In constructing a genetic map utilizing multi-species/genus probe sets, it is desirable to designate loci such that the DNA sources of the markers can be readily identified. Over the past several years, it has been our practice to designate the locus-sites for maize-derived molecular markers placed on the Tripsacum dactyloides genetic map with the prefix letter "t," as in tumc1, to designate the Tripsacum locus-site of high homology to a molecular marker (i.e., umc1) which identifies a homoeologous locus-site in maize. Reciprocally, Tripsacum-derived molecular markers (TDA probe set) are given a prefix letter "z," as in ztda50, when mapped in maize (Zea mays ssp. mays). This creates a four letter locus-site designation that identifies both the DNA source of the molecular marker and the genus-specific locus-site being discussed.

Our justification was that it provides a simplified system that allows for the identification of both the locus and the DNA source of the marker used to identify the locus. This also allows for homoeologous locus identification using a specific molecular marker or cDNA from different species, especially where there may be some degree of lack of exact sequence homology due to the level of hybridization stringency. For example, the zag1 and zag2 genes (for Zea agamous-1 and -2) designated by Schmidt et al. (Plant Cell 5:729-737, 1993) were cloned from a maize cDNA library by low stringency hybridization with the agamous (AG) cDNA from Arabidopsis. In dealing with genomic synteny, the same molecular marker may or may not identify a homoeologous locus region in another species or genus; therefore, each locus in a particular species (or genus) has a given name which identifies the specific locus and the history (source) of the marker used in its identification. 

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