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,
C. E. Durel 3 and
W. E. Van de Weg 4
1Walloon Agricultural Research Centre (CRA-W), Gembloux, Liroux 9, B-5030, Belgium, 2Agroscope Changins-Wädenswil (ACW), Phytopathologie, P.O. Box 185, Schloss CH-8820 Wädenswil, Switzerland, 3Genetics
and Horticulture – GenHort, National Institute for Agricultural
Research, 15 INRA, BP 60057, F-49071 Beaucouzé Cedex, France and 4Plant Research International (PRI), P.O. Box 16, 6700 AA Wageningen, The Netherlands
Open Access article from Bioinformatics 2007 23(7):882-891.
Objective: AppleBreed DataBase (DB) aims to store genotypicand phenotypic data from multiple pedigree verified plant populations(crosses, breeding selections and commercial cultivars) so thatthey are easily accessible for geneticists and breeders. Itwill help in elucidating the genetics of economically importanttraits, in identifying molecular markers associated with agronomictraits, in allele mining and in choosing the best parental cultivarsfor breeding. It also provides high traceability of data overgenerations, years and localities. AppleBreed DB could serveas a generic database design for other perennial crops withlong 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-classesat the physical level: TREE and DNA-SAMPLE. This approach facilitatesall links between plant material, phenotypic and molecular data.The entities TREE, DNA-SAMPLE, PHENOTYPE and MOLECULAR DATAallow multi-annual observations to be stored as individual samplesof individual trees, even if the nature of these observationsdiffers greatly (e.g. molecular data on parts of the apple genome,physico-chemical measurements of fruit quality traits, and evaluationof disease resistance). AppleBreed DB also includes synonymsfor cultivars and pedigrees. Finally, it can be loaded and exploredthrough the web, and comes with tools to present basic statisticaloverviews and with validation procedures for phenotypic andmarker data to certify data quality.
AppleBreed DB was developed initially as a tool for scientistsinvolved in apple genetics within the framework of the Europeanproject, ‘High-quality Disease Resistance in Apples forSustainable Agriculture’ (HiDRAS), but it is also applicableto many other perennial crops.