Project : USDA ARS

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Research Project: Integrated Management of Soybean Pathogens and Pests

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

2020 Annual Report

Objectives
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.

Approach
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
Objective 1. Relate the spatial and temporal dynamics of soybean pathogens, pests, and associated microbial communities to soybean productivity. Soybean thrips are one of the most efficient vectors of soybean vein necrosis virus (SVNV), which can cause severe necrotic symptoms in sensitive soybean plants. To determine which other viruses are associated with soybean thrips, soybean thrips were separated from other insects collected in 2018 by the Midwest Suction Trap Network. Analysis of contigs assembled from total RNA high-throughput sequencing data revealed the presence of near full-length genome sequences of 12 described plant viruses and 10 described arthropod viruses, including five viruses reported from Hubei province in China. The assembled contigs also included sequences representing more than 20 novel viruses with positive-sense, negative-sense and double-stranded RNA and single-stranded DNA genomes. The presence of diverse populations of plant viruses within soybean thrips suggests they feed on and acquire viruses from multiple host plant species that could be transmitted to soybean. Greenhouse grown Glycine latifolia (G. latifolia) were observed to be mildly to severely affected with leaf spot symptoms that included moderate defoliation. Spots were irregularly shaped, approximately 2 to 5 mm by 4 to 8 mm in size, pale, gray or light brown in color and not bounded by veins, but often surrounded by chlorotic haloes and delimited by dark brown or reddish lines within or outside the haloes. Symptomatic leaflets were detached, rinsed with tap water, and incubated in the dark. After one-week, sporodochia formed in and around the leaf spots. Spores were collected and used to generate isolates, which appeared morphologically similar to Myrothecium fungi. Spores were harvested from a culture and misted onto five-week old soybean and G. latifolia plants. Necrotic lesions similar to those on the original plants were visible 2 days after inoculation and severely affected leaflets dropped off within two weeks. Nucleotide sequences of fungal internal transcribed spacers from the cultures were identical to corresponding regions from Albifimbria verrucaria. To our knowledge, this is the first confirmed report of A. verrucaria causing leaf spot on G. latifolia or any perennial Glycine species in natural or controlled environments. Aphis gossypii (A. gossypii) is a highly polyphagous aphid with a worldwide distribution. It is taxonomically challenging due to similar morphology to other Aphis species. It has been recorded throughout most of Africa on cotton, cowpea, cucurbits, and pepper but not on soybean. In March of 2019, immature, adults, and dwarf types of A. gossypii were found on soybean in Mpongwe, Zambia. The sequences of mitochondrial cytochrome oxidase 1 genes from the African isolates were nearly identical to the reference sequence for A. gossypii in GenBank. Morphological observations such as the ratios of antennae processus terminalis and base, and siphunculi and cauda confirmed the identity of this species. Soybean cyst nematode (SCN) occurs widely and is a leading cause of soybean yield losses in the USA. Additional SCN management strategies are needed because sources of SCN resistance have become less effective in keeping SCN populations in check. Arbuscular mycorrhizal fungi (AMF) form symbiotic relationships with roots of most plants including soybean. Research has shown that AMF can reduce disease severity in plants caused by pathogens and pests, including plant parasitic nematodes. The goal was to determine if AMF could suppress SCN. In one experiment, five AMF species significantly reduced the number of cysts on soybean roots compared to soybean roots without AMF. In two other experiments, AMF species reduced the counts of SCN juveniles in soybean roots by 60% and suppressed egg hatching by as much as 30%. These experiments showed that AMF were able to suppress SCN cyst counts and reduce SCN juveniles in roots and suppress egg-hatching. There is increasing interest to incorporate arbuscular mycorrhizal fungi (AMF) into agricultural production because of the benefits they provide, including protection against pathogens and pests. Sudden death syndrome (SDS) of soybean is a devastating disease caused by the soilborne pathogen Fusarium virguliforme (F. virguliforme). The relationship between F. virguliforme and AMF is not well documented. The ability of the AMF species Rhizophagus intraradices (R. intraradices) to reduce SDS severity was investigated. Six soybean genotypes were inoculated with F. virguliforme and with or without R. intraradices in a greenhouse experiment. In the six soybean genotypes assayed, area under the disease progress curve values were significantly reduced in roots of R. intraradices-colonized plants compared to plants without R. intraradices. Root weight of R. intraradices-colonized plants increased significantly compared to plants not colonized by R. intraradices. With the benefits gained from inoculation of R. intraradices, AMF should be considered as a potential strategy to manage the impact of SDS on soybean production. Geographical and temporal variability in the virulence and aggressiveness of Phakopsora pachyrhizi, the fungus that causes soybean rust, make it difficult to develop soybean cultivars with broad and durable resistance. In collaboration with researchers at the University of Georgia, reactions of 52 soybean accessions were assayed for their responses to 13 isolates that caused soybean rust collected 2007 to 2015. All the accessions carried an Rpp3 rust resistance gene. Thirty-two accessions had reaction patterns similar to plant introduction (PI) 462312 (Rpp3), while eight others had reaction patterns more similar to ‘Hyuuga’, a line with resistance genes at the Rpp3 and Rpp5 loci. The remaining 12 accessions had reaction patterns that differed from both PI 462312 and Hyuuga, and that were different from one another in many cases. The accessions with reactions similar to Hyuuga offer breeders alternative sources of broad resistance to soybean rust, but the PIs with unusual reaction patterns to the 13 isolates could be useful for studying genomic differences at the Rpp3 locus that are associated with pathotype recognition. The results also demonstrate that eight isolates collected between 2013 and 2015 were less virulent than a 2012 isolate from north-central Florida that is able to reproduce on plants with genes that condition resistance to most other U.S. isolates of the rust fungus. 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. The genetic base for commercial soybean cultivars is extremely narrow. There are 26 wild perennial Glycine species that potentially have genes of economic importance that could be incorporated into soybean. To take advantage of the diversity present in soybean’s wild perennial relatives, 16 accessions from four perennial Glycine species were evaluated for resistance to soybean cyst nematode (SCN) and to multiple isolates of the soybean rust fungus prior to initiating hybridization with soybean. All 16 accessions were resistant to one SCN biotype with 12 accessions associated with low SCN reproduction and four plant introductions with no cyst reproduction. All 16 accessions were immune to one rust isolate of soybean rust, but none were immune to all three of the other rust isolates. In summary, Glycine accessions with resistance to SCN and to multiple soybean rust isolates may be useful in wide-hybridization programs to transfer resistance into soybean. Soybean vein necrosis virus (SVNV) was first discovered in 2008 in Arkansas and Tennessee and rapidly became widespread in the USA and Canada. Multiple species of thrips transmit this and other tospoviruses with soybean thrips as the most efficient vector for SVNV. This year, 18 soybean genotypes were evaluated in four experiments by infesting plants with non-infected and SVNV-infected thrips using choice and no-choice assays. In both choice experiments with non-infected and SVNV-infected thrips, the lowest number of immature soybean thrips occurred on plant introductions 229358 and 604464 while soybean cultivars supported higher counts of thrips. The counts between the two assays (non-infected and SVNV-infected thrips) were positively correlated. In both no-choice experiments with non-infected and SVNV-infected thrips, counts of thrips did not differ significantly by soybean genotypes. Further studies are needed to characterize the inheritance and mechanisms involved in this antixenosis type of resistance found in the choice assay. Several species of water molds in the genus Pythium cause root rot and “damping-off” (wilting) of soybean seedlings, particularly when soils remain cool and damp. After the Canadian cultivar ‘Maple Isle’ was found to have resistance to an Illinois isolate of P. ultimum var. ultimum and two other Pythium pathogens, elite ARS breeding lines were crossed with Maple Isle and genetically related Pythium-resistant accessions from the USDA-ARS Soybean Germplasm Collection. Some hybrid plants were backcrossed to the ARS parent line or were crossed with a different ARS breeding line to combine increased Pythium resistance with other important resistance and agronomic traits. Selected plants were harvested and advanced to the next generation for preliminary evaluation of yield potential. After further inbreeding, agronomically superior breeding lines will be evaluated for Pythium resistance and yield under different environmental conditions. More than 5,000 breeding lines with at least one germplasm accession in their pedigrees were rated for incidence of bacterial blight, bacterial pustule, frogeye leaf spot, and symptoms resembling sudden death syndrome late in the 2019 growing season.

Accomplishments
1. Monitored seasonal abundance of soybean aphids and other insect species. The abundance of soybean aphids and other insect species that make up the aerobiota in the central United States vary temporally and geographically. The ability to predict damage caused by agricultural insect pests is dependent on detailed information on their abundance and impacts on crops linked to contemporaneous climatological and meteorological factors. To fill this information void, ARS scientists at Urbana, Illinois, collaborated with state researchers, extension specialists, and agriculturalists to analyze insects captured in suction traps located in nine central states, that consisted of vertical tubes that rise up more than 6 meters from the ground. The collected insects have been stored, used for past research, and will serve as a foundation for future research. The suction trap data and its samples have generated publications on modeling distribution and migration patterns for soybean aphids, providing new reports of aphid species beyond their known distributions, and learning more about the distribution of other insect species, such as mosquitoes and thrips. These data are of interest to researchers working to reduce crop damage from insect pests and economists and population biologists who are interested in modelling agricultural production systems.

2. Evaluated soybean lines for incidence and severity of foliar diseases in Zambia and Malawi. Soybean production has expanded worldwide including countries in Sub-Saharan Africa where soybean production is considered important to small-plot farmers. However, few high-yielding disease-resistant soybean cultivars are available that are adapted to the region. To address this short fall, ARS researchers at Urbana, Illinois, collaborated with other national and international agencies and research groups to help improve overall performance of soybean breeding stocks in Africa. High-yielding germplasm from Brazil and the USA were evaluated in Zambia and Malawi for three bacterial diseases, six fungal diseases, one oomycete and viruses as part of the Pan African Soybean Variety Trials. The occurrence of most diseases was high except for soybean rust and target spot. This work provided a bookmark for the status of soybean diseases in Sub-Saharan Africa and will be important to soybean researchers worldwide as well as breeders, pathologists, and farmers in Africa.

3. Developed methods to express cloned gene sequences in plant parasitic nematodes. Plant parasitic nematodes cause millions of dollars of losses in crop productivity each year. However, methods to manipulate gene expression in these damaging pests are limited. To aid in the analysis of interactions between plants and nematodes, ARS scientists at Urbana, Illinois, in collaboration with university researchers, developed methods to express cloned reporter genes in plant parasitic nematodes. To induce nematodes to uptake synthetic gene sequences, nematodes were briefly pulsed with high-voltage electricity. Most nematodes survived the pulses, and expression of the synthetic gene was highest at 24 hours after treatment but was still detected after 72 hours. The techniques were applied to soybean cyst nematode, a root-knot nematode, and a free-living bacterial-feeding nematode. The ability to transiently express synthetic gene constructs in economically important plant parasitic nematodes provides a rapid means to evaluate nematode and/or foreign genes for their potential roles in nematode management. These results will be of interest to scientists studying the interactions between nematodes and plants that lead to crop losses and has broader implications for biotechnologists and farmers that someday may grow soybean varieties with nematode resistance traits.

4. Assessed the resistance of soybean plant introductions (PIs) to soybean rust. In many growing seasons soybean rust (caused by Phakopsora pachyrhizi) threatens the yield of soybean in the southern United States. Rust-resistant cultivars would reduce the complete reliance on fungicide applications to manage this disease. Seedling and detached leaf assays were conducted by an ARS researcher from Urbana, Illinois, in collaboration with University of Illinois scientists to evaluate the reactions of 55 PIs to six fungal isolates (strains) representing four years, three states and several pathotypes varying in their abilities to defeat specific rust resistance (Rpp) genes. Hyuuga, which has two resistance genes, and plant introduction 471904, which has a resistance gene at the Rpp5 locus, were resistant to all six isolates, as were five other PIs. Twenty-six other PIs were resistant to at least four of the fungal isolates. The pathogenic diversity of the soybean rust pathogen makes it challenging to develop cultivars with broad and durable resistance to rust. The results of this study provide breeders developing cultivars for the southern United States with new information about which Rpp genes, gene combinations and germplasm sources to use in their breeding programs.

U.S. DEPARTMENT OF AGRICULTURE

Soybean/maize Germplasm, Pathology, and Genetics Research: Urbana, IL