Virulence Diversity of Phakopsora pachyrhizi Isolates From East Africa Compared to a Geographically Diverse Collection.

Soybean rust, caused by the biotrophic pathogen Phakopsora pachyrhizi, is a highly destructive disease causing substantial yield losses in many soybean producing regions throughout the world. Knowledge about P. pachyrhizi virulence is needed to guide development and deployment of soybean germplasm with durable resistance against all pathogen populations. To assess the virulence diversity of P. pachyrhizi, 25 isolates from eight countries, including 17 isolates from Africa, were characterized on 11 soybean genotypes serving as differentials. All the isolates induced tan lesions with abundant sporulation on genotypes without any known resistance genes and on soybean genotypes with resistance genes Rpp4 and Rpp5b. The most durable gene was Rpp2, where 96% of the isolates induced reddish brown lesions with little or no sporulation. Of the African isolates tested, the South African isolate was the most virulent, whereas those from Kenya, Malawi, and some of the isolates from Tanzania had the lowest virulence. An Argentinian isolate was virulent on most host differentials, including two cultivars carrying multiple resistance genes. Ten distinct pathotypes were identified, four of which comprised the African isolates representing considerable P. pachyrhizi virulence. Soybean genotypes carrying Rpp1b, Rpp2, Rpp3, and Rpp5 resistance genes and cultivars Hyuuga and UG5 were observed to be resistant against most of the African isolates and therefore may be useful for soybean-breeding programs in Africa or elsewhere.

First Report of Phakopsora pachyrhizi Causing Rust on Soybean in Malawi.

Soybean rust (SBR), caused by Phakopsora pachyrhizi, has become established in Africa since the first report in Uganda in 1996 (2). The urediniospores, as windborne propagules, have infested new regions of Africa, initiating SBR in many countries, including Ghana and Democratic Republic of the Congo in 2007 (4) and Tanzania in 2014 (3). No refereed reports have been published about rust in Malawi, but some people have indicated that soybean rust may have been observed as early as 2008. Typical symptoms and signs of SBR, including leaf yellowing and tan, sporulating uredinia, were observed on soybean in May 2014 during field surveys in the major soybean-growing areas of Malawi, including the central (Dowa, Mchinji, and Kasungu) and southern (Thyolo) regions in nine out of 12 sites surveyed. When microscopically examined, urediniospores were elliptical, echinulate, and hyaline to pale yellowish brown. Leaves exhibiting sporuliferous uredinia were sent by APHIS permit to the University of Illinois. To confirm the pathogen, symptomatic soybean leaf tissue of approximately 1 cm2 was excised from each of the samples, and DNA was extracted using the FastDNA Spin Kit (MP Biomedicals, Solon, OH), with further purification using the MicroElute DNA Clean-up Kit (Omega Bio-Tek, Norcross, GA). The resulting DNA was analyzed by quantitative PCR using published Taqman assays for P. pachyrhizi and P. meibomiae, with a multiplexed exogenous internal control reaction to validate negative results (1). P. pachyrhizi DNA was detected in excess of 180,000 genome equivalents/cm2 in all samples, indicating a substantial infection. P. meibomiae DNA was determined to be absent from all samples, within the limit of quantification of ~2 pg DNA/cm2. Urediniospores dislodged from three leaves and inoculated onto susceptible soybean cultivar Williams 82 produced tan lesions after 2 weeks of incubation in a detached-leaf assay. This is the first confirmed report of P. pachyrhizi causing rust on soybean in Malawi, putting at risk 14,000 ha currently under soybean production. The reports of soybean rust in Malawi and adjoining countries will alter soybean production practices and research interests. In some cases, foliar application of fungicides has increased and planting dates have been changed to avoid conditions that are most conducive for rust development. Efforts to understand the virulence and genetic diversity of the pathogen in the region are needed in order to develop and deploy resistant cultivars. References: (1) J. S. Haudenshield and G. L. Hartman. Plant Dis. 95:343, 2011. (2) R. Kawuki, et al. Afr. Crop Sci. J. 11:301, 2003. (3) H. M. Murithi et al. Plant Dis. 98:1586, 2014. (4) P. S. Ojiambo et al. Plant Dis. 91:1204, 2007.

First Report of Phakopsora pachyrhizi on Soybean Causing Rust in Tanzania.

Phakopsora pachyrhizi Syd. was reported on legume hosts other than soybean in Tanzania as early as 1979 (1). Soybean rust (SBR), caused by P. pachyrhizi, was first reported on soybean in Africa in Uganda in 1996 (3), and its introduction into Africa was proposed to occur through urediniospores blowing from western India to the African east coastal areas by moist northeast monsoon winds (4). The fungus rapidly spread and was reported on soybean in South Africa in 2001, in western Cameroon in 2003, and in Ghana and the Democratic Republic of the Congo in 2007 (5). A second species causing SBR on soybean, P. meibomiae, has not been reported in Africa or elsewhere, outside of the Americas. From 2012 to 2014, symptomatic leaf samples were collected in the major soybean growing areas of the Tanzanian Southern Highlands (Iringa, Mbeya, and Ruvuma regions). Symptoms of SBR included yellowing of leaves and tan sporulating lesions. These symptoms were observed at flowering through seed maturity. From fields surveyed in 2012, 2013, and 2014, SBR was observed in 5 of 14, 7 of 11, and 14 of 31 fields, respectively. Some of the leaves sampled had up to 80% of the leaf area affected. When microscopically examined, urediniospores were elliptical, echinulate, and hyaline to pale yellowish brown. In 2014, sporuliferous uredinia were observed on leaf material collected from the Iringa and Ruvuma regions of Tanzania, and a subset of these samples was sent by APHIS permit to the University of Illinois. To confirm the pathogen, symptomatic soybean leaf tissue of approximately 1 cm2 was excised from each of the samples, and DNA was extracted using the FastDNA Spin Kit (MP Biomedicals, Solon, OH), with further purification using the MicroElute DNA Clean-up Kit (Omega Bio-Tek, Norcross, GA). The DNA was subjected to quantitative PCR using published Taqman assays for P. pachyrhizi, P. meibomiae, and a multiplexed exogenous internal control reaction to validate negative results (2). P. pachyrhizi DNA was detected in excess of 66,000 genome equivalents/cm2 in all samples, and P. meibomiae DNA was determined to be absent from all samples (limit of quantification ~2 pg DNA/cm2). Free surviving urediniospores were dislodged from 12 samples and inoculated onto susceptible soybean cultivar Williams 82, which produced sporulating SBR lesions after 2 weeks of incubation in a detached-leaf assay. Thus, Koch's postulates were completed. This is the first report of P. pachyrhizi causing rust on soybean in Tanzania. In vivo cultures have been established from most of these samples, and ongoing research includes an evaluation of the P. pachyrizi virulence on a differential set, and characterization of the genetic diversity. References: (1) D. L. Ebbels and D. J. Allen. Phytopath. Pap. 22:1-89. (2) J. S. Haudenshield and G. L. Hartman. Plant Dis. 95:343, 2011. (3) R. Kawuki et al. Afr. Crop Sci. J. 11:301, 2003. (4) C. Levy. Plant Dis. 89:669, 2005. (5) P. S. Ojiambo et al. Plant Dis. 91:1204, 2007.