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A multiple‐species, multiple‐project database for genotypes at codominant loci
Author(s) -
Reinsch By N.
Publication year - 1999
Publication title -
journal of animal breeding and genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.689
H-Index - 51
eISSN - 1439-0388
pISSN - 0931-2668
DOI - 10.1046/j.1439-0388.1999.00217.x
Subject(s) - biology , genotype , quantitative trait locus , locus (genetics) , genotyping , genetics , marker assisted selection , selection (genetic algorithm) , allele , genetic marker , genome , microsatellite , bottleneck , gene , computer science , artificial intelligence , embedded system
The possibility of identifying chromosome segments which have an important effect on quantitative traits has been greatly increased by the availability of dense marker maps. Crosses between wild ancestors and domesticated breeds (e.g. A ndersson et al . 1994) as well as commercial populations (e.g. G eorges et al . 1995) can be used either to scan the entire genome of livestock species or to investigate single chromosome regions of special interest (e.g. R einsch et al . 1998a). This kind of research makes it necessary to genotype hundreds or thousands of animals for numerous marker loci and consequently a big bulk of genotypic data must be processed. The results of QTL (Quantitative Trait Loci) research are expected to initiate the age of marker‐assisted breeding value estimation (F ernando 1998) and marker‐assisted selection, extending the demand for genotypic data processing to commercial breeding programmes. But even in current selection schemes genotypic data are accumulated, usually for parentage testing and by using DNA probes for the selection against alleles causing unfavourable conditions or diseases, e.g. at the ryanodine receptor locus in pigs (F ujii et al . 1991). New developments like DNA‐chip technology (L ipshutz et al . 1995) or the application of mass spectrometry (H aff and S mirnov 1997; H iggins et al . 1997) aim at the implementation of reliable automated high‐throughput genotyping systems and are likely to drive the mass of available genotypes further, at least until tissue sample collection and DNA preparation become a bottleneck. Keeping this situation in mind this paper gives a description of a database (DB) for genotypes at codominant loci. It was initially developed to collect the marker data from a QTL mapping project initiated by the German Cattle Breeders’ Federation (ADR) in collaboration with several animal breeding institutes, and may also serve as a prototype for unified procedures to process a large variety of genotypic data, such as may occur in a breeding programme. In the first part of the paper the general role of such a database is described, with emphasis on different sources of inconsistencies. The second part is a description of the structure and the relational scheme of ADRDB, followed by a section on consistency checking and error reporting. Finally the use of ADRDB in some research projects is described. Special aspects like the treatment of null alleles or sex‐linked loci are part of the discussion section.