Background and scope

Дата канвертавання25.04.2016
Памер13.11 Kb.
The Populus Genome Science Plan

Panel on Genetic Resources

Panel Members: John Davis, Joerg Bohlmann, Stefan Jansson, Les Pearson, Wan Song,

Barb Thomas, Chung-Jui Tsai, and Marc Villar

A major challenge faced by any scientific research community is to efficiently archive and distribute shared resources. The IPGC encourages active distribution of shared genetic resources in order to minimize unnecessary duplication of effort among research groups, thus maximizing the rate at which new discoveries in Populus biology are made.
Herein we define genetic resources broadly to include: information (e.g., genome sequence, EST sequences, genetic maps, physical maps), cloned DNA (e.g., EST collections, large-insert libraries), other molecular reagents (e.g., gene expression arrays, DNA from mapping populations), and germplasm (e.g., naturally occurring or conventionally bred genotypes, transgenic plant material generated through functional genomics experiments).

Physical Resources
Financial Resources


The scientific objectives being put forth here will collectively lead the Populus community to develop a shared capacity and resource development related with the following areas:

  1. Development and/or preservation of germplasm, mutant collections, virtual stock centers, pedigrees, cryopreserved stocks, & in situ populations and

  1. Repository and/or distribution of BAC libraries, EST libraries, KO/KI & gene trapping resources, etc.

Bioinformatics. The IPGC places high priority on establishing and/or partnering to establish a relational database for Populus molecular genetics that can be supported on a long-term basis. All activities related to the archival and distribution of shared genetic resources must be underpinned by a high quality, robust relational database with a public web browser interface. The database creates a forum for information exchange among community members, and serves as a nucleation point for supporting other community resources including stock centers.

DNA stocks (cDNA and genomic) and other molecular reagents. The IPGC aims to establish two Populus Biological Resource Centers, operated as parallel collections that closely coordinate the collection, maintenance and distribution of DNA stock resources and related molecular reagents. The rationale for centralization is to ensure consistency in material deposition, handling, distribution, and quality. As a general rule, it is expected that one Center will provide services to North America and one Center will provide services to the rest of the world. The primary function of these Centers is to acquire, preserve and distribute DNA stocks and molecular reagents for use by the research community. It is anticipated that these Centers may distribute stocks on a cost-recovery basis. It is also anticipated that at least one, or perhaps both Centers would be housed at institutions where DNA stock resources of other species are collected, maintained and distributed. In other words, the IPGC recognizes the economy of scale that can be accomplished if the Populus community can establish partnerships with existing stock centers, or planned centers that are designed to accommodate multiple species.

Germplasm. The IPGC supports a partially centralized approach to archiving and distributing germplasm, due to practical difficulties in centralizing all Populus germplasm resources. In contrast to Arabidopsis and most annual crop plants, which are propagated and distributed as seed representing accessions, cultivars or wild relatives, Populus germplasm is usually propagated and distributed in the form of dormant stem cuttings. Stem cuttings are placed in soil by the recipient, after which adventitious roots and pre-formed shoots grow and establish a new plant body that is the same genotype as (i.e., a clone of) the donor plant. Propagation of genotypes by stem cuttings requires a good deal more space and effort than seed (which can be stored dry and in small containers). Usually genotypes of interest are maintained in field plots. Selected genotypes are sometimes naturally occurring genotypes from wild stands, although progeny sets from controlled, usually interspecific, hybridizations are often quite valuable resources for the community. Increasingly, transgenic materials are being produced that are valuable resources. The transcontinental range of several Populus species, and the transglobal range of the genus, creates practical difficulties in centralizing germplasm archival and distribution. Not all species and hybrids will survive and grow in a single location. Consequently it seems appropriate to distribute germplasm across a series of field plots around the world. Of course, over the long term, field sites are notoriously lost due to harvest, land sale, etc., and it is difficult to predict with any degree of certainty which sites would be most "stable" for archiving and distributing germplasm. Ownership category options to consider might be university, government, industry or even private lands.
The IPGC recommends that a common registry of germplasm be established that would provide the community with a roster of available Populus material that is available for research. This registry would give the community notice of trial or plantation termination, thereby allowing others to obtain cuttings to continue specific lines. Furthermore, the IPGC recognizes the benefits of rapid and easy exchange of germplasm for research purposes. To this end, the IPGC encourages the development of blanket materials transfer agreement that is acceptable to all parties involved in Populus research. This agreement could be used routinely to document the current sites at which specific genotypes are being used for research, and to accelerate the transfer of scientifically useful germplasm among university, government, and industry research teams.
The IPGC encourages the development of cryogenic storage methods for archiving and distributing germplasm. Cryo methods hold promise for reducing the space and labor requirements associated with maintaining field plantings. Cryo methods as applied to Populus would involve freezing shoot tips after treatment with osmoprotectant compounds. Subsequent revival of the shoot requires some tissue culture steps, however when the methods are well defined for a plant species, they are relatively simple to perform. A centralized location for developing cryogenic storage and regeneration protocols for Populus, material deposition, cryostorage and distribution would be desirable, with potentially several other "inactive" storage facilities elsewhere.

The Populus community is not unique in its need to establish some centralized entities to allow sharing of genetic resources. In particular, archival and distribution of DNA resources could best follow the centralized model adopted by many communities including Arabidopsis. To be successful these Centers should be underpinned by an excellent and robust relational database, and opportunities for partnerships with other communities of researchers should be pursued in order to reduce costs. The Populus community is somewhat unique in the challenges of sharing germplasm, since the germplasm is propagated vegetatively. A common registry and transfer agreement should help facilitate sharing, albeit in a decentralized way. Finally, the development of cryostorage methods is encouraged in order to reduce the overall costs, and increase the overall efficiency of germplasm archival and distribution.

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