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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 » Introduction

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

Breeding cultivated plants and, in particular, apple trees (Malusx domestica Borkh.), has always been an important activity atboth the amateur and professional level. Compared with annualcrops, breeding perennial crops is complex, long-lasting andtime consuming due to their long juvenile phase and long economiclifespan. Cultivars of perennial crops are grown across largegeographical areas and consequently new cultivars and breedingselections have to be evaluated over many successive years invarious localities. The age of the trees has to be taken intoaccount when phenotypically characterizing material becausephenotypic characteristics change with age. Other characteristicsgive perennial crops some advantages in genetic research, suchas their suitability for vegetative propagation. This meansthat many old cultivars and breeding selections still exist,which allows an identical genotype to be tested in various localitiesand in various years. In addition, the simultaneous presenceof various successive generations within a single experimentis possible. All these specific characteristics affect breedingprocedures and genetic experiments and put high demands on thestorage of phenotypic data.

The demands for the storage of genotyping data is also increasingtremendously due to the pace at which high numbers of PCR-basedmolecular markers are being developed. Initially, studies onmarker-trait associations were limited in size, usually involvingjust a single cross. The use of a single cross suffices as longas the genetic basis of a trait is extremely simple (only onelocus with one + allele). In all other cases, multiple crossesare needed if sound conclusions are to be reached on the numberof loci, alleles and mode of action of genes (intra- and/orinter-locus interactions). Studies on multiple crosses thereforedemand high quality and good data management facilities.

In the perennial apple crop, a new concept of gene and QTL identificationwas initiated called Pedigree Genotyping (Van de Weg et al.,2004). This approach aims to identify marker-gene associations,functional allelic diversity and both intra- and inter-locusinteractions by the integrated analysis of multiple plant populations(crosses, breeding selections and commercial cultivars) thatare genetically related by their pedigree. The European projectHigh-quality Disease Resistance in Apples for SustainableAgriculture’ (HiDRAS) (Gianfranceschi and Soglio, 2004),was initiated to test the concept. In this study, more than2000 genotypes are being extensively phenotyped and genotyped,delivering more than 1 million data points. Each phenotypicdata point is associated with its own descriptors for tree,year, sample and locality. Each genetic data point is associatedwith its own descriptors for DNA sample, tree, genotype, markerand map position. To meet the needs for the storage and accessibilityof these data, a database was needed. There are already severaldatabases managing both genomic and phenotypic information forthe plant kingdom. MaizeGDB database (Lawrence et al., 2004),for instance, is a repository for maize sequence, stock, phenotype,genotypic and karyotypic variation, as well as chromosomal mappingdata The GrainGenes database (Matthews et al., 2003) focuseson grasses and cereals storing both genetic and phenotypic information.It holds, amongst others, the genealogy and allelic constitutionof markers and genes from 69 632 wheat accessions. Other databaseshave been developed for managing genome molecular information(Rhee et al., 2003; Schoof et al., 2002) or for storing genesand protein information for Arabidopsis thaliana (ABRC, NASC,MATDB).

All these databases focus on annual plants and most of themmanage genomic or phenotypic information separately. None ofthem allows the management of pluri-annual data on the sameindividual plants (Reiser et al., 2002; Sakata et al., 2000).As none of the existing public databases were able to supportextensive studies on marker-trait associations in pedigreedpopulations of perennial crops, AppleBreed DB was developed.In the context of database construction, apples could serveas a model for perennial crops. Apples are a woody perennialand have a 3–7 year juvenile phase, which is a significanthandicap in combining high fruit quality and durable diseaseresistance by classical breeding. Apples are self-incompatibledue to a gametophytic incompatibility system, and thereforeinbreeding methods are not applied (Lespinasse, 1992). Applesare vegetatively propagated, have an economic lifespan of about15 years during which they produce 13 crops, are economicallyimportant and are highly rated among consumers, being rankedthird in a fresh fruit consumption survey after banana and citrus(Pollack, 2001). Currently, there are more than 10 000 applecultivars (Morgan and Richardson, 2002; Way et al., 1991) throughoutthe world. Nevertheless, world apple production is based ona handful of cultivars that are grown in commercial orchards.The most important commercial cultivars are highly susceptibleto the most important apple diseases (scab, powdery mildew andEuropean canker), and most of the resistant cultivars do notyet meet the quality demands of consumers. The most importantobjective of worldwide apple breeding programmes is thereforeto combine high fruit quality with good disease resistance.To achieve this aim, breeders need a better understanding ofthe genetic basis of fruit quality traits and disease resistance,and to obtain access to molecular markers for the most importantgenes controlling these traits.

AppleBreed DB supports breeders and geneticists in their geneticstudies and in their exploration of germplasm collections. Structuredinformation stored in the database should help them not onlyto elucidate the genetics of complex traits and to assess marker-traitassociations, but also to choose more easily and more quicklythe most interesting genitors to cross with (e.g. with gooddisease resistance, a particular taste, or a skin colour preferredby consumers). In this way, it is expected that breeders willmore easily be able to create new cultivars meeting consumerpreferences and allowing sustainable production systems. Thisarticle describes the database model of AppleBreed DB. AppleBreedDB is sufficiently generic to allow it to be used as a modeldatabase for many other perennial crops.

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