NP 301OSQR review2008 Ken Richards & Peter Bretting USDA Plant Germplasm Operations Committee meeting, Ft. Collins, CO June 2008
General Comments • About 30 NPGS-related Project Plans were reviewed by four different NP 301 review panels. In general, the overall quality of those Project Plans was improved as compared to the first review cycle. Here’s a rough summary of the review results, to date: • No revision: 5 • Minor revision: 16 • Moderate revision: 5 • Major revision: 3 • Infeasible: 0 • “Double-failure” (project re-formulation): 1
General Comments • As requested by customer/stakeholders, during the next 5 years the NPGS plans to expand collections, databases, taxonomic research, characterization, evaluation and molecular analytical efforts. • But, the review panels noted no obvious increases in resources or personnel available for that. Although operational efficiency can be enhanced, it cannot offset customer/stakeholder expectations for expanded service. • Consequently, strategic NPGS-wide analyses and identification of “unnecessary” or lower priority activities are warranted.
Priorities and Linkages • For sites that curate one or a few crops, setting priorities may be simpler than at other sites, such as the PI stations or some clonal sites which curate many crops. • Although there are efficiencies of scale associated with the preceding sites, how can curators and site managers set priorities effectively, and accomplish critical tasks?
Priorities and Linkages • In many cases, it was not clear how priorities were set, or if the crops assigned to sites were optimal from the standpoints of curatorial capacity, and biological/agronomic similarities. • Some crops (e.g., forage and annual clovers, other forage legumes, cucurbits), are split between several sites, and the degree of coordination among those sites is unclear. • Should large collections (i.e., 15,000 + samples) be assigned their own research project, so as to ensure they receive the necessary curatorial attention?
Priorities and Linkages • Setting priorities for hypothesis-driven research may be more challenging than for standard curatorial responsibilities (e.g., regeneration). • In some cases, the reviewers were impressed by the large volume of research proposed, but they were unconvinced that all of it would be accomplished. Nevertheless, aiming high is better than aiming low or missing altogether. • Many of the “service objectives” might have better been formulated as hypothesis-driven research, especially if a research manuscript was cited as the primary ultimate product.
Priorities and Linkages • The customers/stakeholders for some projects were not always clearly and effectively identified. CGCs were frequently mentioned, but their roles in the projects were not always specified, or were their precise names. • CGC input is important, and these committees must be active and effective. The roles, responsibilities and mandates of all CGCs might be reviewed periodically, retaining those which are functional, and terminating those which are ineffective.
Priorities and Linkages • Coordination and project linkages represent a continual challenge for a large, geographically diverse research program such as the NPGS. • The PGOC and more recently the biennial curators meetings serve as useful mechanisms to present, discuss and resolve issues and actions and to learn about new opportunities. • Some of the individual projects (e.g., the sub-tropical /tropical clonal crops projects) emphasize cross-project coordination more than did others. Among some other projects, there may be unnecessary duplication. There are opportunities for efficiency!
Priorities and Linkages • All active sites rely on the DBMU and the NCGRP at least to some degree, but sometimes the project plans did not contain detailed information regarding inter-project coordination among those sites. • Similarly, some research and service activities at the DBMU and the NCGRP depend on material and information from active sites.
Priorities and Linkages • The criteria for setting research priorities for developing in vitro or cryopreservation methods for clonal crops were often not clear, and perhaps worthy of a specific priority-setting workshop. • Many clonal crops require techniques for secure backup (cryopreservation, in vitro techniques, etc), and the lack of such is a bottleneck to progress. • Could graduate students from developing countries be placed at the NCGRP to assist with such research? This would also constitute benefit-sharing /capacity building for the developing countries and may facilitate germplasm acquisitions.
Priorities and Linkages • Currently, crop collections are still expanding, although presumably the rate of expansion has slowed. For some crops, relatively little diversity may remain to be acquired. • What will be the mechanism for switching emphasis from germplasm acquisition to adding value to the collection through more characterization / evaluation? Will this be determined crop by crop and will any protocols or priorities be established? • Staffing vacancies are noticeably affecting project progress at some sites. Hopefully, these positions will be filled soon.
Acquisition / Distribution • All NPGS projects plan to acquire new/priority germplasm. But the rationale/criteria as to how priority, strategic germplasm or specific gaps in collections were identified were consistently not clear and lacked detail. • Assignment of priorities for germplasm acquisition is particularly challenging for sites with large collections with many genera/species. How are such priorities set?
Acquisition/Distribution • Specific crops or species to be targeted for exchange were frequently unspecified, although explorations were described at the level of country to be visited. • PEO might be more proactive with assisting curators with acquisition, in some cases. • Consultation with relevant CGCs was not always cited. Crop vulnerability reports, which themselves may be out of date, were never mentioned.
