GEMS Name Types
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Contents |
Introduction
As of 2009, the naming system of marker detectors (including genes) and their molecular variants (alleles) has been revised in IWIS3-GEMS and IMIS-GEMS to reflect the following name types, all of which are stored in the GEMS_UDFLDS table of the GEMS database:
User-defined fields for GEMS:
Name types for GEMS:
| fldno | fname | fdesc | location in GEMS | example |
|---|---|---|---|---|
| 2 | MARKER NAME | MARKER NAME | name of marker (saved as marker detector; gobjid = mdid) | wPt-9900 SCM009 |
| 3 | ALLELE NAME | ALLELE NAME | allele names, including marker names used as names for their alleles (saved as molecular variant; gobjid = mvid) | wPt-0021 TC408385 |
| 5 | GENE NAME | GENE NAME | name of gene or introgression (saved as marker detector; gobjid = mdid) | Lr19/Sr25 Cre5 |
| 8 | MARKER-SIZE | ALLELE BY SIZE | allele name as determined by allele size, as in the case of SSRs (saved as molecular variant; gobjid = mvid) | dp004-200 SCM009-200 |
| 9 | MARKER#ID | ALLELE BY GEL ID NUM | allele name as determined by an arbitrary number assigned by the laboratory (saved as molecular variant; gobjid = mvid) | gwm577#1 Sr24#12#1 AAC_CAA-1 (AFLP) |
| 10 | TRAIT +/- | ALLELE BY TRAIT +/- | allele name as determined by presence of absence of a trait associated with the marker, i.e. disease resistance/tolerance (saved as molecular variant; gobjid = mvid) | Ppd-D1_insensitive ppd-A1_sensitive |
| 11 | GENE +/- | ALLELE BY GENE +/- | allele name as determined by presence of absence of a gene associated with the marker (saved as molecular variant; gobjid = mvid) | Lr34+ Qu9-5+ |
| 12 | MARKER-BASE | ALLELE BY NUCLEOTIDE BASE | allele name as determined by base change, as in the case of SNPs (saved as molecular variant; gobjid = mvid) | ZHD1.1-T PZA01542.1-A |
Genes vs. Markers in GEMS
Due to the limitations of the existing GEMS ver 5.4 schema, the following standards have been used to capture the relationships of genes and markers in GEMS...
- Genes (or introgressions) are temporarily stored in the GEMS_MARKER_DETECTOR table so that their corresponding genic alleles are stored as molecular variants in the GEMS_MV table. The gntype column in the GEMS_NAMES table will distinguish markers from known genes (or introgressions).
- Associations between genes and markers are stored in the GEMS_MV table. When an allele of a marker is associated to a particular marker of a gene, they will have the same locusid (taken from the GEMS_LOCUS table).
- If two or more alleles have the same "gene +/-" label. this indicates that both or all these alleles are required to signify that the gene is present.
- Because of the one-to-one correspondence between a primer pair (stored as fprimer and rprimer in the GEMS_MARKER_DETECTOR table) and each assigned marker detector (identified by mdid in the GEMS_MARKER_DETECTOR table and linked to gobjid in the GEMS_NAMES table), it is possible for a marker with a particular "name" to be represented several times in gnval of the GEMS_NAMES table.This implies that the same marker was genotyped using different primer pairs.
Genes and Phenotypic Traits in GEMS
There is a suggestion that the relationship between genes and the phenotypic traits they are associated with can be stored in the DMS using this template, following what has been done by AAFC.
However, the gene names must first be stored in GEMS and assigned MDIDs before they are loaded into the DMS.
In the cases where the specific molecular variant of the trait is known to be associated to the gene, the MVID is also indicated in the template, as shown here:
Null alleles and unknown genotype in GEMS
To correctly reflect the nature of markers, the following null alleles were removed from the current IWIS3-GEMS...
These "unknown" or "?" alleles have also been removed from the IWIS3-GEMS database...
Unknown genotypes and null alleles are not stored in GEMS. Instead, they will be stored in the DMS using either the PRESENCE/ABSENCE or INCIDENCE variate.
