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Title: Bulk Segregate Analysis using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Phakopsora pachyrhizi (Soybean Rust) in Soybean

item Hyten, David
item Smith, James - Rusty
item Frederick, Reid
item Tucker, Mark
item Cregan, Perry

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/1/2009
Publication Date: 9/1/2009
Citation: Hyten, D.L., Smith, J.R., Frederick, R.D., Tucker, M.L., Song, Q., Cregan, P.B. 2009. Bulk Segregate Analysis using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Phakopsora pachyrhizi (Soybean Rust) in Soybean. Crop Science. 49:265-271.

Interpretive Summary: Soybean rust (SBR), caused by Phakopsora pachyrhizi Syd., was first discovered in North America in 2004 and has been detected as far north as Illinois and Indiana in the United States. Five known genes that control resistance to soybean rust have been defined. We used a new assay called the GoldenGate assay to localize one of these genes which is known as Rpp3 to a position on a soybean chromosome. Knowing the location for Rpp3 allowed us to further locate the position of Rpp3 between the widely used DNA markers BARC_Satt460 and BARC_Sat_263. These molecular markers can be used to predict which soybean breeding lines carry the Rpp3 resistance gene. The GoldenGate assay is a new tool that geneticists can use to quickly map other single disease resistance genes. In addition, these markers will be useful for integrating the Rpp3 soybean rust resistant gene into modern soybean cultivars, to combine it with other identified soybean rust resistant genes, and to help determine the exact location of this resistant gene for molecular cloning. This information will be used by crop breeders and seed companies to increase the efficiency of finding new resistance genes and incorporating Rpp3 into new soybean cultivars.

Technical Abstract: Few resistance genes 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 SNP genotyping that can be used to rapidly map single gene resistance to SBR. Our objectives were to demonstrate that the high-throughput SNP genotyping method known as the GoldenGate assay can be used to perform bulk segregate analysis (BSA) to find candidate regions to facilitate efficient mapping of one of the dominant resistant genes to SBR designated Rpp3. We used a 1,536 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. This makes the GoldenGate assay a powerful tool for implementing BSA to quickly map other qualitative traits since the GoldenGate assay is capable of screening 1,536 SNPs on 192 DNA samples in three days.