An update and proposal on TESC activities
By Rajeev Varshney (Nov 23, 2004)
A large number of papers have already been published on development and
applications of EST-SSR markers in triticeae as well as other cereal and
plant species (recently summarized in a recent review entitled 'Genic
microsatellite markers in plants: features and applications' authored by
Varshney/Graner/Sorrells due for publication in 'Trends in
Biotechnology', please write to me if you like to read this paper), no
serious efforts have been made to co-ordinate these activities in the
past. Now it is time for us to come forward and participate actively in
coordination activities in order to avoid redundant efforts and to make
a better use of the existing resources in different triticeae (or
cereal) species. After reviewing the status of the activities and
available reports on the TESC page and literature, I summarize the
current status of triticeae EST-SSR research and write my opinion as
following:
Summary:
Here is the list of labs, as per my knowledge, engaged in triticeae
EST-SSR research. In case, your lab is also a part of such activities
and not listed here, please provide us the info on the project(s)
underway in your lab.
(1) Development and mapping of EST-SSR markers:
Wheat: Cornell University (Mark Sorrells), KSU (Bikram Gill/Sukhwinder
Singh), INRA (Pierre Sourdille), Beijing (Jizeng Jia), Colorado State
University (Nora Lapitan)
Barley: IPK (Andreas Graner)
Rye: BAFZ (B Hackauf/ P Wehling), IPK (Andreas Boerner)
Ryegrass: S E Warnke/M A Rouf Mian/ M C Saha
(2) Applications: diversity analysis, transferability, comparative
mapping, etc.
Cornell University (Mark Sorrells), IPK (Andreas Graner), Meerut (P K
Gupta/ H S Balyan), ICARDA (Kamel Chabane/ Michael Baum), Lismore (Garry
Ablett), DIAS-Slagelse (Thomas Lubberstedt), NIAB (Paolo Donini/ Donal
O'Sullivan), SCRI (Wayne Powell/Joanne Russell), Adelaide (Robert
Henry), Wageningen University (Rients Niks).
Proposals:
(1) Need of a database: As it is evident that EST-SSR markers have been
developed in large number in triticeae species, we need to develop a
database for such markers so that other laboratories make a better use
of existing resources. Therefore, I propose all the labs, that have
developed such resources, to submit the sequences of ESTs (SSR-ESTs) in
FASTA format with their corresponding EST-SSR marker name, primer
sequences, chromosome position, PIC value (diversity index),
interspecific transferability and reference so that we can develop a
database. In case, you designed the primer pairs for some EST-SSRs and
you could not get the amplicon or find the polymorphism in parents of
the mapping population, then also provide the information to us. I hope
that the proposed database would be useful to select the markers of
interest for their use for a variety of applications.
(2) BLASTing of SSR-ESTs: After receiving the EST-sequences, we have a
plan to keep them in a BLASTable database on TESC page so that any
laboratory interested in development of new EST-SSR markers may check
their ESTs for redundancy against already mapped EST-SSRs (or SSR-ESTs)
of the respective species. It is really important to develop the novel
and non-redundant markers.
(3) Collaboration: I propose to initiate a multi-laboratory
collaboration on triticeae EST-SSR research and invite you to send your
feedback and suggestions to us. In this direction, after receiving the
EST sequences (SSR-ESTs) of corresponding mapped EST-SSRs of wheat,
barley, rye, etc. from you, we will check them for their in silico
transferability in the triticeae or even different cereal species and
thus we should be able to define candidate EST-SSR markers of wheat,
barley and rye for their use in interspecific transferability and
comparative mapping. For instance, laboratories engaged in barley
research may like to map candidate wheat and rye EST-SSRs and in the
similar way laboratories engaged in wheat research may like to map
candidate barley and rye EST-SSR markers and so on. These collaborative
efforts eventually should provide us a set of anchor markers across the
triticeae species and even cereal species (in case some labs show their
interest in mapping the triticeae EST-SSR markers in rice, sorghum,
oats, etc.) in addition to enrich the existing repository of SSR or
functional molecular markers for a particular cereal species. Thus the
final outcome would be an interesting resource for triticeae/ cereal
community as well as the content of publication (we can plan a joint
publication of different labs).
Once we receive the list of developed EST-SSR markers with their EST
sequences and willingness of interested labs to participate in the
multi-lab collaboration, we can plan comparative mapping experiments by
a number of candidate markers as per the individual and mutual interests
of participating labs. I assume that the laboratories which developed
the markers should be able to distribute an aliquot of their primer
pairs to other labs. I would propose to map the candidate triticeae
EST-SSR markers in standard (or common) mapping populations like ITMI
population (Synthetic X W7984) in wheat, OWB (Dom X Rec)/ Steptoe X
Morex/ Igri X Franka population(s) in barley and P87 x P105 population
in rye, etc. We can discuss these issues in details at a later stage
also. But I believe that my proposed collaboration makes you interested
to be a part of the multi-laboratory collaboration and therefore, I
request you to inform me about your willingness to participate in such
an effort and your interest as well as suggestions so that we can come
up with a final work plan of the proposed collaboration.
You may provide your feedback/suggestions on the above to me
(rajeev@ipk-gatersleben.de) or Dave
(matthews@greengenes.cit.cornell.edu). Once again, I strongly encourage
you to provide your data to us so that we can really avoid the redundant
efforts to develop the markers from the same gene. I am very much
hopeful that with your active participation and cooperation, we can
really make a better use of the TESC's efforts.
We are looking forward for your active participation and co-operation in
the above activities. Thanking you!
***************************************************************
Rajeev Kumar VARSHNEY, Ph.D.
Institute of Plant Genetics & Crop Plant Research (IPK)
Correnstrasse 3,
D 06466 GATERSLEBEN (GERMANY)
Tel: ++ 49 39482 5594(off.),5231 (lab) Fax: ++ 49 39482 5595
E-mail: rajeev@ipk-gatersleben.de / rajeevkvarshney@hotmail.com
Web : http://www.ipk-gatersleben.de/en/ ;
http://pgrc.ipk-gatersleben.de/
***************************************************************
back to TESC Page