Soybean rust, caused by the fungus Phakopsora pachyrhizi Sydow, has been known in Australia, Asia, Africa and South America, and has now become established in North America. Significant yield losses varying from 40 to 90% have been reported in Asian countries when environmental conditions were conducive for disease development. The rapid aerial spread of the pathogen and the potential for high risk of severe yield losses makes this potentially the most destructive foliar disease of soybean. Soybean rust was first observed and officially confirmed in the continental United States in November 2004 near Baton Rouge, Louisiana. For last two years, the disease was found infecting in more than 260 counties of southern soybean growing states (http://www.sbrusa.net/). This indicates that future soybean production in the US could be at a high risk for potential rust epidemics which will have a major impact on soybean production and production costs.
Resistance to soybean rust is controlled by four single dominant genes, Rpp1, Rpp2, Rpp3, and Rpp4. However, single-gene resistance in soybean was reported to be susceptible to certain isolates of P. pachyrhizi in many conditions. It was believed that the fungus P. pachyrhizi had considerable variation in virulence among isolates and was able to effectively overcome single-gene resistance in soybean. Thus, partial or horizontal resistance as indicated by low rust severity and/or fewer lesions may be an efficient approach for developing durable resistance. Since then, many efforts have been made to evaluate the USDA soybean germplasm collection to identify novel sources of resistance to the pathogen.
Soybean researchers of the National Center for Soybean Biotechnology (NCSB) have initiated a project "Evaluating and Breeding for Soybean Rust Resistance with Vietnam, 2005-2007" funded by USDA-FAS (in collaboration with USDA-ARS, University of Illinois-Urbana). A large number of US soybean germplasm and Missouri breeding lines were evaluated in Ha Noi, Vietnam. Several plant introductions (PIs) had disease reactions as good as local checks. These PIs also showed good disease reaction when evaluated in southern Georgia, US. In collaboration with other soybean scientists of the USB-funded project, soybean researchers of NCSB are currently focusing on the development of genetic populations derived from crosses of these resistance sources and elite soybean cultivars in attempts to identify novel genes or quantitative trait loci (QTL) responsible for resistance to the pathogen. Subsequently, fine-mapping using near-isogenic line (NILs) approach will be conducted to map candidate genes for the soybean rust resistance. These efforts aim to the development of gene-based molecular markers, providing efficient tools for marker-assisted breeding in soybean.
Due to the current APHIS restricted regulations for the culture of foreign soybean rust isolates used in US laboratories, soybean scientists rely on foreign nurseries for their phenotyping analysis. Thus, there has been limited information on isolates of P. pachyrhizi found in the continental US. There is an urgent need for knowledge about the population structure of soybean rust isolates in the US as well as abroad. It would allow US soybean researchers to accurately predict the origin and performance of US soybean rust isolates. With these perspectives, efforts of NCSB soybean researchers led by the Stacy laboratory is to conduct a pilot genome sequence project on a domestic P. pachyrhizi isolate to gauge the feasibility of a whole genome sequencing project and identify gene candidates for phylogenetic use. In addition, in hopes of the APHIS permit for the culture of rust isolates, the NCSB soybean researchers will evaluate the genetic diversity of domestic and foreign P. pachyrhizi isolates using sequence characterized amplified region (SCAR) polymorphisms derived from these gene candidates. The hope will be to identify specific sequence markers that can specifically identify US isolates.