00-3213Rpp1, G00-3213Rpp2, G00- 3213Rpp3, and G00-3213Rpp4. Each NIL exhibited resistance to the GA12 P. pachyrhizi bulk isolate equivalent to that of the original resistant sources, and similar agronomic qualities to G00-3213. Marker-assisted selection has become a valuable tool to select value-added quantitative trait loci. A reliable, inexpensive, high-throughput DNA extraction protocol for soybean seed and leaf samples that does not generate hazardous waste was developed,allowing for the leverage of SNP genotyping platforms, including the SimpleProbe Assay and KASPar v4.0 SNP Genotyping System. This methodology allows one to run up to 150 SNP markers from a single seedchip or leaf with a 95% success rate. Germplasms with putatively novel Rpp genes, PI 594796, PI 433972, and PI 605823, were identified. Using BSA with SoySNP50K Infinium Chips, the putative resistance locus from PI 605823 was located on Chr 19. PI 476905A has the Rpp6/Rpp[PI567068A] haplotype, yet has a unique P. pachyrhizi isolate pattern. The resistance of PI 605791A was mapped to the Rpp4 locus, and its haplotype matches the novel PI 423972 (Rpp4[PI423972]) haplotype associated with the resistance allele described here. PI 605791A has a different isolate reaction pattern compared to both PI 459025B (Rpp4) and PI 423972.