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National Program 302: Plant Biological and Molecular Processes
Action Plan
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Action Plan: National Program 302 - Plant Biological and Molecular Processes

December 23, 2004


Goal: National Program (NP) 302, Plant Biological and Molecular Processes, supports fundamental research that creates a knowledge base and research tools that will contribute to greater crop productivity and efficiency, better product quality and safety, improved protection against pests and diseases, enhanced tolerance to abiotic stress, and sustainable practices that maintain or enhance environmental quality.  The rationale for NP 302 is that all plant traits (phenotypes) depend upon genes and gene networks that respond to their environment.


Plant breeding has a long history of improving crop plants for agriculture, usually without fundamental knowledge of how the underlying genes are controlled. However, modern tools of biology offer plant scientists ways to improve plants either by using existing variability in plant properties or by creating new variability when warranted. Knowledge of how biological mechanisms can be modified will provide new and potentially more effective approaches to improve crop plants. Thus, crop improvement will be accelerated and strengthened, as agricultural scientists understand the scientific principles that link molecular and genetic phenomena to phenotype.


Translating research at the molecular level into useful information for problem-solving demands an integrated approach in which the experimental design may range from knowledge development at the level of gene ensembles to yield testing in the field. This NP provides the means for the integration of research. NP 302 scientists will draw upon relevant expertise within NP 302 to coordinate and integrate the use of resources to develop focused strategies for solving specific problems. NP 302 scientists may also attract federal, university, industry and international partners. Objectives of NP 302 collaborative projects will be consistent with constituent ARS base projects and are expected to substantially enhance the impact of research outputs.


Relationship of This National Program to the ARS Strategic Plan: Outputs of NP 302 research support the “Actionable Strategies” associated with the performance measures shown below from the ARS Strategic Plan for 2003-2007, Objective 1.2:  Contributions to the Efficiency of Agricultural Production Systems


Performance Measure 1.2.5:  Provide producers with scientific information and technology that increases production efficiency, safeguards the environment, and reduces production risks and product losses.  Target: Technology will be developed that optimizes management practices for sustainable production with available soil microbial, mineral nutrient (including carbon and nitrogen), and water resources. Production systems and technologies that harness genetic potential will be developed to maximize profits and provide secure supply and market competitiveness. 


Performance Measure 1.2.6:  Improve understanding of the biological mechanisms that influence plant growth, product quality, and marketability to enhance the competitive advantage of agricultural commodities.  Target:  Information will be available to guide manipulation of regulatory metabolic processes that influence plant growth, product composition, product quality, and profitability.


Performance Measure 1.2.7:  Identify genes responsible for plant product quality and resistance to disease, pests, and weather losses.  Target:  A more complete understanding will be developed of the structure and function of genes responsible for quality, growth, and health of crops and how those individual genes are regulated in the context of gene systems or networks.


Component 1. Functional Utilization of Plant Genomes: Translating Plant Genomics into Crop Improvement 


In the past five years, DNA sequencing of model plant genomes such as Arabidopsis (dicot) and rice (monocot) has contributed to an exponential gain in information about plant genes and gene expression. These efforts have produced vast EST resources and extensive amounts of microarray-based transcript expression data. It is now possible not only to observe whole-genome patterns of gene expression in response to treatment variables, but also to differentiate genetic variation in those responses. New technologies for quantifying gene function through changes in mRNA, protein, and metabolites (transcriptomics, proteomics, metabolomics) create additional opportunities to understand how plants convert their genetic potential into form. Confirming the function of specific gene sequences enables advanced strategies for crop improvement that involve the modification of specific gene targets. However, to support useful applications, the information garnered through plant genomics must be reduced to practice in a timely manner.


Problem Statement 1A: Advancing From Model Plants to Crop Plants


Most genomic information is derived from model plants, such as Arabidopsis. However, the extent to which knowledge of model systems can be generalized to the complex genomes of crop plants depends on the degree of synteny or how closely plant species are related on an evolutionary scale. Thus, regulation of many important processes in crop plants often differs from those in model systems. This inadequacy limits the utility of model systems to resolve complex problems in agricultural crops. To remedy this dilemma, ARS research will explore gene-rich regions in important agricultural crops to advance genomics and alleviate the inherent limitations of model plant genomes.   


Research Needs


Knowledge of how important genes function in model plants will be extended to crop plants.  Methods useful in model species, such as gene disruption to identify function, will be modified or extended to systematically define the biological function of crop plant genes. 



·         Description of the function of agriculturally important genes in model plants and agronomic crops.

·         Verified knowledge of gene families or genetic networks that mediate or are associated with important traits in agronomic crops.


