In 5 March 2001, a severe rust outbreak was recorded at Pitapó, Paraguay, and the causal organism was determined to be Phakopsora pachyrhizi using polymerase chain reaction (PCR) and DNA sequence analysis. In May, rust surveys showed spread throughout most of Paraguay and into western and northern Parana, Brazil. In the 2001-02 season, rust was widespread in Paraguay, but losses were reduced due to severe drought; however, in Brazil it spread to more than 60% of the soybean acreage, causing field losses estimated at 0.1 million metric tons (MMT). In 2003, the disease was observed in more than 90% of the fields in Brazil, and the projected losses in Mato Grosso and Bahia alone are 2.2 MMT (US$487.3 million). Approximately 80% of the soybean acreage in Brazil was sprayed twice with fungicides at the cost of US$544 million. Differences in efficacy have been observed among the commercial strobilurin and triazol fungicides.

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Phakopsora pachyrhizi, the cause of soybean rust, is an economically important pathogen of soybean in South America. Understanding the pathogenicity of indigenous fungal populations is useful for identifying resistant plant genotypes and targeting effective cultivars against certain populations. Fifty-nine rust populations from Argentina, Brazil, and Paraguay were evaluated for pathogenicity in three cropping seasons, 2007/2008-2009/ 2010, using 16 soybean differentials. Only two pairs of P. pachyrhizi populations displayed identical pathogenicity profiles, indicating substantial pathogenic variation in the rust populations. Comparative analysis of 59 South American and five Japanese samples revealed that pathogenic differences were not only detected within South America but also distinct between the P. pachyrhizi populations from South America and Japan. In addition, seasonal changes in rust pathogenicity were detected during the sampling period. The differentials containing resistance genes (Rpp: resistance to P. pachyrhizi) Rpp1, Rpp2, Rpp3, and Rpp4, except for Plant Introduction (PI) 587880A, displayed a resistant reaction to only 1.8-14, 24-28, 22, and 36 % of South American P. pachyrhizi populations, respectively. In contrast, PI 587880A (Rpp1), Shiranui (Rpp5), and 3 Rpp-unknown differentials (PI 587855, PI 587905, and PI 594767A) showed a resistant reaction to 78-96 % of all populations. This study demonstrated that P. pachyrhizi populations from South America vary geographically and temporally in pathogenicity and that the known Rpp genes other than Rpp1 in PI 587880A and Rpp5 have been less effective against recent pathogen populations in the countries studied.