from Dave Matthews, 5 Jan 1994 revised 3 Feb 1994 [NOTE, 28 Nov 1994: The concept of a "GrainGenes-name" described below is being revised to take advantage of new features in the database software. For now, the discussion of GrainGenes-names should be disregarded.] NAMING GENETIC LOCI There are two distinct systems for naming genetic loci in use among Triticeae scientists, the wheat system and the barley system. Since these systems are both in wide use in the literature, GrainGenes will include names under both systems as correct names. In addition, it is desirable to assign each locus a "GrainGenes name" for purposes of comparing loci that are likely to be homologous between genomes and between organisms, as described below. The primary differences between the wheat and barley systems are for DNA markers (loci mapped with molecular probes), and can be exemplified in the following names. Assume the anonymous probe DEM123 maps three RFLPs in the T. tauschii genome, one on chromosome 2D and two on 5D. The wheat rules would name the third of these markers: Xdem123-5D.2 The barley rules would call it: DEM123C Major differences are, 1. Wheat includes the chromosome location as part of the name, barley doesn't. 2. Wheat prepends the name of such markers with "X", barley doesn't. 3. For probes that identify multiple markers, wheat numbers them sequentially on a per-chromosome basis whereas barley assigns sequential letters on a per-genome basis. For DNA markers mapped with known-function probes, but which have not themselves been shown to correspond to known genes, there is an additional difference. The wheat name is based on the name of the probe, with the gene symbol included in parentheses. The barley name is based on the gene symbol, followed by a numeral to differentiate such DNA markers from genes with the same symbol and from each other. For example a locus mapped with an Adh clone named DEM456 might be called Xdem456(Adh)-4D by wheat, and Adh4 by barley. RULES FOR CONSTRUCTING GRAINGENES-NAMES FOR LOCI The GrainGenes database software can be very helpful in showing possible homologies in locus order and location between different genomes, but only for loci that have the same name. Therefore it is desirable to enter all loci under a "GrainGenes name", as well as under their correct names in the wheat and/or barley systems. The following rules are designed to maximize the likelihood of homologous loci being assigned the same name. 1. Anonymous molecular markers: Use "abc123", "abc456A", "abc456B". I.e. like the barley system, except: - Use lower-case, to distinguish locus names from probe names better. 2. Known-function-probe markers: Use "XAdh". - "X" distinguishes these markers from genes mapped by function. Then add just the name of the gene or gene-class recognized, to maximize the database's ability to show possible homologies. - "XAdh1" would indicate that the probe used can distinguish gene Adh1 from Adh2 etc. - For multiple loci detected by these probes, use "XAdhA" or "XAdh1A". For the multi-locus probes, the loci may be lettered in any order. Later, these will be renamed based on a comparison of the maps in GrainGenes, so that the homoeologous loci are given the same name. ADDENDUM, 3 FEB 94: NUMBERING Under ALL naming rules, the use of constructions in which the numbers contain leading "0"s, such as "abc001", should be avoided. This kind of name leads to inconsistencies in which the marker is sometimes called "abc001" and sometimes "abc1".