The "International Rice Microsatellite Initiative", (IRMI), is a consortium of public and private research groups that are working together to generate new microsatellite markers for rice based on publicly available sequence.

We hope that our work will provide a valuable set of highly informative PCR-based markers that will bridge information derived from sequencing, genome mapping and phenotypic evaluation for use in breeding and genetics.

Our institutional membership currently includes Cornell University (CU),the International Rice Research Institute (IRRI,) Huazhong Agricultural University and RiceTec, Inc. Three new groups have recently applied for membership and we are negotiating with Monsanto/Pharmacia for release of additional SSR-containing sequence information as template for primer design that will enable these groups to proceed.

The objectives of the project are:

a) to develop and test a set of broadly useful SSR markers from publicly available sequence data and

b) to make the primer sequences and map positions of these markers publicly available.

The working arrangements are as follows:

1) A web-accessible data management tool was designed and implemented by the USDA Center for Agricultural Bioinformatics (CAB) and the Cornell Theory Center (CTC). This tool is being used to coordinate the entry and editing of data generated on this project.

2) SSR primer pairs are designed from publicly available sequence information using the Primer 0.5 program and distributed in non-overlapping sets to IRMI participants.

3) The lab groups involved in the consortia agree to work on non-overlapping subsets of SSR containing sequences (minimum of 500 sequences each) assigned to them by the coordinating group at Cornell.

4) Each lab group agrees to test primer pairs using a standard PCR protocol and a standard panel of rice lines to facilitate multiplexing and automation.

5) Groups may use either silver-staining of PAGE gels or fluorescent-based detection on automated sequencers as the basis for allele size estimation. (Due to the requirement for accurate allele size estimations, the use of EtBr stained agarose gels is not recommended for sizing alleles.)

6) Members agree to report their results on a weekly basis (more frequently if possible) by submission of data in a web-based format to the IRMI data management tool (http://scylla.tc.cornell.edu/irmi/ ). The IRMI data management tool is password protected and serves only as a holding repository for data entry and editing. All submittors are responsible for the accuracy and reliability of their own data. Data editing is permissible only by the submittor.

7) Public access to the newly developed SSR markers and related information will be through the Gramene database (www.gramene.org). Data will be transferred from the IRMI data management tool into Gramene on a monthly basis.

8) All members of the consortium will finance their activities independently but all results will be shared openly.

9) All members of the consortium will be publicly recognized as contributors to IRMI.

Please note: all published rice SSR markers previously developed in the McCouch lab are available at http://www.gramene.org/microsat/

Additional information about SSR primer pairs developed from other sources of sequence or SSR allele profiles of rice accessions not included in the standard panel can be submitted to the Gramene database. If you would like more information about rice SSR markers, about SSR marker data submission, or about joining about IRMI , please contact Susan McCouch (srm4@cornell.edu). We will be happy to discuss arrangements that will facilitate your participation in the initiative.

Acknowledgement: We are grateful to Gerard Barry at Monsanto/Pharmacia for negotiating the release of the SSR sequence data that inspired the formation of this consortium.