R I C E
Report on QTL nomenclature
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R I C E |
SR McCouch (1), YG
Cho (2), M Yano (3), E Paul (4), M Blinstrub (1), H Morishima (5)
and T
Kinoshita (5)
1) Plant Breeding
Dept., Cornell University, Ithaca, NY USA;
e-mail: srm4@cornell.edu
and marcib@nightshade.cit.cornell.edu
2) Genetics Division,
NIAST, RDA, Suwon 441 707, KOREA;
e-mail:
ygcho9@chollian.dacom.co.kr
3) NIAR/MAFF, 1-2,
Kannondai 2-chome, Tsukuba, Ibaraki 305, JAPAN;
e-mail:myano@abr.affrc.go.jp
4) GeneFlow, Inc., 503
Mt. Vernon Ave, Alexandria, Va USA;
e-mail:
epaul@nightshade.cit.cornell.edu
5) National Institute of
Genetics, Mishima 411, JAPAN;
e-mail:
hmorishi@lab.nig.ac.jp
6) Faculty of
Agriculture, Hokkaido University, Sapporo 060, JAPAN
The following is a set of recommendations for QTL nomenclature in rice agreed on by the authors of this report. We are submitting these recommendations for publication in RGN14 to invite comments from other rice researchers aimed at further refinements of this first draft.
We also recommend that if people want to see how the QTLs are
being modeled in the RiceGenes database, that they consult the
database on the WWW at:
RiceGenes is no longer up.
An archive version is available here.
The database schema is temporarily viewable on Gramene here.
In addition, we encourage people to consult the electronic
version of the RGN, volumes 1-12, over the WWW by going into:
http://probe.nalusda.gov:8300, then to the ABOUT link under
RiceGenes. Using the electronic version of the RGN makes it
possible to search all 12 volumes based on any key word of
interest.
We aim to define a QTL nomenclature system providing the simplest possible naming strategy that would still allow each unique QTL to be distinguished. We suggest using CAPITAL LETTERS for the locus name so that it does not confuse QTL names with other gene nomenclature in rice. We agree that a designated database curator will determine the final numerical identifier of a QTL when it is entered into a genome database so that the authors of a particular study only need to concentrate on distinguishing QTLs within their own study.
Keeping these concepts in mind, we suggest the following as a
guide to QTL nomenclature in rice and welcome suggestions from
our readers.
2) Use a 2-5 letter name IN CAPITAL LETTERS to designate the trait actually measured. There will undoubtedly be variations in nomenclature for some of the same traits when they appear in publications, but we will adopt a standard nomenclature when the information is entered into a genome database (i.e. RiceGenes). The CAPITAL LETTERS will make the QTL name stand out clearly, facilitating recognition of the trait under consideration.
3) Add a dash (-) and a number to the end of the locus name to designate the rice chromosome (1 - 12) on which it has been mapped. If more than one QTL for the same trait is identified on the same chromosome in the same study, then the author should add a second numerical identifier (i.e., another dash (-) and a new number following the chromosomal designation) to differentiate the individual QTLs.
4) When QTLs from different studies are integrated into a single genome database, the database curator will ensure that the numerical code at the end of the QTL name makes it possible to uniquely identify QTLs for the same trait on the same chromosome in different studies. If the author of a study has already attempted to do this (see 3 above) the number assigned in the publication may be adjusted to distinguish a new QTL from what is already in the database.
5) When QTLs are entered into the RiceGenes database, they will be assigned a "general trait" category [i.e. biotic resistance, abiotic resistance, plant architecture, yield, etc.] so that users can perform the appropriate queries. This assignment will be reflected within the qtl record, but not in the name itself.
6) Here's an example of how a QTL name would appear using this system:
