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AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple …


Biology Articles » Agriculture » Plant Production » A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: the AppleBreed DataBase » Discussion

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

AppleBreed DB is, as far as the authors know, the first databaseto store both genetic and phenotypic data up to the level ofindividual observations. This combination of data makes AppleBreedDB a powerful tool for extensive genetic studies directed atthe assessment of marker-trait associations, for candidate genevalidation and for allele mining. AppleBreed DB takes into accountthe particularities of perennials such as: (1) vegetativelypropagated, allowing the same genotype to be present at variouslocalities, (2) long juvenile phase, (3) multi-annual crop,(4) long economic lifespan and (5) simultaneous availabilityof successive generations in the same plot of breeding programs,experimental stations and gene banks. These aims and particularitiesdetermined the general structure of the database, and have resultedin a framework quite distinct from models in use for annualcrops, such as the ZmDB database (Dong et al., 2002; Du et al.,2003; Gai et al., 2000) or the MaizeGDB database (Lawrence etal., 2004).

AppleBreed DB is built on a relational model. The structureof its conceptual model allows for the flexible addition ofnew entities. In other words, the AppleBreed DB structure allowsdata with new characteristics to be easily and quickly integratedinto the database, at least as long as the database integrityrules are respected. The ability to encode new data into thedatabase is checked by the database structure itself.

Due to the relational structure of the database, users’queries are easily handled through SQL requests. Other potentialreal-time query tools can be easily added, such as specificmultiple-choice questionnaires for different views of the requestedinformation. Modules to export data in ‘à la carte’output formats are also under development, making data directlycompatible for a wide range of software packages, includingpackages for QTL mapping. An interesting point for geneticistsand breeders is that it is possible to manage traceability ofplant material, a genotype or a family and to follow the parentsand their descendants. In addition, the flexibility of the datamodel makes it possible to adapt this system for other multi-annualbotanical species. Unfortunately, one characteristic of relationaldatabases might represent an inconvenience. Direct encodingof results is not allowed, for example, for new genotypes ormarkers. It is always necessary to insert new data in a particularand logical order and according to a specific and defined format.

AppleBreed DB can store phenotypic data at the level on whichthey were originally assessed, including at the level of individualsamples. In addition, the position of trees in the orchard andthe genetic relationships among genotypes are documented. Together,this allows in-depth analysis of the data because experimentaldesign, position effects, genetic relationships and experimentalvariation can be taken into account.

This not only allows in-depth classical analysis of the phenotypicdata itself, such as heritability estimates and the effect ofdifferent cultivation practices and environments, but also ensuresa high-power detection of marker-trait associations. As it standsAppleBreed DB will be a powerful tool for resolving the geneticbase of horticulturally important traits. In addition, it hasthe potential to support valorization of EST and genome sequencingprojects, since its phenotypic and genetic data can be helpfulin the identification of the candidate genes validated by geneticists.

Currently, there are various public databases for perennialcrops that are related to different aspects of genetics andbreeding. The USDA-ARS Germplasm Resources Information Network(GRIN http://www.ars-grin.gov/npgs/) is a database which storesinformation about clonal germplasm in the USDA system, includingvarious tree species as apples, pears stone fruits, grapes,etc. The Genome Database for Rosaceae (GDR, http://www.mainlab.clemson.edu/gdr/)is a curated and integrated web-based relational database. GDRcontains data on physical and linkage maps, annotated EST sequencesand all publicly available Rosaceae sequences. Although thisdatabase started as a database for Prunus, it is now extendingto other families of the Rosaceae. Various databases for themanagement of genetic resources were created by the EuropeanCooperative Programme for Plant Genetic Resources Networks (ECP/GR).These databases are crop specific and include Apple (http://www.ecpgr.cgiar.org/databases/Crops/Malus.htm[Maggioni et al., 2002]), Pear (http://pyrus.cra.wallonie.be/)and various stone fruits (http://www.bordeaux.inra.fr/urefv/base/).The HiDRAS SSRdb (http://www.hidras.unimi.it/) contains detailedinformation on more than 300 SSR markers that have been mappedin apple. The AppleBreed DB is currently uploading the HiDRASdata, most of which are likely to become public. All these databasesare relational, curated and web based. They are continuouslyextending in content and functionality. Much synergism couldbe obtained by tuning into their policies, content and formats,and much added value could be obtained if private databasessuch as the HortResearch Apple EST Database (Crowhurst et al.,2005) became part of the network.

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