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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Research Project #422909


Location: Soybean/maize Germplasm, Pathology, and Genetics Research

2014 Annual Report

1. Identified and named a new fungal species that causes soybean anthracnose. Anthracnose of soybean was first reported in Korea in 1917, and now is known to occur wherever the crop is grown. The disease has been reported to cause significant yield losses in soybean in southern areas of the USA. The most common pathogen that causes soybean anthracnose is Colletotrichum truncatum. In 2009, an ARS scientist at Urbana, Illinois in cooperation with a University of Illinois scientist surveyed the distribution of Colletotrichum species in soybean fields in Illinois and characterized the collected species using traditional morphological observations and molecular characteristics of multiple gene sequences. Multiple-gene sequence analyses identified one isolate that was genetically distinct from other established Colletotrichum species. The isolate was further examined closely for its morphology, growth characteristics in culture, and pathogenicity on soybean. Based on the molecular phylogenetic, morphological and pathogenicity analyses, a new species was proposed named Colletotrichum incanum. This information is important for the development of soybean cultivars that are resistant to anthracnose, which will reduce the use of fungicides to control this disease thereby reducing costs of production for soybean growers and enhancing environmental quality.

2. Confirmed that the 2013 population of the soybean rust fungus in north-central Florida was less virulent than the 2012 population. Soybean rust, a potentially devastating foliar disease, is currently managed using fungicide applications, but previous studies discovered soybean genotypes with resistance to the disease. ARS scientists from Urbana, IL collaborated with researchers from the University of Florida and the University of Georgia to evaluate the reactions of historically resistant soybean germplasm accessions in 2013. These accessions developed much less disease in the field in Quincy, FL in 2013 than most of them had in 2012, while known susceptible lines had severe rust symptoms in both years. This dramatic decrease in virulence was unexpected, and is an important discovery because it indicates that loss of rust resistance in one growing season does not necessarily mean that the resistance genes will fail to provide protection in the following season. It also demonstrates that the virulence of the rust population at a location does not always increase from one season to the next. These results suggest that rust-resistant soybean cultivars maybe effective longer than previously thought for reducing yield losses from the disease and the economic and environmental costs of fungicide applications to manage soybean rust.

3. Compared the genome organizations of soybean and one of its wild perennial relatives. Soybean, like many cultivated crops, lacks genetic diversity for some economically important traits, while soybean’s wild perennial relatives are more genetically diverse and show high levels of resistance to multiple soybean pathogens and pests. However, it has been extremely difficult to cross soybean with its wild perennial relatives to capture genes for these valuable traits. ARS scientists at Urbana, Illinois, in collaboration with researchers from the University of Illinois, investigated differences in chromosome structure between soybean and one of its perennial relatives, Glycine latifolia, and showed that 12 of 20 soybean and G. latifolia chromosomes were very similar. The remaining eight chromosomes appeared to contain multiple interchromosomal rearrangements, which could reduce the fertility of offspring between the two species. The results from these experiments will aid in the development of methods to transfer genes from soybean’s wild perennial relatives to improve soybean yields and resistance to pathogens and pests thereby reducing both costs of production and applications of chemicals applied to the crop that will in turn enhance rural economies and environmental quality.

4. Aggressiveness of the fungus that causes soybean rust from Nigeria and the United States assessed using quantitative traits. Soybean rust is one of the most important foliar diseases of soybean worldwide. An ARS scientist at Urbana, Illinois cooperated with University of Illinois scientists to compare isolates of soybean rust from Nigeria and the U.S. for six quantitative traits to assess aggressiveness on two soybean genotypes. Five of the six quantitative measures were significantly different among the isolates within each soybean genotype within each country. By defining and understanding the traits used to measure aggressiveness, comparisons among fungal isolates can be used to determine if geographic or environment differences are associated with quantitative aspects of aggressiveness. This research will allow scientists to develop soybean cultivars to better manage pathogenically diverse populations of the soybean rust pathogen, which will reduce the need for costly fungicide applications and in turn enhance rural economies and environmental quality.