Anticipated Impact


Innovative research strategies will yield more comprehensive information about gene action in crops, enabling researchers to directly modify genetic processes governing or influencing crop productivity and quality.


Problem Statement 1B: Applying Genomics to Crop Improvement


Gene families or gene networks in crop plants often control complex traits, such as seed quality and vigor, flower color and scent, mineral nutrient use efficiency, and forage digestibility.  Knowledge of how these genes interact to influence gene expression in crops is essential to understand inheritance and regulation of traits.  Without this knowledge, inheritance of such traits is hard to predict, and assembling the required genes in an improved genotype is difficult.  ARS research will analyze, interpret and use the voluminous increase in crop genomic resources to characterize gene networks governing fundamental processes in crops and identify opportunities for crop improvement.   


Research Needs


Transcript and protein expression profiles associated with genetic variation in complex traits will be determined to identify genes that control phenotypic expression. DNA sequence differences (polymorphisms) associated with variants of complex traits will be identified to enable mapping, inheritance studies, and eventual manipulation of valuable traits. Multiple sets of information within and across species and environments will be “mined” to relate gene action to plant phenotype and productivity. Quantifying gene action and crop biological processes that contribute to productivity will require application of new algorithms and computational tools for data analysis and integration.




·                     Identification of specific genes that mediate end-product traits desired by consumers, such as nutritional content, oil and grain quality, and disease resistance and abiotic stress tolerance in agricultural crops.

·                     Voluminous expansion of genomic information on the function and regulation of gene systems that govern the expression of important traits in agricultural crops. 

·                     Expanded macro-array and micro-array capabilities to visualize functional changes in gene expression during the development of agronomic crops species.

·                     Proteomic technologies to extend genomic understanding to the level of gene products.


Anticipated Impact


·                     Gene discovery will provide new sources of enhanced crop traits for incorporation into breeding programs.

·                     New genetic strategies resulting from expanded genomic knowledge will accelerate the enhancement of crop productivity and the exploitation of nutritional and healthful properties of foods.



The following ARS locations have research projects that are coded to contribute to National Program 302 identified under Component I.  ARS scientists who are assigned to these projects include:

Albany, CA     

Fletcher, Jennifer C.; Hake, Sarah C.; McCormick, Sheila M.

Ames, IA

Wise, Roger P.


Columbia, MO

Flint-Garcia, S; Herman, E.; McMullen, Michael D.; Oliver, Mel;  Shaefer, M.


Ithaca, NY        

Giovannoni, James J.; Kochian, Leon; Li, Li, Thannhauser, Theo; Yang, Yong


 West Lafayette, IN  Hudson, Karen; Dunkle, Larry

Component 2.  Biological Processes that Improve Crop Productivity and Quality


Crop productivity is determined by a plant's capacity to convert energy, nutrients, and water into harvestable yield of high quality and high value. Thus, ample supply of harvestable products is a function of a plant’s genetic potential to capture energy, and use available water and nutrients. The molecular and biochemical factors that actuate regulatory mechanisms are poorly understood for fundamental biological processes that underpin crop plant productivity and the production of high-value end-products.  A highly coordinated integration of research is needed to develop knowledge of how biological processes may be regulated to overcome factors that limit crop yield and quality in a manner that reduces costly inputs, expands area suitable for production, and protects the environment.


Problem Statement 2A: Understanding Growth and Development 


Biological processes that regulate crop plant growth and development include photosynthesis (conversion of sunlight energy to chemical energy); initiation and growth of reproductive tissues; root and shoot growth; transport of metabolic assimilates from leaves to and among plant organs; seed development and maturation. These processes often are inefficient or poorly adapted to agricultural growing conditions that may seriously restrict productivity and crop quality. ARS research will develop a better understanding of the fundamental principles governing these processes and findings will be applied to improve crop quality, increase product value, and achieve more sustainable production systems.


Research Needs


Knowledge of the processes that regulate growth and development is necessary to develop effective strategies for enhanced crop productivity under variable growing conditions. Hormonal signals that trigger important developmental changes, and the genes that control the signaling pathways will be identified. The potential of gene modification to beneficially influence the performance of biological processes will be assessed for ability to enhance crop quality and production efficiency. 



  • Improved knowledge of how genes and gene networks that mediate crop development and productivity are regulated.
  • Improved knowledge of how metabolic processes that mediate crop quality and productivity of agricultural commodities are regulated.
  • Technology to enhance flavor, nutritional value, or other quality traits of plant products.


Anticipated Impact


·                     Ability to regulate fundamental biological mechanisms will enable technologies that beneficially alter processes such as photosynthesis, cellulose and lignin accumulation, carbohydrate partitioning to harvested organs, and fruit ripening. 

