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Title: Development of a grape genomics database using IBM DB2 content manager software

Author
item HUANG, H - Florida A & M University
item LU, J - Florida A & M University
item Hunter, Wayne
item DOWD, S - Spiro Stat Technologies
item KATSAR, C - Animal And Plant Health Inspection Service (APHIS)
item JORGENSON, C - Florida A & M University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/22/2009
Publication Date: 12/15/2009
Citation: Huang, H., Lu, J., Hunter, W.B., Dowd, S., Katsar, C.S., Jorgenson, C. 2009. Development of a grape genomics database using IBM DB2 content manager software. Acta Horticulturae. 827: 87-92.

Interpretive Summary: A relational database was created for the North American Grapevine Genome project at Florida A&M University’s Viticultural Research Center. The collaborative project with USDA, ARS researchers is an important resource for viticulture production of new grapevine varieties which will be adapted and grown across the southern USA. Diseases are a limiting factor in production of non-native grapes in many areas of the United States. For example, Pierce's disease limits the production of European grapes in most part of the southeastern United States. Disease resistance of non-native grapevines could be enhanced by incorporation of the resistance traits discovered in native American grapevine species. These native varieties are providing new genetic resistance through the use of cross pollination in plant breeding programs. Alternatively, a 'molecular breeding approach' will accelerate these conventional breeding programs. The recent development and availability of genomic grapevine data resulted in the need to stream line a system which researchers could use to access and apply this growing informational resource. Thus, a collaborative effort of researchers at Florida A&M University (FAMU) and ARS resulted in a relational grape genomics database using IBM DB2 Content Manager to store genetic sequences such as Expressed Sequence Tags (EST), genomic sequences, molecular markers, chromatograms, graphic information, blast hits, and functional annotations in an organized and coherent fashion. The system provides a convenient way to associate heterogeneous data sets such as genetic sequences and various annotations with extensive search capabilities. This database system will better serve the use and applications of biological data integration and information retrieval relative to Vitis spp. in the creation of new grapevine varieties for the U.S. market.

Technical Abstract: A relational database was created for the North American Grapevine Genome project at the Viticultural Research Center, at Florida A&M University. The collaborative project with USDA, ARS researchers is an important resource for viticulture production of new grapevine varieties which will be adapted and grown across the southern USA. Diseases are a limiting factor in production of non-native grapes in many areas of the United States. For example, Pierce's disease limits the production of European grapes (Vitis vinifera) in most part of the southeastern United States. Disease resistance of non-native grapevines could be enhanced by incorporation of the resistance traits discovered in native American grapevine species, such as Vitis shuttleworthii, V. aestivalis, V. riparia, and V. rotundifolia. These native varieties are providing new genetic resistance through the use of cross pollination. Alternatively, a 'molecular breeding approach' could be used to assist and accelerate these conventional breeding programs. The recent development and availability of a large number of gene sequence data makes the molecular approach more realistic than ever before. Florida A&M University (FAMU) has developed a relational grape genomics database using IBM DB2 Content Manager to store genetic sequences such as Expressed Sequence Tags (EST), genomic sequences, molecular markers, chromatograms, graphic information, blast hits, and functional annotations in an organized and coherent fashion. The system provides a convenient way to associate heterogeneous data sets such as genetic sequences, and various annotations with extensive search capabilities. This database system will better serve the use and applications of biological data integration and information retrieval relative to Vitis spp. in the creation of new grapevine varieties for the U.S. market.