Acquisition / Distribution • Moving high-priority germplasm through quarantine continues to be challenging because of the cost of quarantine for some crops, and lack of capacity at some quarantine sites. Reducing the requirements (resources, quota) for processing clonal crops through quarantine via acquiring seeds versus whole plants needs further evaluation and assessment. • The responsibilities (who, what, where, when) for acquiring heirloom germplasm from within the US were not clear. Collaborative arrangements with NGOs, Plant Material Centers and private industry may help with acquiring unique germplasm in some cases.
Acquisition/Distribution • Project plans rarely mentioned the FAO International Treaty on Plant Genetic Resources for Food and Agriculture or the Convention on Biological Diversity. • Even though the US has not yet ratified/signed these agreements, US agriculture and the NPGS are and will be affected by them and must comply with their terms and conditions including access and benefit sharing regimes. • Opportunities for facilitated germplasm acquisition and distribution and for creative access and benefit-sharing packages exist.
Acquisition/Distribution • An NPGS-wide policy on acquiring genetic stocks and mapping populations is needed. Previously they were not considered a priority for some crops, but now some sites are actively acquiring them. • They may be challenging to manage, so some NPGS-wide discussion is needed.
Acquisition/Distribution • Applying GIS technologies to identify gaps in collections, to understand the ecogeographic distribution of germplasm and to link these variables to observed genetic variation (using molecular techniques) might be emphasized. The technologies may help us to better understand why the variation exists.
Maintenance • Do genebanks have back-up electrical generators for cold storage rooms? • Many Project Plans for sites with “active collections” lacked milestones describing the amount of germination testing actually occurring. • Increased germination testing at active site may help the NCGRP develop management models and may also reduce the amount of testing at NCGRP.
Maintenance • De-accessioning: Relatively few Project Plans discussed this important topic in-depth. The criteria and priority for de-accessioning should be stated clearly, because this process may become increasingly prominent as molecular marker data accumulate, and the cost of maintaining materials rises. • When does it become worthwhile to devote substantial time and resources to identifying true duplicates, via passport data, phenotypes, and genetic markers? Is this more challenging for large collections? Is it worth the time/resources to identify true duplicates by genetic markers, if the accessions don’t cost much to maintain? • Some users (e.g., breeders) apparently do not mind receiving duplicate samples because they can easily identify and cull “identical” material.
Maintenance • Given other demands on resources, the lack of emphasis on in situ conservation may be understandable. Yet the NPGS has some expertise to help identify native plant species and perhaps in situ management sites. Unique (rare, threatened, endangered) native species (secondary or tertiary gene pool material) need conservation. Can cross-Agency collaboration help secure more resources for this purpose? • International assistance for determining or establishing in situ sites may be another form of access and benefit sharing for specific countries. North America is a centre of origin for some crop species, yet little to no effort is being made to conserve agriculturally important germplasm, except indirectly through national parks, state parks or other protected areas. Does the PEO have the resources and capacity to lead an “in situ initiative?”
Maintenance • Many clonal genebanks are seeking alternatives to duplicate local orchard plantings for backing-up their collections, e.g., via developing cryopreservation or in vitro maintenance in collaboration with the NCGRP or by establishing duplicate orchard plantings at other sites. • Research for developing techniques for conserving clonal crops from seed seemed lacking. Although this approach may not be feasible or biologically sound (recalcitrant versus orthodox seeds, genetic integrity issues) for some crops, it may be possible for other species or populations.
Regeneration • Some Project Plans state that one “trigger” for regeneration is when seed viability drops to or below 60%. But the international standard for regeneration is 85% viability (FAO 1995) because below this level some degree of genetic erosion is believed to occur. • Why is the 60% threshold level used? Is there any research that supports this lower level?
Regeneration • Few Project Plans mention regeneration capacity at Parlier or Palmer. The role of these sites should be better defined. Both sites may be isolated from some disease or pests, and the Palmer site may provide capacity for evaluating materials for cold hardiness. [Note: This is partially because the Parlier Project Plan was not reviewed with the rest of the plans, due to personnel vacancies.]
Characterization • All review panels commented on how the words characterize (“genotype”) and evaluate (“phenotype”) were used in the Project Plan objectives. They believed these terms were misleading and differed from common usage. • To the panels, characterization meant analyzing characters which are highly heritable, that can be seen easily by the eye (except molecular characters) and that are expressed in all environments (color and morphology). Evaluation referred to analyzing characters not as easily observed visually, such as pathogen or pest resistance or quality characters (oil or protein content, fiber content, fatty acid profile). The preceding terms must be applied consistently.