·                     Improved efficiency of nutrient assimilation and metabolism will support higher crop productivity and nutritional value.



Problem Statement 2B: Understanding Plant Interactions with Their Environment


Abiotic and biotic stresses during a growing season can significantly limit agronomic crop yield and alter the population dynamics of plant species. Natural plant defense mechanisms often provide only limited protection, and the process of how crops adapt to unfavorable growth environments is poorly understood.  ARS research will establish knowledge of how gene networks for fundamental biological processes perceive and translate ‘signals’ in response to environmental stimuli. Innovations governing fundamental processes that influence crop performance will be incorporated into useful crop protection strategies. 


Research Needs


Genes important to crop adaptation, tolerance and defense will be identified. The capacity these genes confer on crops to withstand stress or attack will be determined. How crop plants and the organisms that affect them “recognize” and respond to each other will be assessed. Critical sites for intervention will be distinguished by disrupting interactions between organisms.  




  • DNA markers for genes that confer resistance or tolerance to abiotic and biotic stresses.
  • Discovery of genes that govern processes involved in plant adaptation and response to environmental stimuli.
  • Knowledge of biological mechanisms and regulatory processes that condition crop response to abiotic and biotic stresses. 
  • Discovery of genes that condition biological processes associated with crop plant interactions with weeds, fungi, and bacteria.

Anticipated Impact


  • Knowledge of the basis for crop - environment interaction will lead to enhanced stress tolerance and enhanced ability to maintain productivity in unfavorable growth environments.
  • Breeding for pest and pathogen resistance will be more effective as a result of identifying and characterizing new sources of resistance. 

Problem Statement 2C: Developing High-Value Products


Plants are increasingly being recognized as sources of compounds that have important roles in nutrition, medicine, or industrial products. Frequently, new phytochemicals are produced as organisms interact with each other, but many materials of interest are produced without external stimulus. ARS research on natural products will help develop new high-value feedstocks for biobased products and pharmaceuticals. 


Research Needs


New sources of novel phytochemicals will be identified.  Constituent compounds will be isolated and characterized for appropriate chemical and biological activities.  This information will be related to the biosynthetic pathways, genes that control those pathways and the development of probes to enable rapid screening of plants for new sources of high-value compounds.



  • Tools and methods to identify specific genes that mediate secondary end-product traits desired by consumers, such as nutritional and pharmaceutical compounds. 
  • Identification and characterization of functional compounds and components in agricultural commodities and their byproducts that provide the basis for enhanced crop value.  New sources of valuable bioactive compounds and potential sources for commercialization identified.

Anticipated Impact


Natural products will embody valuable biological, nutritional, pharmacological, or other beneficial materials including domestic source of feedstocks for biobased products. 




The following ARS locations have research projects that are coded to contribute to National Program 302 identified under Component II.  ARS scientists who are assigned to these projects include:


Albany, CA

Altenbach, Susan; Blechl, Ann E.; Hurkman, William J.; Theologis, Athanasios; Vensel, William; Whalen, Maureen


Beltsville, MD

Cooper, Bret; Ehlenfeldt, Mark; Rowland, Lisa.; Kuykendall, Larry; Matthews, Benjamin F.; Mattoo, Autar K.; Slovin, Janet P.; Smigocki, Anna C.; Tucker, Mark L.


Columbia, MO

Beuselinck, Paul R.; Bilyeu, Kristen; Herman, Eliot; Krishnan, Hari B.; Miernyk, Jan A.


Corvallis, OR

 Scagel, Carolyn F.; Schreiner, Roger


Dawson, GA

Rowland, Diane; Sobolev, Victor, Lamb, Marshall C.; Dang, Phat


Fargo, ND

Dahleen, Lynn S.; Klotz, Karen L.


Gainesville, FL

Chourey, Prem S.; Teal, Peter



Hilo, HI


Gonsalves, Dennis; Albert, Henrik

Ithaca, NY

Kochian, Leon V.; Gioavnnoni, James


Kearneysville, WV

Artlip, Tim; Bassett, Carole L.; Norelli, John; Wisniewski, Michael


Lubbock, TX

Burke, John J.; Chen, Junping; Mahan, James; McMichael, Bobbie; Payton, Paxton; Velten, Jeffrey; Xin, Zhanguo


Madison, WI

Henson, Cynthia A.; Skadsen, Ronald W.; Wise, Mitchell

New Orleans, LA

Lingle, Sarah E.; Triplett, Barbara A.


