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problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/14ed25cc0598531dbc60be74e2016ebbproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/267ec68c8c7aed7c532264241e14ab6fproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/2848bfe066f82fb93e1cab002695362cproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/2e6e978fb80e06b1fc39f0bc0387ace2problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/43b6bb2b4ba9028dacb0975a0f5e65e0problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/61e65e674b0a9e7af4ea6ba5bae00b48problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/7697f9e882c2a24450db29ae29fd12c1problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/7f9365057886e30ebc0f7aa179cbbf29problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/9b871a2c0628c4b722fce326a38d57b8problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/bbcb87e5d71ae017a02008caf13c287bproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/c98c28b9c55577dbdadf71c1c08a802cproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/d1d4fd9470fb106ecf347e59fab4a8fcproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/f16c65c68809d874dea7b8b5e1066e82problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/14ed25cc0598531dbc60be74e2016ebbproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/267ec68c8c7aed7c532264241e14ab6fproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/2848bfe066f82fb93e1cab002695362cproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/2e6e978fb80e06b1fc39f0bc0387ace2problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/43b6bb2b4ba9028dacb0975a0f5e65e0problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/61e65e674b0a9e7af4ea6ba5bae00b48problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/7697f9e882c2a24450db29ae29fd12c1problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/7f9365057886e30ebc0f7aa179cbbf29problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/9b871a2c0628c4b722fce326a38d57b8problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/bbcb87e5d71ae017a02008caf13c287bproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/c98c28b9c55577dbdadf71c1c08a802cproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/d1d4fd9470fb106ecf347e59fab4a8fcproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/f16c65c68809d874dea7b8b5e1066e82problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/14ed25cc0598531dbc60be74e2016ebbproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/267ec68c8c7aed7c532264241e14ab6fproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/2848bfe066f82fb93e1cab002695362cproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/2e6e978fb80e06b1fc39f0bc0387ace2problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/43b6bb2b4ba9028dacb0975a0f5e65e0problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/61e65e674b0a9e7af4ea6ba5bae00b48problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/7697f9e882c2a24450db29ae29fd12c1problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/7f9365057886e30ebc0f7aa179cbbf29problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/9b871a2c0628c4b722fce326a38d57b8problems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/bbcb87e5d71ae017a02008caf13c287bproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/c98c28b9c55577dbdadf71c1c08a802cproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/d1d4fd9470fb106ecf347e59fab4a8fcproblems clearing cache file /home/httpd/projectos/coec/cache/refTableSQL/f16c65c68809d874dea7b8b5e1066e82
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Polymorphism detection and validation

Abstract

The cork oak (Quercus suber) forest (the “montado”) is a unique and emblematic resource for Portugal, due to its ecological and socio-economic significance, and the commercial value of cork. Portugal is the main cork producer (about 1/3 of the world production). Little is known about Q. suber germplasm diversity, stress plasticity and cork formation, though this species has recently become in Portugal, a priority target of several research projects on ecophysiology and selection.

Mediterranean evergreen oaks (holm and cork oak) are being threatened by damaging policies of land use, by climate change, biotic stresses and fire. To urgently defend the richness of these forests in Portugal and southern Europe, research on these trees should be implemented. The responses to abiotic and biotic stress, and developmental processes such as vegetative and reproductive development, acorn production, and the mechanisms of cork formation are subjects that deserve to be investigated.

 

Research on oaks, specifically cork oak, would greatly profit from the construction of a gene chip for transcriptomic studies. Transcriptomics forms a dynamic link between genome, proteome and cellular phenotype, and thus will allow the assessing of differential gene expression along development or in response to varying environmental conditions. The production and sequencing of expressed sequence tags (ESTs), in order to construct a cork oak gene chip, will support such studies and, furthermore, will provide useful information for a cork oak genome sequencing project.
A Portuguese Functional Genomics Platform Consortium has been established as a concerted effort to contribute with ESTs for the construction of the cork oak gene chip. Affymetrix was chosen to produce the chip after careful evaluation of the microarray technology available. With this concerted initiative new competences will be established at national level, while stimulating cooperation and increasing the number of teams conducting research on this highly valuable national resource. Moreover, team organization as a Consortium will guarantee an ensuing minimum utilization of the cork oak gene chip.
The Consortium organized 12 projects, involving different partners, to cover as many different conditions as possible, and guarantee the expression of the maximum number of Q. suber genes to enrich the gene chip. Each project counts with researchers with specific experience for the project, who will prepare the plant material and extract total RNA. Normalized cDNA samples from the total RNA isolated will be prepared in a lab recognised for this service (Evrogen), in order to reduce losses of low abundant transcripts. The normalized cDNA will be sequenced by 454 technology (to be centralized at the BIOCANT Technological Park), with theoretical yields of 1 million bases, 500 Mbp per sample, 400 bp/sequence. Assembly of EST contigs and preliminary annotation will be performed at BIOCANT. A dedicated bioinformatics team will implement databases and data pipelines to organize and analyze the large volume of information to be generated and make it available to the community. The created public platform, CorkOakDB, will serve as an important research tool for the biotechnology communities, and will showcase this first Portuguese large-scale genomic project.
The 12 projects that integrate the Consortium, identified as SOBREIRO/##/2009, are: 14 (Biotic stress: roots response to infection by Phytophthora cinnamomi); 17 (Cork production); 19 (Male and female gametophyte development); 25 (Acorn germination); 29 (Fruit and embryo development); 30 (Bioinformatics platform); 33 (Abiotic stress: drought, salt and oxidative stresses); 34 (Mycorrhizal symbiosis); 35 (Abiotic stress: heat and cold stresses); 36 (Polymorphism detection and validation); 38 (Cork quality); 39 (Bud sprouting and foliar development).
Within the specific project here presented, the focus will be on polymorphism detection within the multiple sequence alignments obtained from the 454 technology outputs, from all the other consortium projects. The aim is to adapt a bioinformatic pipeline for automated detection and classification of the Single Nucleotide Polymorphisms (SNPs) and to produce a list and location of the putative variation within the ESTs. Consequently these results will allow a better design of the oligonucleotide chip. In order to increase the depth of coverage and the potential detection of genetic variation, an additional pyrosequencing plate of ESTs from the final stage of foliar tissue development will be added to the other two already dedicated to the same process in another project of the Consortium, with samples from different geographic origins.

 

Involved Groups:

Computational Biology & Population Genomics Group (CoBiG²)

 

Members:

Octávio S. Paulo

Dora Batista

 

Involved Institutions:

Faculdade de Ciências da Universidade de Lisboa

Centro de Biologia Ambiental

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