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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Research Project #432114

Research Project: Integrated Management of Soybean Pathogens and Pests

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

2021 Annual Report

Objective 1. Relate the spatial and temporal dynamics of soybean pathogens, pests, and associated microbial communities to soybean productivity. Subobjective 1.A. Determine if novel virulent or resistance-breaking soybean pathogens/pests have emerged within the U.S. and other parts of the world. Subobjective 1.B. Determine the impact of selected biocontrol and beneficial microbes to reduce the impact of soybean pathogens and pests. Subobjective 1.C. Characterize variability and shifts in the pathogenicity of Phakopsora pachyrhizi populations in the southern U.S. to guide breeding program decisions. Objective 2: Identify, characterize, and develop improved resistance in soybean that can be used for sustainable disease management strategies that include effective host resistance and biological control. Subobjective 2.A. Identify or characterize pathogen/pest resistance using annual and perennial accessions from the USDA Soybean Germplasm Collection and selected breeding lines. Subobjective 2.B. Develop agronomically competitive soybean breeding lines with disease- or pest-resistance genes from adapted or unadapted germplasm accessions in the USDA Soybean Germplasm Collection. Subobjective 2.C. Investigate relationships between soybean yields and resistance to soybean cyst nematode and Phytophthora sojae in public breeding lines from the Northern Uniform/Preliminary Soybean Tests.

The distribution and abundance of soybean pathogens and pests will be monitored on multiple geographic scales using pathogen-specific and metagenomic assays. The impacts of beneficial and insect-borne microbes on soybean diseases and yields will be characterized in replicated trials over multiple years. Changes in pathogen virulence over time will be assessed using soybean lines expressing different pathogen resistance genes and pathogen populations collected from soybean fields each year. New sources of resistance to pathogens and pests will be identified and characterized in cultivated soybean and related annual and perennial accessions from the USDA Soybean Germplasm Collection through field and greenhouse evaluations. Regions of soybean chromosomes associated with pathogen/pest resistance will be identified using phenotypic assays and molecular marker analyses of derived mapping populations. Soybean lines shown to be resistant to soybean pathogens/pests will be used to produce breeding lines with enhanced resistance using phenotypic and marker-assisted selection techniques as appropriate.