Phoenix, AR

Salvucci, Michael


Raleigh, NC

Burton, Joseph W.; Carter, Tommy; Israel, Daniel W.; Kwanyuen, Prachuab; Taliercio, Earl;  Upchurch, Robert


St. Paul, MN

Vance, Carroll


Oxford University, MS

Baerson, Scott; Dayan, Franck E.; Duke, Stephen O.; Pan, Zhioang


Urbana, IL

Huber, Steven; Ort, Donald R.; Ainsworth, Elizabeth


 Washington, DC

 Kamo, Kathy; Hammond, John


 West Lafayett, IN


Component 3.  Plant Biotechnology Risk Assessment


Genetic engineering offers tremendous promise for improving crop production and protection, making production systems more efficient and sustainable, and providing high-value and high-quality products needed by the world’s burgeoning population of consumers. These products can range from foods with enhanced nutrients to biomedical reagents. However, the science of recombinant DNA, both creating the genetically engineered plants and evaluating their impact is in an early stage. Methods used for genetic engineering need to be improved, and the principles that determine the risks of transgenic plants in the environment need to be better elucidated. Research that integrates product development with risk assessment is needed to develop data that will help guide regulatory decisions on management of transgenic crops in a manner that builds public confidence in the safety of products derived from biotechnology.


Problem Statement 3A: Improving and Assessing Genetic Engineering Technology


The utility of plant transformation protocols often is limited by low recovery of transformed cells, unpredictable expression of transgenes, inability to control transgene expression, residues of unneeded selectable marker-genes, and limited ability to introduce multiple genes.  ARS research will characterize the genetic changes that accompany transformation, determine the mechanisms that alter gene expression and metabolic processes, and elucidate the biological consequences of those alterations. 


Research Needs


Methods will be developed that reliably and reproducibly insert single copy genes into a host genome, that limit gene expression, and that remove transgenes from harvested materials once their usefulness is over. Methods will be developed for “pyramiding” multiple genes so that multigenic traits can become feasible targets for transfer. Baseline data will be collected on the changes in global gene expression patterns when plants undergo through a vegetative or sexual reproductive process, for comparison to changes that accompany recombinant DNA manipulation. The deviation of global gene expression patterns from normal will be correlated with plant performance, so that unacceptable levels of variability can be defined. 




·         Improved gene constructs and plant genetic transformation systems that efficiently incorporate genes and enable their stable expression, and that allow expression of multiple genes and limit expression to specified tissues.

·         New processes placed in the public domain to the extent possible, promoting public access to them. 

·         Data that define genetic and epigenetic effects of transformation and comparison of those effects to similar effects of natural reproductive processes, so that thresholds of acceptability can be identified.


Anticipated Impact


·         Accomplishments will establish a basis for interpreting variability in global gene and protein expression, as well as shifts in metabolism associated with biotechnologically derived traits.

·         New procedures will expand the scope and reduce the cost of genetic engineering, potentially making it more useful for a wider array of crops.


Problem Statement 3B: Interaction of Transgenic Plants with Their Environment


Unbiased and rigorous information is needed to guide regulatory agencies that oversee the deployment of transgenic crops. The possibility of unintended ecological effects of transgenes needs to be maintained as low as possible, using the likelihood of effects from non-transgenic crops as a benchmark for comparison.  These include such concerns as deleterious effects from the introgression of transgenes, effects of plant-incorporated protectants, or induced weediness or invasiveness. ARS research will focus on ways to accomplish appropriate recommendations of the National Research Council for biological confinement of transgenic material. 


Research Needs


The evaluation of gene flow from transgenic crops needs to be accompanied by analysis of the ecological effects and the persistence of those genes. Methods will be developed to eliminate transgenes from pollen or, like male sterility, otherwise prevent transgenes from being transmitted during reproduction. The molecular basis of pollen-stigma compatibility will be characterized, so that pollen from transgenic plants can be made incompatible with potential female receptors. 




·         Greater knowledge and technology to remove transgenic DNA from pollen, or other approaches likely to help contain transgene flow in the field and control gene spread.  Ability to characterize the nature and likelihood of persistent changes in ecosystems as a result of introducing new transgenic plants, in support of science-based regulation of transgenic crops. 


Anticipated Impact


·         New technology will be advanced that will reduce or eliminate the movement of transgenes from transgenic crops to areas where they are unwanted.

·         Data will help determine whether transgenic crops pose environmental risks.  These data will provide a scientific basis for regulatory consideration of transgenics.




The following ARS locations have research projects that are coded to contribute to National Program 302 identified under Component I.  ARS scientists who are assigned to these projects include:


Albany, CA

Blechl, Ann E.; Ow, David W.; Thilmony, Roger; Thomson, James


Beltsville, MD

Lewers, Kim; Natarajan, Savithiry; Polashock, James


Ithaca, NY

Hokenga, O.; Li, Li


Madison, WI

Brunet, Johanne; Simon, Philipp W.






Last Modified: 4/15/2009
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