Fine Mapping Rpp6, a Valuable Soybean (Glycine max L. Merr.) Rust Resistance Gene for the Southeastern USA

Soybean rust (SBR) is the most destructive foliar disease of soybean, and is caused by the obligate fungal pathogen Phakopsora pachyrhizi, which entered the continental USA in 2004. SBR can cause severe yield losses and genetic resistance is the most sustainable solution. The sixth discovered resistance gene to P. pachyrhizi (Rpp6) from PI567102B is a dominant resistance QTL. PI567102B produced a red-brown resistance or immune reaction to SBR in greenhouse assays (2008-2013), and had the fewest lesions and no detectable sporulation under high disease pressure in a two-replication field experiment in Attapulgus GA in 2012. Using Rpp6 alone, or in a pyramid with Rpp1 and/or Rpp3 is a breeding objective in the southeastern USA. We phenotyped and genotyped 140 F_2:3 families from an elite susceptible (G00-3213) by resistant (PI567102B) population using a Georgia rust population collected in 2012. A novel “super bulk segregant analysis” method for soybean confirmed the relative position of Rpp6 using only two samples (all homozygous susceptible and resistant families). The entire population was genotyped with 19 SNP polymorphic markers within the known interval (Gm18: 5.89 – 9.97 Mbp) using KASP assays designed from the SoySNP50K Infinium Chips. The 4.08 Mbp interval of the Rpp6 locus was reduced to 1.192 Mbp (Glyma_275_V2.0) flanked by the SNP markers Gm18_5,961,229 and Gm18_4,784,486. Breeder friendly SNP marker assays for marker-assisted selection, and backcrossing were developed. Candidate genes (e.g. Glyma.18g059600.Wm82.a2.v1, a leucine-rich repeat receptor-like protein kinase) have been identified in the region (5.033 to 5.597 Mbp (Glyma_275_V2.0) for designing functional marker assays.