Skip Navigation



Bioinformatics Advance Access published online on January 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm013
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
23/7/882    most recent
btm013v2
btm013v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Antofie, A.
Right arrow Articles by Van de Weg, W.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Antofie, A.
Right arrow Articles by Van de Weg, W.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase

A. Antofie 1,*, M. Lateur 1, R. Oger 1, A. Patocchi 2, CE Durel 3 and WE Van de Weg 4

1Walloon Agricultural Research Centre (CRA-W), Gembloux, Liroux 9, B-5030, Belgium
2Plant Pathology, Institute of Integrative Biology (IBZ), ETH Zurich, Universitätstasse 2, CH 8092 Zurich, Switzerland.
3Genetics and Horticulture – GenHort, National Institute for Agricultural Research, 15 INRA, BP 60057, F-49071 Beaucouzé Cedex, France
4Plant Research International (PRI), P.O. Box 16, 6700 AA Wageningen, The Netherlands

*To whom correspondence should be addressed. A. Antofie, E-mail: antofie{at}cra.wallonie.be


  Abstract

Objective: AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple pedigree verified plant populations (crosses, breeding selections and commercial cultivars) so that they are easily accessible for geneticists and breeders. It will help in elucidating the genetics of economically important traits, in identifying molecular markers associated with agronomic traits, in allele mining and in choosing the best parental cultivars for breeding. It also provides high traceability of data over generations, years and localities. AppleBreed DB could serve as a generic database design for other perennial crops with long economic lifespans, long juvenile periods and clonal propagation.

Results: AppleBreed DB is organized as a relational database. The core element is the GENOTYPE entity, which has two sub-classes at the physical level: TREE and DNA-SAMPLE. This approach facilitates all links between plant material, phenotypic and molecular data. The entities TREE, DNA-SAMPLE, PHENOTYPE and MOLECULAR DATA allow multi-annual observations to be stored as individual samples of individual trees, even if the nature of these observations differs greatly (e.g., molecular data on parts of the apple genome, physico-chemical measurements of fruit quality traits, and evaluation of disease resistance). AppleBreed DB also includes synonyms for cultivars and pedigrees. Finally, it can be loaded and explored through the web, and comes with tools to present basic statistical overviews and with validation procedures for phenotypic and marker data to certify data quality.

Associate Editor: Chris Stoeckert

Received on November 20, 2006; revised on January 11, 2007; accepted on January 12, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.