Progress Report
For Objective 1, we conducted a nematode survey in certified organic soybean fields in northern and central Illinois to determine the frequency and population densities of plant-parasitic and free-living nematodes. Fields surveyed included both long-term, 5 years or longer rotation with soybean, and short-term, every 3 years with soybean. Common plant-parasitic nematode taxa included spiral, lesion, cyst, stunt, dagger, and pin nematodes. Among the taxa, spiral, lesion and dagger nematodes were above previously reported damage threshold levels in some fields. Cyst nematode population densities were significantly higher in fields under short-term rather than long-term rotation with soybean. These results provide information about the occurrence of plant-parasitic nematodes and the soil ecosystem in organically farmed soybean fields and is useful information for disease management. To determine how the phenology of three agriculturally important aphid species varied with seasonal temperature and precipitation between 2005 and 2019, more than a half a million aphid observations from the US Midwest Suction Trap Network were examined with other scientist from the University of Georgia. Climate change projections with climate-aphid phenology models predicted shifts in aphid phenology by 2050 and 2080. While there is growing evidence that early flights of aphids are advancing in response to warming winters, little is known about how the many dimensions of aphid phenology will respond to the combined effects of changing temperature and precipitation. Overall, the climate-aphid phenology models predict that changes in climate will advance and therefore extend the period of crop colonizing flights for three aphid species, despite differing life histories and climatic drivers. Soybean production in Sub-Saharan Africa has been increasing in recent years and has led to several facets of research such as cultivar development to increase yield. Several abiotic and biotic stresses can decrease yield, including pathogens and pests that attack seed. While evaluating seed lots from 30 Pan-African Soybean Variety Trial locations, we identified bruchids and/or bruchid damaged seed in nine locations in four countries (Cameroon, Malawi, Mozambique, and Rwanda). The most severe damage and infestation was recorded in Bwanje, Malawi with 28 of the 40 seed lots infested. Seed damage ranged from 0.6-100% among the 28 infested seed lots. Adult bruchids discovered at the Bwanje location were identified as Callosobruchus chinensis, or the Chinese bruchid. No adults were found in other locations. Bruchids are a destructive storage pest of legumes and monitoring the different species attacking soybean will help researchers and producers understand the potential threat of bruchids to soybean production as well as help implement the best management practices. Soybean rust is one of the most devastating diseases of soybean worldwide. A field experiment was conducted with collaborators at Jimma and Metu Agricultural Research Center’s sites in Southwestern, Ethiopia for two years during the main cropping season using three soybean cultivars and six fungicide treatments to determine how fungicides and cultivar selection can reduce losses. Disease severity ranged from 6% to 52%. The highest seed yield (3.2 t/ha) was observed with one fungicide treatment, whereas the lowest seed yield (2.0 t/ha) was from the non-fungicide control. Of the three soybean varieties, the highest mean yield was observed on cultivar Clark 63K (2.72 t/ha) followed by cultivar Afgat (2.7 t/ha). The highest recorded yield loss (56.3%) was recorded on variety SCS-1 at Jimma. Pythium species cause seed rot and damping-off in soybean that results in significant economic losses, and are controlled by breeding resistant cultivars and fungicide applications. Research was conducted in FY2021 to evaluate 14 isolates from five Pythium spp. for their pathogenicity on six cultivars reported to have different levels of resistance in greenhouse and Petri plates assays. The objective of this study was to evaluate the aggressiveness of the Pythium isolates in causing seed rot during seed germination and root rot during seedling growth. For Objective 2 some plant introductions (PIs) from the Soybean Germplasm Collection are resistant to soybean rust. Disease ratings and DNA marker data from 255 PIs not previously known to be resistant, 16 susceptible checks and 15 resistant lines with known Rpp resistance genes, were analyzed in a genome-wide association study to detect regions of the soybean genome associated with resistance. Disease data were collected in 15 different year-location environments in the southeastern United States in collaboration with colleagues from the University of Georgia, the University of Florida, and Auburn University. Attention was paid to the geographical origin of resistant germplasm accessions, since almost all of the most resistant accessions were from either southern Japan, northern Vietnam, or central Indonesia. A manuscript is in preparation to report the results. Some cultivars in the USDA Soybean Germplasm Collection were previously discovered to have resistance to three species of Pythium, a soil pathogen that can cause seed rot and poor seedling stands. Experiments were conducted to better characterize the resistance of these and other accessions to 14 isolates representing five species of Pythium. Arkansas isolates of P. aphanidermatum, P. spinosum and P. ultimum var. ultimum were the most aggressive. Cultivars ‘Maple Isle’ and ‘Maple Glen’ were most resistant. Compared to the most susceptible lines, ‘Williams’ had lower disease severity, similar to that of ‘Archer’, which has moderate resistance to some species of Pythium. The objective will be to identify genomic regions associated with resistance to different species of the pathogen and to determine whether more than one isolate of each species is required for effective genetic analyses. Identification of germplasm accessions with broad resistance to Pythium would be useful in current breeding programs. Red leaf blotch, caused by the fungus Coniothyrium glycines, is an important disease of soybean across soybean growing regions in Africa. Fifty-nine soybean entries were evaluated for red leaf blotch severity in nine field locations in Ethiopia, Kenya, Uganda, and Zambia. Disease incidence was 100% and disease severity differed among entries at eight of the nine locations. Mean severity ratings ranged from 1.4 to 3.2 based on 0 to 5 scale with higher disease severities recorded in Ethiopia, followed by Zambia. The cultivar SC Signal had the lowest red leaf blotch severity ratings in the combined analysis. This is the first extensive report evaluating soybean genotypes for resistance against red leaf blotch under multiple environments. Perennial Glycine species are potentially valuable genetic resources that can improve disease resistance in soybean. The goal of this research, in cooperation with other scientists at the University of Illinois, is to discover novel quantitative trait loci (QTL) for resistance to Meloidogyne incognita from perennial Glycine spp.. From our initial screening of 18 accessions of 10 perennial Glycine species for resistance to M. incognita, we discovered that G. latifolia PI 559300 has a higher level of resistance to M. incognita. To identify QTL associated with resistance to M. incognita in G. latifolia, we conducted a QTL analysis using recombinant inbred lines derived from resistant (PI 559300) and susceptible (PI 559298) G. latifolia accessions and single nucleotide polymorphism markers generated through genotyping by sequencing. The initial analysis identified a single QTL on G. latifolia chromosome 13. The QTL interval spans a region from about 7.8 to 11.2 Mbp, explaining 34% of the phenotypic variation. This QTL contains at least 73 genes, including at least three putative disease resistance genes that have not been examined for their functions against M. incognita. We expect that the QTL on G. latifolia chromosome 13 is a major QTL responsible for resistance to M. incognita and contains novel genes that confer this resistance. We also anticipate that G. latifolia PI 559300 is a good candidate for utilizing genes that are effective against M. incognita and could be used to improve soybean resistance to M. incognita. We are proposing to release soybean germplasm lines LB18-58, LB18-65, LB18-49, LB18-52, LB18-57, LB18-67 and LB18-75 in FY22. These large seeded, non-GMO soybean lines range in maturity from maturity group (MG) 00 to MG IV. Each line contains a single gene for resistance to soybean aphid or Phytophthora root and stem rot. Lines LB18-58 and LB18-49 have resistance to soybean aphid biotype 3 provided by LD06-16721. Soybean aphid resistance to biotype 2 was derived from LD08-12441 or LB18-65. LD08-12582 provided resistance for lines LB18-52 and LB18-57. Williams 82 was the source of the PRSR resistance gene, Rps1k. Large seeded cultivars Tohya (MG 00), BeSweet 2001 (MG II), Gardensoy 24 (MG II) and Gardensoy 41 (MG IV) served as recurrent parents with pest resistant donor lines to develop large seeded, pest resistant soybean lines in a range of maturity groups. The combined pest resistance and large seed size, in a range of maturities, will be valuable for breeders developing large seeded pest resistant cultivars. A germplasm release notice and registrations of these lines are in progress.

1. Discovered a new virus infecting soybean. Soybean production in the USA is negatively impacted by an ever-changing population of pathogens and pests that are influenced by climatic changes. In experiments to monitor commercial fields for the emergence of new soybean pathogens, ARS scientists in Urbana, Illinois, in collaboration with University of Illinois researchers, discovered a new virus in soybean and named it soybean carlavirus 1. Based on encoded proteins and low nucleotide and amino acid sequence, the phylogenetic grouping of soybean carlavirus 1 showed it to be a new member of the Carlavirus genus, some members of which are capable of inducing significant crop losses. Further work will determine the importance of the new virus on soybean production. These results will be of interest to soybean producers, breeders, and other scientists working on virus identification and epidemiology of virus diseases of soybean, including the identification of its biological vectors.

2. Documented the ability of the soybean aphid to overwinter on glossy buckthorn. The soybean aphid is a major pest of soybean, both in Asia where it is native, and in the U.S. where it is adventive. The rapid spread and establishment of the soybean aphid in the U.S. since its discovery in 2000 was successful because of extensive soybean production in the Midwest and the wide distribution of common buckthorn, its preferred primary winter host. Both common buckthorn and glossy buckthorn are widely distributed in the U.S. and Canada, but the ability of aphids to overwinter on glossy buckthorn has not been described. We compared the survivorship of four soybean aphid biotypes on common and glossy buckthorn. Results showed that nymphs of all four soybean aphid biotypes reached adulthood and produced eggs on glossy buckthorn and that soybean aphid biotypes 2 and 3 males reproduced on both common and glossy buckthorn. This finding suggests that the density of glossy buckthorn in midwestern states may be important in the spread of aphids on soybeans. This work will be of interest to entomologists that study the overwintering of insects, to ecologists, and to soybean production.

