Minutes for the Soybean Genetics Committee meeting
16 February 2009
Sheraton Westport, St. Louis, Missouri, U.S.A.
2008-2009 Members (all in attendance):
Rouf Mian (co-chair)
David Walker (co-chair)
David Sleper
David Hyten
Bill Schapaugh
Gary Stacey
Jim Narvel
David Grant (ex-officio)
Randy Nelson (ex-officio)
Also in attendance: Jennifer Yates, Pengyin Chen, and several guests.
Brief review of cases and SGC decisions from Feb 08 to Feb 09
1. Confirmation of two recessive seed phytic acid QTL: cqPha-001 (on Chrom 3/LG N) and cqPha-002 (on Chrom 19/LG L). Confirmation status was requested by Andrew Scaboo (former M.S. student with Vince Pantalone at the Univ. of Tennessee) in February 2008 (Manuscript: Scaboo et al.; submitted to Crop Sci.).
2. Recommended and approved naming a soybean rust resistance gene Rpp1-b.
Brian Diers (Univ. of Illinois) had requested approval to name a resistance gene on Chrom 18/LG G of PI 549538A Rpp1b in June 2008 (Manuscript: Chakraborty et al.). The SGC recommended insertion of the dash to comply with nomenclature rules.
3. Recommended adoption of the name Ncl2 for a dominant salt tolerance gene from G. soja accession PI 483463, and assigning Ncl1to a previously reported salt tolerance gene from G. max line S-100. Grover Shannon (Univ. of Missouri, Portageville) had requested permission to assign the symbol Ncl-Gs to the G. soja gene in July 2008 (Manuscript: Lee et al.). Authors concluded from 15:1 segregation for tolerance:sensitivity among F2:3 families from a cross of G. max S-100, PI 483463 that the G. soja gene was different from a salt tolerance gene previously identified in S-100.
4. Recommended naming a newly mapped maturity gene locus E8E8 on the basis of evidence that it is independent from previously named maturity loci. Elroy Cober (Agriculture and Agri-Food Canada) requested advice on naming the new locus in September 2008. (Manuscript: Cober et al.)
5. The SGC received a manuscript from Curt Hill (Univ. of Illinois) in September regarding an aphid resistance gene from PI 200538 that maps to the same region on LG F as Rag2 (from PI 243540). The SGC decided that this did not really fall under the Committee's jurisdiction, since the authors were not proposing a new name for the gene that they had mapped.
6. Approved recognition status and naming an SCN resistance QTL on LG D2 as cqSCN-005. David Lightfoot (Southern Illinois Univ.) requested recognition of confirmation status for this QTL in December 2008 (Manuscript by Kazi et al.).
7. Received requests from Dechun Wang (Michigan State Univ.) for approval of gene symbols for recessive aphid antibiosis resistance genes from PI 567598B (rag1b on LG M), PI 567541B (rag4 on LG F, and rag1c), and for a recessive aphid antixenosis gene from PI 567543C (rag3b). The Committee did not make a ruling on these requests, but they were discussed at the meeting, and they illustrated the need for nomenclature that can be applied to genes and QTLs that have not yet been confirmed by the SGC, but which scientists may want to include in presentations prior to an SGC ruling. (More information on the discussion is provided below.)
C. General issues discussed and/or voted on:
1. Dr. Jennifer Yates (Monsanto, Galena, MD) and Dr. Pengyin Chen (Univ. of Arkansas) were confirmed as the two new members from North America.
2. A motion was passed to increase the number of members in the Soybean Genetics Committee to include members from outside of North America. Another motion was passed to expand the committee by four international members, adding two in 2009 and two more in 2010. After that, additional international members would be elected to replace members rotating off of the Committee, in order to maintain a complement of four international members. The intent of the motion passed is to keep a balance between the number of representatives from Asia and South America, since these are the other continents on which extensive soybean genetic research is being conducted.
3. Bill Schapaugh and David Walker were elected as co-chairs of the SGC to serve from February 2009 to February 2010. Rouf Mian and Jim Narvel rotated off of the Committee.
4. The proportion of SGC members needed to support a proposed gene name or on confirmation status for a QTL before it could be considered an SGC decision was discussed, and a motion was passed to adopt decisions based on a simple majority (i.e., >50% of the members supporting it).
5. A motion was passed to give the ex-officio members (currently Randy Nelson and David Grant) voting rights. Although this privilege had been assumed, there was apparently nothing in writing to confirm it.
6. A discussion was initiated about the need to revise the existing gene nomenclature rules from 1997 in order to solve incompatibility problems between some of the existing nomenclature rules and the SoyBase database. David Grant, Dave Hyten and David Walker will draft a revision of the rules to submit to the SGC for commentary.
7. A need for nomenclature rules for gene names proposed by researchers, but not yet confirmed by the SGC, was also discussed. This was prompted by Dechun Wang's request to have several aphid resistance gene names approved prior to a presentation that he was to give the following day. In other cases, researchers may wish to 'reserve' a name when they feel that they have sufficient data to support either a novel locus or likely allelism with a previously reported gene. There was some concern about using the proposed name without any indication that it had not yet been approved by the Committee. Some SGC members advocate using a unique gene name for unconfirmed genes, an arrangement with precedence in some other plant genetics communities. Other members were concerned about the fact that the name initially used for a gene tends to stick, and that having two unique names for the same gene might cause unnecessary confusion. A compromise was proposed in the use of the postscript '_provisional' to indicate that a particular gene name had not yet been confirmed by Committee vote. For example, the aphid resistance gene from PI 567598B would be named 'rag1-b_provisional'. A suggestion was also made that authors be allowed to use this 'provisional' nomenclature in only one manuscript, and that the next manuscript should provide evidence for confirmation or rejection of the original name. This proposed nomenclature rule was accepted tentatively, but appeared to warrant further debate and discussion.
8. There was also a discussion about the used of chromosome numbers and linkage group designations, and the need for a Soybean Genetics Committee policy regarding this. A debate took place about the validity of chromosome numbers that had been assigned on the basis of genetic length instead of using cytogenetics studies with primary trisomics. The point was raised that the DOE-Joint Genome Institute sequencing project had insisted on using chromosome numbers instead of molecular linkage group names, which had forced the issue. The JGI might have assigned numbers arbitrarily to the nine unnumbered linkage groups if members of the soybean genetics community had not advocated assignment of chromosome numbers to the remaining linkage groups on the basis of genetic length. Although some members were uncomfortable with the method used, a majority agreed that with the release of the Williams 82 sequence by the JGI, it would be difficult or impossible at this point to halt the use of the chromosome numbers used in that project. However, it was also pointed out that with the extensive use of Linkage Group names in the literature, it will be helpful to provide both Chromosome number and Linkage Group name in articles. Therefore, the Soybean Genetics Committee voted to encourage authors to use the appropriate Chromosome number followed by the corresponding Linkage Group name.