Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/1/2024
Publication Date: 4/3/2024
Citation: Kendrick, M.D., Ramachandran, S.R., Wright, A.L., Lincoln, L.M., Whitham, S.A., Graham, M.A., Pedley, K.F. 2024. The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi. Molecular Plant-Microbe Interactions. https://doi.org/10.1094/MPMI-01-24-0007-R.
DOI: https://doi.org/10.1094/MPMI-01-24-0007-R

Interpretive Summary: Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean production throughout the world. While most soybean germplasm is susceptible to the disease, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. However, the actual genes that confer resistance are largely uncharacterized. We utilized two soybean accessions, PI 462312 (Ankur) and PI 506764 (Hyuuga), to identify and characterize candidate Rpp3 resistance genes. Ankur is the original source of Rpp3 and Hyuuga is known to carry an allele of Rpp3 and a second resistance gene at the Rpp5 locus. In this study we identified a single candidate resistance gene for Rpp3 and show that it is identical in both of the resistant lines. Rpp3 is an effective source of resistance towards P. pachyrhizi strains in the southern U.S. Our findings will enable plant breeders to identify Rpp3 in uncharacterized soybean germplasm and to differentiate novel Rpp3 alleles.

Technical Abstract: Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max (L.) Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371 kb region on chromosome 6 (Gm06). The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance.