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United States Department of Agriculture

Agricultural Research Service

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The mission of the Crop Production and Pest Control Research Unit is to conduct research to minimize crop losses due to insects and pathogens and improve soybean quality. Specific projects are directed toward discovering the genetic, biochemical, and molecular mechanisms that confer insect resistance in cereals, disease resistance in grain crops and soybeans, and influence the chemical composition of soybean seeds. The information is applied to devise innovative strategies for insect and disease control and develop germplasm with improved quality traits, pest resistance, and agronomic characteristics.

There are five CRIS projects in the Crop Production and Pest Control Research Unit:
Enhancing Resistance to Root Rot Pathogens of Soybean 
Teresa J. Hughes (Research Plant Pathologist) - The soybean pathology lab personnel consists of Wad Crochet and T.J Fleury (ARS Technicians). The primary focus of the project is to identify and define the role(s) of fungal pathogens infecting soybeans. Host resistance is a major emphasis for Phytophthora root rot and sudden death syndrome. In order to evaluate soybean germplasm and breeding lines for disease resistance, a culture collection of soybean pathogens is maintained and utilized to identify and describe mycological and physiological characteristics of the biotypes associated with each disease. An additional activity involved in improving disease resistance and yield in soybeans is the project's responsibility for coordinating the Uniform Soybean Tests for the Northern Region.
Hessian Fly Resistance in Soft Winter Wheat
Brandon J. Schemerhorn(Research Entomologist) - Population biology of Hessian fly.
Richard H. Shukle(Research Entomologist) - Our long-term goal is to ensure effective and durable resistance in wheat to Hessian fly. One approach we are taking toward this goal is to test combinations of effective undeployed Rgenes using F 1plants and Hessian fly collections from different locations across the Southeast. Results will test the hypothesis that deployment of a combination of two highly effective Rgenes will be more efficacious and potentially more durable than single gene releases. We are also employing an in plantabioassay with Hessian fly larvae to discover toxic proteins that could be utilized in transgenic resistance. Using this assay we are testing lectins for toxicity as well as various Bacillus thuringiensisCry ?-endotoxins. These results are testing the hypothesis that toxic proteins can provide effective transgenic resistance to Hessian fly that can be pyramided with combinations of native genes for resistance. A third approach to develop novel resistance in wheat to Hessian fly is the application of RNA interference (RNAi). We have used RNAi as a functional genomics tool with Hessian fly larvae and recently developed what appears to be a simple and effective approach to eliciting RNAi knockdown of targeted transcripts. Preliminary results with RNAi suggest we have identified a secreted salivary gland protein (SSGP) that is a virulence effector involved in the stunting of seedling wheat by Hessian fly larvae. When the gene encoding this SSGP is silenced by RNAi larvae appear to be unable to stunt wheat and cannot develop properly. We propose to test the hypothesis that plant mediated RNAi silencing of this gene can provide effective resistance to Hessian fly.
Christie E. Williams(Research Molecular Biologist) - The goal of Dr. Williams research is to better understand the basis of wheat resistance and susceptibility to Hessian fly and to apply this knowledge toward improving the durability of resistance in the wheat field. The Williams lab has identified Hessian fly-responsive wheat genes that contribute to plant defense and lead to larval death on resistant plants.
Several of these genes encode lectins and components of oxidative stress, which appear to act as feeding deterrents or disrupt the ultrastructure of the larval midgut. Other wheat genes have been identified that are suppressed by larvae, resulting in physiological changes that benefit the insect. These genes include several involved in maintaining integrity of leaf surface defenses through production and transport of cuticular waxes and cutins, or cell wall cellulose. These and other genes are being identified through the use of quantitative real-time PCR, microarrays and high-throughput DNA sequencing. Proteomics approaches characterize the encoded proteins, determine lectin activity and identify likely glycan targets. For deployment of new types of resistance, Hessian fly-induced wheat gene promoters are being characterized to drive transgenes that can be pyramided with conventional R genes. In addition, new R genes conferring Hessian fly-resistance are being mapped and molecular markers designed for wheat breeding programs.
Manipulation of the Quality and Flavor of Soybean Proteins
Karen Hudson(Research Molecular Biologist) - The goal of Dr. Hudson's research is to improve multiple aspects of soybean seed composition including protein and oil content. They will be using expression microarrays to characterize gene expression during soybean seed development in subdomains of the developing seed, as well as to identify genes that are regulated by diurnal cycles in developing soybean embryos. This will further our understanding of how these processes within the seed itself influence composition traits. They are focusing on studying the function, expression and effects on soybean seed of a number of transcription factors known to affect seed development in Arabidopsis. This translational research aims to study the effects of these regulatory genes on accumulation of seed storage proteins in order to develop biotechnology and conventional approaches to fine-tune soybean protein composition.
Soybean TILLInG
Dr. Hudson's lab is developing a chemically mutagenized TILLInG population that will allow us to study the function of genes that are required for normal soybean seed development. The population will allow us to take a reverse-genetic approach to determine what effect the loss of a given gene has on soybean seed development and composition.
Molecular and Genetic Mechanisms of Fungal Disease Resistance in Grain Crops
Vacant(Supervisory Research Plant Pathologist) - Research in the Corn and Sorghum Pathology Lab is focused on analyzing genes involved in light-regulated conidiation and secondary metabolism in the maize gray leaf spot pathogen, Cercospora zeae-maydis. Light conditions during growth and development of this fungus influence these two processes differentially. Blue light suppresses sporulation but promotes biosynthesis of the phytotoxin cercosporin, while red light has the opposite effects. Mutants disrupted in genes encoding putative blue-light receptors, cryptochrome (CRY-1) and white collar ortholog (CRP-1), have been obtained and phenotypically characterized. The other major project involves a microarray approach to analyze gene expression during gene-for-gene responses that determine the outcome of the interaction between maize and the northern leaf blight pathogen, Setosphaeria turcica.
Stephen B. Goodwin(Research Plant Pathologist) - Classical and molecular genetics of host-pathogen interactions between wheat and the Septoria tritici blotch pathogen, Mycosphaerella graminicola; Pathogen phylogenetics and speciation mechanisms; Genetic mapping and analysis of resistance genes; Gene expression during R-gene and non-host resistance responses of wheat and barley; Genomics.
Charles F. Crane(Geneticist - Bioinformatics) - Currently Dr. Crane is investigating cell-wall degrading enzyme loci and repetitive elements in the genomes of Mycosphaerella graminicola and Mycosphaerella fijiensis, which respectively cause destructive diseases of wheat and banana. He is also investigating the relationship of microsatellite motif frequency and codon usage in EST collections from 25 plant genera. All of this work is computational, and the microsatellite study involves extensive simulation of EST collections generated at random according to codon usage frequencies.
Molecular and Genetic Mechanisms of Resistance to Barley Yellow Dwarf Virus
Vacant(Research Molecular Biologist) - The primary focus Small Grain Virus-Host Interaction Laboratory is to identify and integrate into small grain germplasm, disease resistance traits with a primary focus on resistance to Barley and Cereal Yellow Dwarf viruses (YDV). The disease caused by this set of viruses has been particularly severe in recent years, reaching epidemic proportions in many parts of Indiana and surrounding states and resulting in significantly lower yields. Through a collaborative project with the Purdue University small grains breeder, Dr. Ohm, wheat varieties have been developed that are highly resistant to these viruses. These lines are available for planting by wheat producers. Anderson and his colleagues have determined that this host plant resistance blocks the virus from spreading from the initial site of infection by YDV-carrying aphids. In addition to analyzing the mechanism of this resistance, they have also developed a virus detection method which will determine if wheat leaf samples contain any of eight different viruses that infect wheat. This method was developed to determine which of these viruses are present in wheat fields. Understanding more about the virus diseases within a field and across a state such as Indiana will determine resistance required in future elite wheat lines. Initial results show that wheat plants expressing virus disease symptoms typically contain two and as many as four different viruses. Producers and wheat scientists are very interested in this disease test and the lab is currently examining samples from many Indiana counties and research plots in West Lafayette, Indiana, Georgia and North Carolina.
Steven R. Scofield(Research Geneticist) - Dr. Scofield's research program is focused on achieving two major objectives: increasing our understanding of the molecular signaling pathways that lead to the activation of defense pathways in plants, and applying this knowledge to improve disease resistance in cereal crops. The work is carried out in collaboration with other researchers of the USDA-ARS Crop Production and Pest Control Research Unit and the Small Grains Research Group, at Purdue, that study a range of agriculturally significant fungal, viral and insect diseases of cereals.

