Nom du corpus

Corpus Systématique Végétale

Titre du document

Computer-supported gene bank management

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Éditeur
Springer (journals)
Langue(s) du document
Anglais
Type de document
Research-article
Nom du fichier dans la ressource
Syst_veg6_v2_007509
Auteur(s)
  • Stig Blixt
Affiliation(s)
  • Nordic Gene Bank for Agricultural and Horticultural Plants, Box 41, S - 230 53, Alnarp, Sweden
Résumé

Man's interest in plants goes back to times immemorable. The collecting of useful plants to improve the output from agriculture is likewise very ancient. A clear purpose to utilize became apparent at the end of the last century and a purpose to also preserve came withVavilov in the 1930-ies. Preservation became a pressing necessity as the agricultural development after the Second World War accelerated and this necessity became very apparent as the Mexican wheats were introduced, which resulted in systematic efforts to establish national and regional gene banks all over the world. It soon became clear that the establishment of gene banks among other things led to a massive accumulation of data which could not possibly be handled with traditional manual field book and recording systems. The computer was introduced to support the information handling. This lecture presents an overview of the major components to consider in designing a computerized gene bank management system. One consideration forwarded is that such a system should be utilizable not only on a recording and retrieval-level (R&R-level) but also used for analysis, producing new data for further interpretation (A-level). To ensure utility as well as safety aspects, a collection of genetic resources material could be preserved as different collections-alternatively as parts of one collection-for different purposes, Duplicate Base Collection for long-term safety, Base Collection for rejuvenation, Active Collection for multiplication and distribution, characterization, research, etc., the organization implemented to be reflected in the designing of databases. An attempt is made to discuss what material should come under the responsibility of gene banks for preservation. Arguments are given for excluding plant breeding material, plant introductions, commercial seed and ordinary agricultural products from the gene bank's responsibilities. It is further argued that the samples, accessions, preserved in the gene bank are vehicles for the genes, which are the units of variation, recombined and selected on. The justification for preserving an accession can therefore be expressed in terms of it being a vehicle for specific genes, geneblocks, chromosomes, genotypes or groups of genotypes. The preservation of genetic resources may be handledex situ orin situ, and an accession can be preserved in either way or by a combination of both, the most appropriate mode depending on what the accession is supposed to preserve, which again has to be considered in designing a management system. The information relating to the material to be stored and handled by a gene bank management system is often categorized, based on content and use, into passport, management and character data. An argument is put forward in favour of regarding gene and taxonomic data also as categories of their own, since the utilization of such data can become a powerful tool but will require specifically programmed software. The description of an accession in terms of genes using gene symbol descriptors is considered the superior method, to which taxonomic infraspecific classification offers a good substitute for species lacking detailed genetic information. Least preferable is to rely completely on unorganized character descriptors; it is pointed out, however, that carefully designed character descriptors in combination with competent observations for those descriptors would result in information needed to elaborate an infraspecific classification. Finally, some more important auxiliary databases used in a computerized gene bank management system are briefly mentioned, for instance code keys in general and such for genes and taxa in particular. Man's interest in plants in general and cultivated plants in particular goes back to times immemorable, for obvious reasons. Collecting of plants for purposes that we would to-day call plant breeding has probably also taken place for thousands of years though records of these activities are scarce. At the end of the 19th century, after the work of theVilmorin-brothers became known and plant breeding activities were attempted in different European countries, systematic and sometimes well recorded collecting activities were initiated. Land-races of most crops were collected and screened, selected upon and crossed with. After the rediscovery ofMendel's results the breeding work, having obtained a scientific basis, accelerated and in the two first decades of this century new cultivars appeared to replace, at an increasing rate, the old land-races. In this process, little attention was given to the material brought together-modern material was to replace the old and obsolete, and what became of the old and obsolete was of no great concern. A change in this attitude came in the 1930-ies withVavilov and his scientific contributions. Among other things he made clear that the old land-races were, in fact, a phylogenetic record to be interpreted and a valuable, adapted material for use in plant breeding. Systematic collecting activities to cover different geographic areas were again carried out but this time with the clear intention to save the material for the future; the collections then established are the first gene banks, though that name was not yet thought of. The gene bank concept was borne as a consequence of the