General modus operandi

Any group that wants to participate in this scheme places a request for a certain number of contigs (20 is perhaps a suitable number). The group is sent a list of the next 20 contigs (or however many they requested) in the database. The database is then marked that these 20 contigs are 'under investigation'.

The group receiving the 20 contigs then sorts them into categories
a) non-exploitable - only one example of the sequence
b) non-exploitable - all sequences in contig identical, no polymorphism
c) non-exploitable - homoeologous groups apparent, but no variation within homoeologues
d) non-exploitable / incomplete - some polymorphisms, unclear variation between homoeologues and SNPs
e) exploitable - differentiation between homoeologues, potential polymorphism within homologues.

For the sequences classified as exploitable, the next step is to verify that the polymorphisms are real, and usable as markers. Successful locus-specific primer sequences will be filed in the validation report. Amplifications will be carried out using the locus specific primers on 30 genotypes (these will include the genotypes that provided the ESTs, mapping parents of commonly used populations (eg. the ITMI population, the Canadian populations, the Australian populations). The primers will then be scored for the number of samples that amplified, whether a single band was amplified, whether the fragment was the expected size, and if the amplification was judged strong, OK or weak. These assessments can be carried out on an agarose gel. Assuming that some amplification was achieved, the presence or absence of the SNP needs to be shown.

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