To achieve the first goal, Scofield's group has developed a high-throughput virus-induced gene silencing (VIGS) system to identify genes encoding functions required for disease resistance. They will then begin to investigate how the gene products function in resistance, and determine if they may be useful in achieving the second objective. The VIGS system is based on barley stripe mosaic virus (BSMV) and has proven very useful in the analysis of disease resistance pathways in hexaploid wheat. Results of work employing this system to identify genes required for leaf rust resistance in wheat was  published (Scofield et. al., 2005). 

Scofield's approach to the second goal is to harness the power of naturally occurring disease resistance pathways, which are able to provide highly effective resistance to specific pathogens. These resistance systems have been used for decades to provide protection against particular "target" pathogens. Unfortunately, there are many significant pathogens for which no corresponding plant resistance systems are known. However, recent work demonstrates that some resistance pathways can, in fact, provide resistance to a broad-spectrum of "non-target" pathogens when they are engineered to be activated when the plant is attacked by "non-target" pathogens. To this end, Scofield and his team are using the tools of genetic engineering to test existing resistance pathways for the ability to provide defense against agriculturally important "non-target" pathogens, and developing strategies so that these pathways can be appropriately activated by these "non-target" pathogens.

Research Leader:Steven R. Scofield 
Scientists:Teresa J. HughesSoybean Disease Laboratory
VacantSmall Grains Viral Disease Laboratory
VacantCorn and Sorghum Fungal Disease Laboratory
Stephen B. GoodwinSmall Grains Fungal Disease Laboratory
Karen HudsonSoybean Quality Improvement Laboratory
Brandon J. SchemerhornHessian Fly Resistance Laboratory
Steven R. ScofieldFunctional Genomics Laboratory
Richard H. ShukleWheat/Hessian fly Interactions Laboratory
Christie E. WilliamsHost Plant Resistance to Insects Laboratory

Last Modified: 8/13/2016
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