realization that the post-war efforts to increase the per-capita agricultural production in the world had to include a massive input in plant breeding resulting in new varieties which would threat with extinction a large part of the hitherto cultivated material. The more general awareness was, however, slow in coming and several examples of emergency situations were encountered, for instance when the new Mexican wheats began to spread. It was only in 1974 that the Consultative Croup on International Agricultural Research (CGIAR) sponsored by FAO, the World Bank and United Nations Development Programme established the International Board for Plant Genetic Resources (IBPGR) to aid in the world-wide preservation of plant genetic resources. One of the means used by IBPGR became the support for establishing national and regional gene banks. Many gene banks with a history as what may be called Vavilovian seed collections had well established management systems, usually manual, while many newly established gene banks had no tradition, no system at all to fall back on, neither manual, nor computerized. In fact, a generally agreed, scientifically founded genetic resources concept, giving genetic resources preservation a scientific standing similar to e.g. ecology, has yet to be presented and implemented. This explains largely the present situation with respect to computer supported gene bank management systems. Despite efforts from different organizations to uniformize and coordinate the work, almost every gene bank that acquired computers and acquired or developed software started out by computerizing whatever manual system that was already in use or, where no system existed, were satisfied with piecemeal solutions to the most pressing problems, offered by available standard software packages. Within the framework of consultancies to IBPGR and to the Nordic Gene Bank and as a plant breeder having also since 1962 served as curator for a quite old collection with a since 1973 completely computerized management system, the author has had opportunity to give the problem considerable attention. The following presentation therefore contains elements of a gene bank management system which have been tested and implemented as well as such which have not yet but are considered essential for a system adequately meeting scientific as well as practical needs. Firstly must be emphasized that bringing in the computer as a tool in the gene bank management introduces an enormous new potential in processing data and handling information, not only quantitatively but also qualitatively. The computer can, of course, do nothing that can not be done manually and by using the brain, since the computer works with a software produced by man (leaving out for the time being the more extreme prophecies on Artificial Intelligence). In contemplating how to design a computerized gene bank management system it is very useful to think in terms of computerization on different levels: -The recording and retrieval level (R&R), at which the data and the processing are not used for creating new data, and -the analytical level (A), where data are used to create new data and new information to be interpreted. Most of the discussion going on to-day regarding computerization of gene bank management relates to the R&R-level at which advantages and gains are mainly of a practical nature, such as timesaving and better overview and insight. Most of the scientific advantages of the computerization are, however, to be had at the A-level. This, however, requires that the practical management of the material is so organized as to yield high level quality data with high level information content. Needless to say, costs and competence required are major factors to be considered. Competence is expensive, and particularly so in the field of computer software and this in itself can be enough to justify for the gene banks to develop inhouse computer competence. The decisive factor to strongly recommend the gene banks to have an own programming competence is really another, viz., that programming for the A-level and for an A-level prepared R&R-level requires a combination of biological specialized gene bank competence combined with the computer competence, since the A-level calls for biologically “intelligent” programs. The first considerations concern the organization of collections. In the long term, one has to achieve adequate longevity of the stored material, safety from losses by accidents, adequate quantities for distribution, efficiency in recording data and economy with funds and competence. At the same time the current situation needs to be considered, since changes in an existing gene bank management system necessarily have to be evolutionary rather than revolutionary. The following kinds of collections—or functions within one physical collection—are considered normally to be needed in a full-scale gene bank.

Catégories INIST
  • 1 - sciences appliquees, technologies et medecines
  • 2 - sciences biologiques et medicales
  • 3 - sciences biologiques fondamentales et appliquees. psychologie
Catégories Scopus
  • 1 - Life Sciences ; 2 - Agricultural and Biological Sciences ; 3 - Plant Science
  • 1 - Life Sciences ; 2 - Agricultural and Biological Sciences ; 3 - Agronomy and Crop Science
  • 1 - Life Sciences ; 2 - Biochemistry, Genetics and Molecular Biology ; 3 - Genetics
  • 1 - Life Sciences ; 2 - Agricultural and Biological Sciences ; 3 - Ecology, Evolution, Behavior and Systematics
Identifiant ISTEX
010865FCFE0CE63626E0F7E101CA998EC48F4E55
Revue

Die Kulturpflanze

Année de publication
1988
Présence de XML structuré
Non
Score qualité du texte
10
Version PDF
1.3
Type de publication
Journal
ark:/67375/1BB-0PKH2HDM-5
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