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Library Generation and Sequencing:
The objective of this component of the project was the production of high quality full-length cDNA libraries, generating at least 100,000 EST sequences. At least part of the intent was to be able to contribute to the pool of public knowledge. The development of tuber skin, suspension culture, mixed floral, low molecular weight and pathogen-challenged tuber cDNA libraries, within the context of the CPGP, represent novel cDNA libraries not included in public databases, such as the TIGR/NSF project. A wide range of potato tissues were targeted for library construction, containing both regular, normalized and full-length libraries. The potato variety Shepody was chosen as the target for the CPGP’s sequencing effort. Clone 1756 was obtained as sterile, disease-free, in vitro nuclear stock, from the New Brunswick Department of Agriculture and Aquaculture Plant Propagation Centre and grown at the Bon Accord Elite Seed Potato Farm. Approximately 5,000 individual putative recombinant colonies were picked from each library. Colonies isolated from each library were sent for sequencing at The Atlantic Genome Centre (TAGC) in Halifax. Details on the libraries are reported in the section on Library Information.
Bioinformatics Operations/ LIMS/ Website:
The objective of this work was to develop a core bioinformatics network essential to underpin the genomics programs and provide long-term data storage, retrieval, and display. The output of this work is reflected in the gene information section.
The objective of this work was to produce tools related to the needs of the CPGP, with specific emphasis on sequence management and annotation tools that were used by the CPGP Bioinformatics Operations group. The work led to the training of several graduate students in the discipline, and the development of two protoypes, reported in the publications and presentations section.
GE3LS research refers to the Ethical, Environmental, Economic, Legal and Social issues related to Genomics research. For the CPGP, the research objective was to address the scope, protection and development of intellectual property issues relating to potato/crop genomics and biotechnology. This work is documented in the publications and presentations section, as well as the GE3LS biobliography.
The objective of this work was to produce a large mutant population of potato using activation tagging. The work involved choosing the best potato variety to produce this population, to produce up to 10,000 lines, to develop a long term storage strategy for the population, and to screen several thousand lines to establish proof-of-concept on this unique global resource. This information is documented in potato mutant lines section of this website. This was a group effort via a multi-institutional team across three Canadian provinces.
The objective of this work was to produce a micro-array chip with no less than 10,000 unigenes, and to use this for expression profiling of some tuber health and tuber quality traits. You can view the information on this 44K oligochip in the micro-array section of this website.