It is critically important that QTL be clearly differentiated from genes, especially when they are related to similar phenotypes. For example, names for genes and QTL related to fatty acid content need to be clearly different.
The Soybean Genetics Committee recommends that QTL be identified by prepending a lower case q to whatever nomenclature seems appropriate.
For example, a QTL for corn earworm resistance is currently named CEW 3-2 (the 2nd QTL identifed in the 3rd corn earworm paper in SoyBase). After adopting a nomenclature similar to that recommended for molecular mrkers it would become qCEW003_02 (note the zeroes added to pad the length to 3 and 2 characters, ensuring that we won't run out of numbers for a given type). If and when the underlying gene is isolated it would be named using the usual soybean rules, possibly Cew3_2 for historical reasons.
There is a need for nomenclature to distinguish QTL that have been confirmed from those that have not. The Committee recommends that when QTL are confirmed, they be given a new name and be listed under a separate heading in SoyBase. The original names for these QTL would be maintained, and the entry would both contain the original data and point the reader to the new name.
The evidence used to confirm the QTL should include the following:
1. The confirmed QTL nomenclature will use the same trait abbreviations and unique numerical identifier format as nonconfirmed QTL but without the 2 digits that indicate more than 1 QTL for a trait in a single publication. The confirmed QTL will have names that start with cq for "confirmed QTL". The 3 digit number used to identify each confirmed QTL will be assigned in the order that they are approved by the Soybean Genetics Committee. Multiple confirmed QTL in the same paper will be named with consecutive 3 digit identifiers. For example, the first reported confirmed QTL for corn earworm resistance would be cqCEW-001 and if there was a second confirmed QTL in the same paper it would be cqCEW-002.
2. The QTL can only receive the confirmed designation when it is tested in a separate set of meiotic events and environments than it was originally mapped in. The separate set of meiotic events may be, but not limited to:
* a new set of F2s from the original cross
* a new backcross population
* lines derived from a plant in the original mapping population that was heterozygous for the region carrying the QTL
3. The QTL will be confirmed only when an experiment-wise error rate of 0.01, or lower, is used in the confirmation study.
4. At least one parent, and preferably both parents, must be in common between the original mapping study and the confirmation study. An example of when one parent in common is acceptable would be the mapping of QTL for disease resistance. If the same QTL is mapped in two populations developed from crosses between one resistance source two susceptible sources, this would be sufficient for confirmation purposes. To confirm a QTL, the reviewers need to be convinced that alleles at the same locus are segregating in both populations.
5. Evidence supporting QTL confirmation, usually in the form of a manuscript, will be reviewed by the SoyBase Curator.
Nomenclature revised March, 2007
The Soybean Genetics Committee