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Development, optimization and validation of molecular techniques for the measurement, characterization, evaluation and accessing of biodiversity


A proposal is presented here to combine the work described in three complimentary projects, independently submitted to area 7.4 of the BIOTECHNOLOGY programme, into one coordinated programme. The three projects referred to are: (1) Project P, Coordinated by A. Karp, and submitted as the main part of this application (Title: Development, Optimization and Validation of Molecular Techniques for the Measurement, Characterization, Evaluation and Accessing of Biodiversity); (2) Project F, coordinated by F. Scholz, submitted separately (Title: Development, Optimization and Validation of molecular tools for assessment of biodiversity in forest trees); (3) Project A, coordinated by G. Hewitt, submitted separately (Title: Development, Optimization and Validation of Molecular Techniques for the Measurement of Genetic Diversity in Domestic Ungulates).
Incentive for this proposal of a combined project is partly borne from previous experience in the FPIII programme, where the integration of four independently approved projects into one generic programme was extremely successful. Outputs from the generic FPIII project include: a quarterly newsletter (Molecular Screening News) with a current international circulation of currently 135; a practical training course; a complete manual of protocols and case studies (to be published by Chapman and Hall Ltd. UK ) the establishment of an extended audience (the Biotechnology for Biodiversity Platform). The combining of the three proposals above would enable these successful activities to continue.
The added benefits of supra-integration of the three above proposals into one project are: 1. The integration of plant and animal research activities provides an unique partnership, enabling the participants investigating plant species to benefit from the technological developments which are often in advance in animal systems, whilst at the same time, enabling the participants investigating animal species to benefit from the broader scope of the plant projects and the wider range of techniques being compared.
2. The integration of the three projects increases the scientific scope of the programme by coalescing groups working on forest tree species, botanic garden species, crop plants, farm animals and wild relatives. This confluence is important for the development and optimization of techniques with the widest range of applications possible. It is pertinent to recognise here that the targets for biotechnology in the area of biodiversity are very diverse, as is made evident when the range of possible end-users is considered (eg, breeders, seed companies, variety testing organizations, gene banks, conservation agencies, agricultural advisory agencies, seed orchards, forestry managers, zoos and botanic gardens). As a result of the proposed integration, technologies will be developed with application to the broadest range of end-uses in biodiversity.
3. The profile of the project, and the perception of biotechnology's role in conservation of biodiversity, gains strength from the involvement of different european partners and the implementation of pan-european coordinated actions. A larger integrated programme, relating to forestry, plant and animal agriculture and natural bio-diversity in plants and animals, will achieve greater impact than might be achieved by any of these areas separately. 4. The sub-project proposals have shared objectives, although the species studied are different. Integration of efforts will ensure that maximum benefits are gained from the developments in any one area and will eliminate any unnecessary duplication of effortó.
Advances in DNA sequencing, data analysis and PCR have resulted in powerful techniques which can be used for the screening, characterization and evaluation of genetic diversity. Nevertheless, there are still problems to be addressed before the full potential of these techniques, and their effective transfer to potential end-users, can be realised. The difficulties faced relate to both the variety of molecular tools available (and the different ways they assess diversity) and to the diversity of end- users. The objectives of this proposal are, firstly, to develop further, and optimise, those technologies identified by previous work (FPIII) to be most applicable for wide-scale diversity screening (AFLPs, nuclear and organellar sequence PCR analysis and microsatellites\SSRs) and, secondly, to validate the use of molecular tools by testing their application in a selection of diversity problems relating to different end-users. The end-users represented are: (A) Botanic gardens; (B) Gene banks and (C) Plant Breeding Companies.
The first objective is pursued in part 1 where efforts of the participating laboratories are aimed at (1) Development of universal tools, involving (a)identification of SSRs with different map locations and transferability across species; (b) identification of conserved single copy nuclear (scn) and organellar (sco) sequences polymorphic below the species level; (c) development of universal AFLP primers; (2) Optimization of technologies, involving:(a) automation of DNA extraction; (b) assembly of 'on-the-shelf kits'; (iii) non-radioactive methodologies, (iv) reproducibility and transferability and (3) Sampling and data handling, involving within genome and between and within population sampling strategy development. Comparisons for different SSR, scn and sco marker sequences (including developmental and fitness-related ones) will be made with morphological and eco-geographic variation. Combinations of markers will be tested for their ability to give accurate pictures of genome diversity that may be interpreted biologically. The second objective is to validate the use molecular tools by testing their application in a selection of diversity problems relating to different end-users represented by: (A) Botanic gardens; (B) Gene banks and (C) Plant Breeding Companies. Validations will comprise measurable on-site activities, involving direct inputs (including loan of instrumentation) from commercial companies, and off-site activities involving networks of participating laboratories. The molecular data generated from AFLPs, SSRs and sequence-PCR will be extensively analysed and linked to the existing morphological and eco-geographical data.
This project aims at reaching a consensus on the applicability and reproducibility of the whole range of molecular tools, both pre-existing and new ones being developed within the proposal, for answering different questions relating to biodiversity. An indication will be given of the extent to which these molecular tools are able to quantify genetic diversity. New developments in the project are focused on universal, or wide-ranging tools that will be useful for researchers working on as wide a diversity of plant species as possible, e.g., scn sequences and SSRs with high cross-transferability and on developments that will suit the widest range of operational systems, from high-investment to low budget laboratories. Most studies, to date, have used molecular techniques as arbitrary markers of genetic diversity. In this project, with the development of scn sequences and SSRs of different nuclear locations, the possibility of developing molecular markers relating to adaptive variation and functional characteristics at the organismal level will also be tested. These developments are needed for the tools to be most effectively used in helping to make sound decisions concerning the validity of ex situ conservation strategies involving gene banks and other living collections, or in situ conservation strategies involving natural populations. Good feed-back and dissemination with the widest range of end-users is assured by association of the project with an extended audience (The Biotechnology for Biodiversity Platform).

Funding Scheme

CSC - Cost-sharing contracts


Institute of Arable Crops Research
Long Ashton Research Station
BS18 9AF Bristol
United Kingdom

Participants (1)

Kobenhavns Universitet
140,Gothersgade 140
1123 København K