Characterization • Efforts to review and update descriptor lists with input for the relevant CGC were applauded, as was industry involvement in regeneration and characterization for some crops. • If germplasm users have input on determining descriptors, germplasm use will likely increase.
Characterization • Considering its global importance, it was striking that climate change was not mentioned in most Project Plans. Curators should assume a proactive role in preparing for this, via a longer-term strategy for the NPGS. Relevant germplasm should be acquired, new descriptor criteria (eg. resistance to drought, salinity, identification of stress tolerant genes) should be developed, and germplasm evaluated for those factors. • Gene bank managers must anticipate future requests for germplasm and have germplasm and relevant data available. Acquiring germplasm and appropriately evaluating it before users start requesting it will be challenging.
Characterization • Reviewers were enthusiastic about the increased emphasis on digital imaging, especially when images of different organs (seed, flower, roots, cross sections) are captured. The next step will be to apply new technologies to numerically scan the images and generate numerical data as well. • For some crops (beans, canola, sorghum, etc.), information about photoperiod sensitivity should be added to descriptor lists. • More core (or sub-core) subsets are needed for more crop species. Core subsets provide one rational mechanism for managing the genetic diversity within a collection.
Characterization with genetic markers • Since the last project review cycle, germplasm characterization with molecular genetic markers has increased substantially throughout the NPGS. Although genetic marker information provides new insights into intrinsic genetic variability, the analyses and application of genetic markers involve many challenges which were not adequately addressed in most Project Plans. • An NPGS-wide workshop to discuss these challenges would be valuable. It would address the optimal types of marker, strengths/weaknesses for specific purposes, the appropriate number of markers, etc. • For some crops, it may be more efficient to involve industry or university partners or to farm-out genetic marker analyses rather than to develop the expertise “in-house.” This approach may increase interaction, take advantage of their expertise, and increase utilization of collections.
Evaluation • Curators must be aware of germplasm users’ (especially breeders) needs for information required to register new cultivars. Agronomic and horticultural data are high priorities, but quality traits and disease-resistance data are also highly desired. • Curators must be well-aware of new diseases and respond quickly with evaluations for host-plant resistance. Some sites may not be devoting enough time/resources on evaluating germplasm for disease resistance or product quality, sometimes because a standard sets of differential lines (isolates) for certain pathogens are lacking.
Evaluation • “Highly heritable horticultural and morphological traits” were cited as priorities, but sometimes there was little evidence for how these traits will be determined. • It was not clear how germplasm would be evaluated for reclamation/re-vegetation needs, or how priorities would be established for testing viruses present in clonal germplasm.
Documentation • The reviewers were concerned about the current NPGS capacity to handle an increasingly large database management work-load (molecular data, international demands, and web-based query applications, etc.). [Reviewers were unaware of the GRIN-Global effort, because it began after the reviews.]
Documentation • The major effort to incorporate genetic marker data into GRIN, and the NPGS-wide genetic marker committee were encouraged, Incorporating the sometime massive quantities of genetic marker data managed in local site databases into GRIN will be challenging • Data management back-logs already exist and, with the new data being generated over the next five years, the capacity of GRIN staff and data management staff throughout the NPGS will be taxed. A user-friendly format would help sites load genetic marker data, but the potential for bottlenecks are evident.
Documentation • “GRIN taxonomy” is rapidly becoming the international standard for accuracy and completeness. “Botanical customer/stakeholders” may not be as well informed about GRIN taxonomy as are agriculturists. • Perhaps the visibility of GRIN taxonomy at universities, libraries, botanic gardens, etc., could be enhanced by providing dedicated (and perhaps less powerful) computers for their use or by advertising its existence through press releases or publications such as USDA/ARS Agriculture Research magazine.
Documentation • An increasing number of sites are developing and managing site-specific databases. What is the policy regarding this? This information is usually not internet accessible and may divert resources from incorporating data into GRIN. • Temporary holding files are needed for efficient collection management, but how much effort should be devoted to this? How can efficiency be increased and duplication decreased?
Documentation • How is information collected from germplasm users analyzed and disseminated? Where is the information collated and stored? Is it incorporated into GRIN and, if so, where? If only in “comment fields” these tend to be limited and are not easily searchable or data are not comparable among accessions. • Should there be a “special area” within GRIN for depositing this information and the source? How reliable is such information?
Documentation • Mechanisms for more timely input about user needs for GRIN would be desirable. The ad hoc genetic marker committee will be important. International input would be desirable. [Since the review, a Technical Steering Group has been formed for GRIN] • How are data loaded into GRIN? Apparently, some sites depend on the DBMU, but can the DBMU do so? Some larger sites have a dedicated IT specialist for this, but it may be a challenge for the smaller sites. Loading linkage map data may be particularly challenging.