3. Identified 155 novel virus sequences associated with soybean thrips. Soybean thrips are one of the most efficient vectors of soybean vein necrosis virus, which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, ARS scientists in Urbana, Illinois, in collaboration with University of Illinois researchers, analyzed the meta-transcriptome of soybean thrips collected by the U.S. Midwest Suction Trap Network. Contigs assembled from the data revealed a remarkable diversity of virus-like sequences. Of the 181 virus-like sequences identified, 155 were novel and associated primarily with taxa of arthropod-infecting viruses, but sequences similar to plant and fungus-infecting viruses were also identified. Sequences represented 12 previously described arthropod viruses including eight viruses reported from Hubei Province in China, and 12 plant virus sequences of which six have been previously described. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that potentially could be transmitted to soybean. Assessment of the virome of soybean thrips provides us, for the first time, with information on the diversity of viruses present in thrips. This information will be of interest to researchers studying the diversity and distribution of insect and plant viruses in insects that feed on crop plants.

4. Showed that changes in climate could alter aphid pest lifecycles. Many animals change feeding habits as they progress through life stages, exploiting resources that vary in space and time. ARS scientists at Urbana, Illinois, collaborated with scientists from universities in Arkansas, Florida, Georgia, and Illinois to track aphid species in three regions of the world. There were 300 aphid species tracked at 75 individual sites for 10 to 50 years that showed populations declined with median changes of -8.0, -5.6, and -0.2% per year in the central U.S., northwestern U.S., and the United Kingdom, respectively. Warming temperatures through time were associated with aphid decline, although at higher latitudes, there were some aphid increases. Overall, a warming world were associated with a decline in most aphid species, especially those that had time-sensitive movements among multiple host plants. Aphids species that alternate between host plants annually, and those that were agricultural pests, exhibited the steepest declines relative to other species that persist on the same host plant year-round or those in natural areas. In summary, most aphid species that had time-sensitive movements among multiple host plants faced a greater risk of decline as the environment warms. This information is useful for studying population dynamics and forecasting future population dynamics based on climate changes, and indicates overall that climate change will affect aphid populations with a general decline of some species as the world warms.

Review Publications
Paul, C., Harris, D.K., Li, Z., Bollich, P.A., Walker, D.R. 2021. Reactions of 52 soybean germplasm accessions with Rpp3 alleles to a panel of 13 Phakopsora pachyrhizi (soybean rust) isolates from the southern United States. Journal of General Plant Pathology. 87:55-70.
Thekke-Veetil, T., Lagos-Kutz, D.M., McCoppin, N.K., Hartman, G.L., Ju, H., Lim, H., Domier, L.L. 2020. Soybean thrips (Thysanoptera: Thripidae) harbor highly diverse populations of arthropod, fungal and plant viruses. Viruses. 12(12). Article 1376.
Crossley, M.S., Meier, A.R., Baldwin, E.M., Berry, L.L., Crenshaw, L.C., Hartman, G.L., Lagos-Kutz, D.M., Nichols, D.H., Patel, K., Varriano, S., Snyder, W.E., Moran, M.D. 2020. No net insect abundance and diversity declines across US long term ecological research sites. Nature Ecology and Evolution. 4:1368-1376.
Herman, T.K., Han, J., Singh, R.J., Domier, L.L., Hartman, G.L. 2020. Evaluation of wild perennial Glycine species for resistance to soybean rust nematode and soybean rust. Plant Breeding. 139(5):923–931.
Lagos-Kutz, D.M., Hartman, G.L. 2021. Survivorship of soybean aphid biotypes (Hemiptera: Aphididae) on winter hosts, common and glossy buckthorn. Insecta Mundi. 0870:1-8.
Thekke-Veetil, T., McCoppin, N.K., Hobbs, H.A., Hartman, G.L., Lambert, K.N., Lim, H., Domier, L.L. 2021. Discovery of a novel member of the Carlavirus genus from Soybean (Glycine max L. Merr.). Pathogens. 10(2). Article 223.
Crossley, M.S., Smith, O.M., Davis, T.S., Eigenbrode, S.D., Hartman, G.L., Lagos-Kutz, D.M., Halbert, S.E., Voegtlin, D.J., Moran, M.D., Snyder, W.E. 2021. Complex life histories predispose aphids to recent abundance declines. Global Change Biology. 27(18):4283-4293.