Stock Acquisition and Deaquisition Policy
- General Considerations for All Donations
- Acquisition of Stocks
- Requirements Regarding Form and Quantity of Seed and DNA Donations
- Deacquisition of Stocks
General Considerations for All Donations
Guidelines regarding suitability of stock for inclusion in the collection are provided below. For seed and DNA stocks meeting these guidelines, ABRC will accept the stocks in quantities large enough for preservation of the stock and distribution to researchers provided in containers suitable for permanent storage. If a donor is unable to provide the stock(s) in the needed quantity and form, it is possible for the stock(s) to be processed for distribution at ABRC, and the donor should contact us regarding the circumstances. The quantities and form appropriate for donation for different types of stocks are outlined in section II.C. below. Based on this, budgeting of costs can be made for materials and labor associated with preparation of donation quantities and packaging of the donation. Also note, as outlined below, the schedule and timing of donations should be coordinated with the Center.
Acquisition of Stocks
The ABRC accepts seed stocks that are unique and which either are likely to be useful to researchers and/or possess genetic attributes which should be preserved. Arabidopsis seeds of the following general categories are collected: 1) mutants, 2) ecotypes, 3) mapping lines and populations, 4) T-DNA lines, 5) transposon lines, 6) transgenic lines, 7) chromosomal variants, 8) background and reference lines and 9) related species. Stock acquisition goals are set by the ABRC Advisory Committee. The above basic criteria for suitability of stocks translate to somewhat different specific consideration for each class of stocks as follows:
- Mutants: New mutants should be for a locus not in the collection, or a allele of a locus which has effects differing from existing stocks; or a double or multiple mutant line of an already collected loci is desirable if the phenotypic effect of the double mutant is unique. It is preferable that mutant stocks be described in a refereed publication. Unpublished mutants judged to have high interest to the user community will be accepted. It is also preferable that mutants be mapped, as is the case for publications of mutants. Exceptions can be made.
- Ecotypes: Since it is difficult to judge the potential value of natural variants, the acquisition criteria are general and non-restrictive. A naturally collected strain of Arabidopsis thaliana will be accepted if it is not a duplicate of an existing member of the collection. Ecotypes having published characteristics will be sought and given priority for reproduction and distribution. Strains collected as part of a systematic study/collection expedition, so that they represent part of an organized group, will also be given priority over random single strains.
- Mapping lines and mapping populations: Mapping lines not duplicating others will be accepted. Mapping populations will be assessed individually. The criterion for acceptance will be that it appears to be useful to users. The Advisory Committee will be consulted, as necessary.
- T-DNA lines, sets of transposon lines and transposon tagging stocks: It has been the goal of the Center to make available genome-saturating collections of insertional lines and to include a variety of construct expression types in this collection. We plan to acquire such stock for the near term until this goal is reached and to the extent that we can grow and distribute this material. The Advisory Committee is consulted annually on policy toward such stocks. Stocks for transposon experiments, such as mapped Ds lines, etc., are sought as long as they do not duplicate other such stocks. Specific criteria for judgement are uniqueness and usefulness of construct and need for transposon lines having a specific map position.
- Related species: Several genera are closely related to A. thaliana. Lines of such species are accepted if they do not duplicate collections maintained elsewhere.
- Background and reference lines: Ecotypes, mutant or transgenic stocks often are used as references/controls in publications. Such stocks are collected by the Center, since obtainment of these is essential for reproduction of published results and often for extension of published research. Hence, new lines of this type are accepted.
- Transgenic stocks, chromosomal variants and other stocks: Stocks of these types, which have unique genetic/phenotypic characteristics, or serve as reference stock, or have special potential uses to the user community are accepted.
The criteria of usefulness to the community and our ability to accommodate the stocks have been employed for DNA stock acquisitions. With the increasing efforts being concentrated on genomics, the DNA acquisition sought and acquired reflect this trend. General acquisition requirements for DNA are as follows: 1) DNA must be characterized in some way so that it has some potential interest to the Arabidopsis community, 2) DNA should be free of contamination from other DNA sources and 3) it should be provided in a stable form so that decomposition does not occur during storage. Attributes affecting acquisition decisions for specific classes of stocks are as follows:
- Individual clones: Clones should represent a cloned sequence of a gene or cDNA not yet in the collection, or a clone of a unique allele, or be useful for physical or genetic mapping, or be of special use for Arabidopsis researchers. It is preferable that new clone acquisitions be described in a publication; exceptions are made for stocks of special interest.
- Clone collections and libraries: Criteria for accepting such stocks are uniqueness relative to existing stocks, usefulness to researchers and potential impact on the work load of the Center's personnel. In general, all acquisitions of large collections are reviewed with the Advisory Committee.
- DNA isolated from T-DNA lines, etc., for PCR screening: The principles of usage and preparation time will govern acquisition of these stocks. These stocks are discussed in the T-DNA seed acquisition section.
Requirements Regarding Form and Quantity of Donations
Seed Stock Donations
- Mutants, ecotypes and most single lines: For most seed stocks maintained as single lines, a total of at least 20,000 seeds (= 800 microliters = 400 mg) is required for preservation, to provide a moderate number of distributions and provision of seeds to NASC. While distribution can be initiated with fewer seeds for stocks for which high demand is not anticipated, 20,000 seeds are usually needed. These quantities are also considered sufficient for lines maintained as heterozygous, assuming that such lines are donated as F2-equivalent populations so that one-fourth of seeds are expected to be homozygous mutants.
- Complex stocks such as T-DNA pools, etc.: The seeds per sample to be distributed is calculated so that the probability of finding a homozygote of any particular line is at least 0.95. Hence for pools of 10 T-DNA lines, we distribute 125 seeds per pool, and 1250 seeds are sent for pools of 100 T-DNA lines. If such lines are expected to have high demand, as is often the case, the seed quantities required for robust distribution are substantial. For high-demand pools of 10 lines, approximately 5 milliliters of seeds per pool are required, and 15 milliliters per pool of each pool of 100 lines are needed. Note that the quantity mentioned for pools of 10 is calculated so that re-pooling to generate pools of 100 can be achieved with the mentioned quantity. Given these donation quantities, ABRC would not have to conduct seed increases to distribute the pools.
Any donors wishing to provide such stocks in lesser quantities are urged to contact us well in advance, as the space required for seed increase of such pools is substantial.
- Number of stocks in the donation: If the number of stocks to be donated exceeds 100, donors are requested to contact the Center six months in advance of the anticipated donation date to coordinate receipt and any participation of ABRC in increase of the stocks.
- Donation/release schedule: Included in the initial communications with potential donors will be establishment of suitability of the stocks for donation and determination of the arrangements for seed increase, release schedule for distribution, etc. Coordination of efforts between ABRC and donors is vital, as is the development of a schedule for delivery and eventual stock distribution.
- Costs to donor developing seed donations: In the case where preservation/distribution quantities of seed are provided, the costs to donors associated with producing these quantities need to be budgeted. These may vary depending on individual circumstances, so researchers should develop their own estimates for these costs. As a guide, production of distribution-quantities of single lines requires at least one 10-cm pot per line. Seed production for pools of 10 lines typically need to be conducted in 20 x 40 cm flats, and pools of 100 require two such flats.
Seed donations should be provided in standard, ring-sealed cryovials of a size appropriate for the quantity of seeds provided. Seeds received in any other type of container will require transfer to such vials at the Center, which involves substantial time when the number of donated stocks is large. Hence, funds should be budgeted for cryovials and 100-tube storage racks when large quantities of stocks are to be donated.
Quality of donated seeds: Seeds donated should have germination rate greater than 90%, be dried to less than 6% seed moisture content and be free of debris, including chaff from the siliques. Guidelines and procedures for achieving these conditions can be obtained from the Center.
DNA stock donations
- Individual Clones: Individual clones should be donated in the form of duplicate glycerol stocks in cryovials and a sample of isolated DNA. If there is intention to provide stocks in any other form, please contact the Center regarding suitability.
- Collective stocks, including clone collections and libraries: Please contact the Center before determining the form in which these stocks will be donated. The preferred form depends on the exact nature of the stock and its expected level of distribution. For arrayed clones such as BAC libraries, etc., acceptable forms may include duplicate glycerol stocks in microtiter plates or duplicate glycerol stocks in individual cryovials. The most suitable form for donations should be determined in conjunction with the Center prior to donation.
- Cost to donors of preparing donations: As mentioned, the DNA donations are expected to be received in a form suitable for donation and distribution. Costs of vials and boxes for storing vials should be budgeted by the donor.
Material Transfer Agreements and Stock Acquisition
It is current ABRC policy not to accept stocks which for which MTAs are associated, unless the MTA is specifically approved by the Advisory Committee. It is not likely that new stocks will be accepted for which an MTA isrequired.
Deacquisition of Stocks
Arabidopsis seed and many DNA stocks are long-lived and can be stored relatively cheaply. Seeds can be stored for decades in standard freezers, and isolated DNA may last even longer under similar conditions. For any stock of these types, the possibility exists to maintain a stock but forgo distribution. Thus discarding of such stocks should not be necessary. Some DNA stocks, such as YAC libraries, are labor intensive to maintain. Policies regarding continued maintenance of such items must be different
For the great majority of ABRC seed stocks, currently large (ca. 1 ml) quantities of high viability seeds are in cold storage and should meet preservation and distribution demands for many years. It would not seem reasonable to discard these seeds for any reason. If some stocks lose viability, the choices for propagation are similar to those for acquisition.
Many DNA stocks are maintained as or can be converted to isolated DNA. All cloned genes in plasmids are maintained in this fashion. For any such cases, the choices regarding maintenance and distribution are similar to those for seeds. In other words, it is not anticipated that discard of such stocks would be considered, although the distribution could be curtailed.
Regarding DNA stocks with high maintenance costs, choice of maintenance versus discard might become necessary. In this case, an assessment of the exact size of collection that could be maintained would have to be made, and the size of the collection adjusted accordingly. In general, it should be assumed that these stocks would be maintained if they are currently or forseeably useful for any significant segment of users. Also, discard of high-storage-cost stocks could be considered at any time that the stocks clearly become obsolete. Obsolescence is here defined as a stock(s) being completely redundant with newer stocks that are easier to handle and/or are more useful. Any deacquisition is conducted under advice of the Advisory Committee, a thorough, formal review by Center personnel and notification of the user community (e.g., via the newsgroup). Finally, no stocks would be discarded if they could be transferred to an individual willing to maintain them in a fashion consistent with NSF resource philosophy.