From: Nils Stein <stein@ipk-gatersleben.de> Date: Wed, 07 Aug 2002 19:09:25 +0200 Subject: EST-SSR coordination To: Gary Ablett <gablett@scu.edu.au>, "P.K. Gupta" <pkgupta36@hotmail.com>, Perry Gustafson <pgus@missouri.edu>, Bernd Hackauf <b.hackauf@bafz.de>, Robert Henry <rhenry@scu.edu.au>, Pat Heslop-Harrison <phh4@mail.cfs.le.ac.uk>, Ramesh Kantety <rk80@cornell.edu>, Joerg Schondelmaier <schondel@saaten-union-labor.de>, Trude Schwarzacher <ts32@leicester.ac.uk>, Jorge A daSilva <jadasilva@taexgw.tamu.edu>, Sukhwinder Singh <ssingh@ksu.edu>, Mark Sorrells <mes12@cornell.edu>, Pierre Sourdille <pierre.sourdille@clermont.inra.fr>, Nils Stein <stein@ipk-gatersleben.de>, Pauline Stephenson <pauline.stephenson@bbsrc.ac.uk>, Ju-Kyung Yu <jy89@cornell.edu>, Wenchun Zhou <wzhou3@students.uiuc.edu>, Imad Eujayl <ieujayl@wsu.edu>, Harindra Singh Balyan <hsbalyan@rediffmail.com>, Sachin Rustgi <rustgi2001@yahoo.com>, "Rajeev K. Varshnej" <kumar@ipk-gatersleben.de>, Dave Matthews <matthews@greengenes.cit.cornell.edu> Dear colleagues, I apologize for not replying earlier to the feedback or interest on coordination of efforts in the field of EST-based SSR marker development. Most of the replies were posted at the graingenes EST-SSR webpage - thanks to Dave Matthews who already established the option of doing Blast searches of your candidate EST against UNI-EST-SSRs from five species defined by the Sorrells group. From direct correspondence to Dave Matthews or to myself I extracted a few topics that are maybe of the major concern at the moment. Most efforts are currently in wheat (based on the replies). So it seems that for wheat EST-SSRs there is the highest need for coordination for the moment. Prof. Balyan mentioned i.e. that some of the candidate EST-SSRs overlap with some present in the wheat UNI-EST-SSR of the Sorrells lab, so my concerns from the beginning are confirmed. For these cases of maybe redundant marker development I would suggest that everybody who would like to improve the situation would make a statement under which conditions it would be possible to share what kind of data. I.e. Pierre stated that in genoplante he would have to clarify which data he could release to the public. For data of the IPK it would not be possible to immediately post unpublished data to graingenes, but on an MTA basis most data can be shared at least on a bilateral (finally multilateral) way. This might be possible with data from other labs as well? Every data that can be made public immediately is highly appreciated and I would like to call again to post it/send it to Dave Matthews. He once made the following suggestions: - As additional EST-SSRs are found they can be added to the BLAST database. Then anyone else can test their own set to see which ones have been already discovered. - The current status of each unicluster can be given in the corresponding GrainGenes record, e.g. www.graingenes.org/cgi-bin/ace/tree/graingenes?class=Probe&name=[Bcl401ct816cn3385]. The information here could tell which research group is working on it, and add results as they become available. - A list of uniclusters that no one is known to be working on might be defined , and people could "claim" them if they find some of theirs on the list, or want to sign up for some. I would recommend to implement these options. If one would intend to saturate the wheat genome with EST-SSRs it might be important to cluster again all public wheat ESTs / and maybe not yet public (O.Anderson/T.Close?), define UNI-EST-SSRs, subtract the already mapped ones and define claims/sets of candidates which would be selected or distributed among collaborating labs. The final outcome would be an interesting resource and content of a publication. All I wrote about so far was only concerning coordinating efforts in wheat. As no other lab replied which is involved in large scale EST-SSR development in barley I wonder, if there is something to coordinate. We would be happy to share information on a MTA basis with anyone who was involved in development of this kind of barley markers to reduce redundant efforts in our lab. Me, I would highly be interested in collaborating with other labs for mapping of interspecies-UNI-EST-SSRs (barley/wheat/rice/...). Who else would be interested in a concerted attempt of mapping such a set of probes? Rajeev, a postdoc from our lab is currently scanning the Sorrells UNI-EST-SSR contigs for overlaps with our mapped markers as well as to estimate the number of superclusters that has been already adressed by our efforts. Looking forward to your feedback, Nils ____________________________________________________________________________ Dr. Nils Stein Institute of Plant Genetics and Crop Plant Research (IPK) Department Genbank, AG MOM Correnstr. 3 D-06466 Gatersleben Tel.: +49-39482-5522 Fax.: +49-39482-5595 email: stein@ipk-gatersleben.de http://www.ipk-gatersleben.de/en/ http://pgrc.ipk-gatersleben.de/