5. Identified additional soybean germplasm accessions with resistance to soybean rust. Populations of the rust fungus in different locations in the southern USA have shown considerable variation in terms of their ability to cause disease on plants with genes for resistance for soybean rust. To develop soybean cultivars with broad and durable resistance to soybean rust, it is important for breeders to have different resistance genes available. ARS scientists at Urbana, Illinois collaborated with researchers from the University of Georgia and the University of Florida in 2013 to identify 47 rust-resistant soybean plant introductions previously unreported to be resistant in the United States. The resistance of 31 of these was subsequently confirmed in greenhouse assays, and experiments have been started to determine which of these have unique resistance genes that differ from those reported in other plant introductions. The potential to reduce fungicide use by planting resistant crop cultivars developed from these and other sources has economic benefits for growers in addition to environmental benefits.

6. Identified regions of the soybean mosaic virus (SMV) genome that are required for transmission of SMV through seed. SMV is a seed and aphid-transmitted virus that can cause significant yield reductions and reduce seed quality in soybean. In North America, seed transmission serves as the primary source of inoculum for SMV. ARS scientists at Urbana, Illinois, in collaboration with researchers from the University of Illinois, investigated the roles of SMV encoded proteins in seed and aphid transmission. The results showed that some mutations that reduced transmission of SMV through seed also reduced transmission of SMV by aphids, which suggested that specific interactions between SMV-encoded proteins are important for multiple functions in the virus life cycle. The results of this study will help scientists develop soybean cultivars that reduce economic losses caused by SMV and thereby enhance rural economies.

7. Characterized the infection process of the fungus that causes soybean rust in different soybean genotypes. Soybean rust is an economically important disease of soybean with potential to cause severe epidemics resulting in significant yield losses. Host resistance is one of the management tools to control this disease. ARS scientist at Urbana, Illinois, cooperated with University of Illinois scientists to study in detail the infection process of the fungus in soybean using microscopic observations and quantitative measures of changes in the amounts of fungal DNA in soybean plants over time. Differences in infection among soybean genotypes were evident once the fungus invaded the leaves. Soybean genotypes completely or partially resistant to soybean rust had significantly lower quantities of fungal sporulation and fungal DNA than soybean genotypes with lower levels of soybean rust resistance. These results demonstrated that resistance in soybean results from restricted fungal development because plants kill infected cells to reduce disease spread. This information is important for the development of soybean cultivars that are resistant to soybean rust, which will reduce the use of fungicides to control this disease thereby reducing costs of production for soybean growers and enhancing environmental quality.

8. Developed a novel assay method to screen soybean germplasm for resistance to Phomopsis seed decay (PSD). PSD is a fungal disease that causes soybean seeds to become moldy when harvest is delayed by rain, thereby decreasing seed weight and oil and protein contents, which can result in substantial economic losses to producers. Because PSD is a seed disease, assessment of plant resistance is more difficult than it is for root or foliar diseases that can be seen prior to maturity. Furthermore, maintaining adult plants under conditions that promote the disease is difficult in the field and expensive in the greenhouse due to space requirements. ARS scientists from Urbana, Illinois developed a novel greenhouse assay in which soybean plants were grown to maturity at high densities in sand under a misting system that enhanced PSD infection. This method kept the plants diminutive but healthy, and allowed 20-30 plants to be grown to maturity in the same area that a single mature plant grown in standard potting mix would have required. Use of greenhouse space and overhead sprinklers was more efficient with the smaller plants, and plants could be induced to flower early by imposing a shortened photoperiod. Seed harvested from plants known to be susceptible to PSD exhibited higher than 90% disease incidence. These methods will facilitate the development of PSD-resistant soybean cultivars, which will maintain the quality of soybean seed through harvest, and in turn support soybean profitability and the health of rural economies.

Review Publications
Hartman, G.L. 2014. Phoma glycinicola (Red Leaf Blotch): A threat to soybean production in the USA. In: Liu, Dongyou, editor. Manual of Security Sensitive Microbes and Toxins. Boca Raton, Florida, CRC Press. p. 801-806.
Fox, C.M., Cary, T., Colgrove, A., Nafziger, E., Haudenshield, J.S., Hartman, G.L., Specht, J., Diers, B.W. 2013. Estimating soybean genetic gain for yield in the northern United States – Influence of cropping history. Crop Science. 53:2473-2482.
Yang, H., Haudenshield, J.S., Hartman, G.L. 2014. Colletotrichum incanum sp. nov., a curved-conidial species causing soybean anthracnose in USA. Mycologia. 106(1):32-42. DOI: 10.3852/13-013.
Vittal, R., Paul, C., Hill, C.B., Hartman, G.L. 2014. Characterization and quantification of fungal colonization of Phakopsora pachyrhizi in soybean genotypes. Phytopathology. 104:86-94.
Paul, C., Hartman, G.L., Marois, J., Wright, D., Walker, D.R. 2013. First report of Phakopsora pachyrhizi adapting to soybean genotypes with Rpp1 or Rpp6 rust resistance genes in field plots in the United States. Plant Disease. 97:1379.
Yang, H., Stewart, J.M., Hartman, G.L. 2013. First report of Colletotrichum chlorophyti infecting soybean seed in Arkansas, United States. Plant Disease. 97:1510. Available:
Radwan, O., Rouhana, L., Hartman, G.L., Korban, S.L. 2013. Genetic mechanisms of host-pathogen interactions for charcoal rot in soybean. Plant Molecular Biology Reporter. 32:617-629. DOI 10.1007/s11105-013-0686-9.
Xiang, Y., Herman, T., Hartman, G.L. 2014. Utilizing soybean milk to culture soybean pathogens. Advances in Microbiology. 4:126-132.
Diers, B.W., Kim, K., Frederick, R.D., Hartman, G.L., Unfried, J.R., Schultz, S.J., Cary, T.R. 2013. Registration of eight soybean germplasm lines resistant to soybean rust. Journal of Plant Registrations. 8:96-101.
Bonin, C.M., Kim, K., Cregan, P.B., Hill, C.B., Hartman, G.L., Diers, B.W. 2013. Inheritance of soybean aphid resistance in 21 soybean plant introductions. Theoretical and Applied Genetics. 127(1):43-50.
Hill, C.B., Bowen, C.R., Hartman, G.L. 2013. Effect of fungicide application and cultivar on soybean green stem disorder. Plant Disease. 97:1212-1220.
Lygin, A., Zernova, O., Hill, C., Kholina, N., Widholm, J., Hartman, G.L., Lozovaya, V. 2013. Glyceollin is an important component of soybean plant defense against Phytophthora sojae and Macrophomina phaseolina. Phytopathology. 103:984-994.
Marvelli, R.A., Hobbs, H.A., Li, S., McCoppin, N.K., Domier, L.L., Hartman, G.L., Eastburn, D.M. 2014. Identification of novel double-stranded RNA mycoviruses of Fusarium virguliforme and evidence of their effects on virulence. Archives of Virology. 159(2):349-352.
Kim, K., Chirumamilla, A., Hill, C.B., Hartman, G.L., Diers, B.W. 2014. Identification and molecular mapping of two soybean aphid resistance genes in soybean PI 587732. Theoretical and Applied Genetics. 127:1251-1259.
Twizeyimama, M., Ojiambo, P., Bandyopadhyay, R., Hartman, G.L. 2014. Use of quantitative traits to assess aggressiveness of Phakopsora pachyrhizi isolates from Nigeria and the United States. Plant Disease. 98:1261-1266. Available:
Jossey, S., Hobbs, H.A., Domier, L.L. 2013. Role of Soybean mosaic virus-encoded proteins in seed and aphid transmission in soybean. Phytopathology. 103(9):941-948.
Kuhn, J.H., Bekal, S., Cai, Y., Clawson, A.N., Domier, L.L., Herrel, M., Jahrling, P.B., Kondo, H., Lambert, K.N., Mihindukulasuriya, K.A., Nowotny, N., Radoshitzky, S.R., Schneider, U., Staeheli, P., Suzuki, N., Tesh, R.B., Wang, D., Wang, L., Dietzgen, R.G. 2013. Nyamiviridae: Proposal for a new family in the order Mononegavirales. Archives of Virology. 159(10):2209-2226.
Chang, S., Thurber, C.S., Brown, P.J., Hartman, G.L., Lambert, K.N., Domier, L.L. 2014. Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One. 9(6):e99427.