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Comparative genome analysis and mapping in conifers

Objective



Conifer trees are major components of forest ecosystems throughout the EU, both in its Southern and Northern regions, and provide a major source of wood and cellulose products whose demand is continuously increasing. Despite their economic and ecological relevance there is very limited information on the organization of protein coding sequences within chromosomes, the structural basis of metaphase chromosomes, the type and function of non coding DNA sequences and more generally on the genetics and genome structure of this group of species. This project will address basic and applied aspects of Conifer biology in the area of genome analysis and mapping and will aim to get a better understanding of how the conifer genome is organized in order to allow its efficient manipulation either via marker assisted breeding or genetic transformation. This in consideration of the fact that biotechnological tools are more and more frequently applied to forest tree breeding and that the huge size of Conifer genomes (8 x human, 250 x Arabidopsis thaliana genomes) makes it necessary to have a deep knowledge of their structure in order to be able to successfully manipulate them.
Four work packages have been devised in this Proposal aimed to i) provide a more comprehensive and comparative understanding of the structure and organization of Conifer genomes in terms of type and distribution of repetitive sequences, distribution of coding sequences and relationships between genetic and linkage maps (Work Package l); ii) construct second-generation linkage maps based on PCR markers and on anchor loci provided by cDNAs to define syntenic relationships among species (Work Package 2); iii) verify the feasibility of exploiting synteny to identify the genomic regions and genes involved in the determination of important traits such as "growth capacity" in a single "model" Conifer species (Work Package 3); iv) provide an easy way to disseminate results to potential end-users both from academia and private companies through the creation of a Web site for Conifer genome research (Work package 4). By analysing the genomes of three species belonging to two different genera (Picea abies, Pinus sylvestris, Pinus pinaster) we will gain a comparative view of genome organization. The comparative mapping approach will also verify the possibility of concentrating efforts in this area on a single species selected as a "model" and then being able to transfer the obtained results to any of the other Conifer species that are of economic and/or ecological importance in the EU. A deeper knowledge of genome and gene structure in Conifers will also provide an opportunity to determine how closely related gymnosperms are at the molecular level to angiosperms and to establish how relevant programmes on gene discovery and mapping in model angiosperm species such as rice and Arabidopsis are to Conifers. Knowledge of genome structure will also aid rational strategies for searches of useful genes in this group of species as well as lead to an improvement in molecular marker technology. This will in turn increase the ability to map genes of major economic importance. The proposed project, by bringing together a highly qualified group of laboratories with complementary expertises, will therefore attempt to provide a competitive advantage to the EC industries that are active in the area and to compete with the major research efforts in the area of Conifer tree mapping and gene discovery that are underway both in North America and Pacific-Rim countries.

Funding Scheme

CSC - Cost-sharing contracts

Coordinator

UNIVERSITA DEGLI STUDI DI UDINE
Address
Via Delle Scienze 208
33100 Udine
Italy

Participants (5)

INSTITUT NATIONAL DE LA RECHERCHE AGRONOMIQUE
France
Address
Domaine De L'hermitage
33611 Canejan
JOHN INNES CENTRE
United Kingdom
Address
Colney Lane - Norwich Research Park
NR4 7UH Norwich
Scottish Crop Research Institute
United Kingdom
Address
Invergowrie
DD2 5DA Dundee
Stiftelsen Skogsbrukets Forskningsinstitut
Sweden
Address
Glunten
751 83 Uppsala
The Swedish University of Agricultural Sciences
Sweden
Address
2C,baeckloesavaegen
750 07 Uppsala