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Activity 3.1.2

Marker Services

Introduction

The number of marker laboratories able to do genotyping as a service is increasing. Some are generalists and can accommodate genotyping works with several technologies and materials. Others specialise in plants and plant breeding applications in particular. Among them, some offer only the generation of genotyping data, while others offer also corresponding data analyses.
At the same time, more and more researchers worldwide appreciate that keeping laboratory facilities up to date in their own institutions is not cost-effective. Equipment becomes quickly obsolete; marker technologies evolve, some continue to be useful and new ones become available based on newer platforms and equipment. Furthermore, modern developments are more demanding on specialised technician staff to do the work.
This activity will identify, through actual contacts or Internet searches, relevant laboratories able to provide services for genetic diversity analysis and plant breeding applications. It will gather information about characteristics of the services provided (such as type of markers available, data delivery timetable and conditions, approximate costs, and quality control procedures). This information is very dynamic. In most cases the cost structure is dependent on the request (marker type, size, timing, crop, etc).  Therefore, the compilation of information in this Activity will only have value as long as routine and frequent updates are done. The goal will be to update information every 6 months. 
It provides the link with the laboratories, templates to request services, and relevant policies for DNA/germplasm exchange. Very importantly, this Activity will also provide the support to negotiate, depending on the individual service request, the most suitable provider and conditions. It will include guidance to meet the legal requirements for the safe movement of DNA resources, markers and data. The platform management will not take on any legal responsibility regarding the choice of service provider by users, but will only facilitate bilateral contracts.

SNP Marker Conversion

The IBP is in the process of converting SNP markers for use in KBioscience's KASPar System. So far the following SNP sets have been converted or are being converted currently.

Crops Partners No. of SNPs Status
Maize Converted by CIMMYT in early 2010 1250 Available for genotyping
Cowpea UC-Riverside - Jeff Ehlers 1122 Available for genotyping
Chickpeas ICRISAT - Rajeev Varshney 2005 Available for genotyping
Pigeonpeas ICRISAT - Rajeev Varshney 1616 Available for genotyping
Rice IRRI - Michael Thomson et al. 805 Available for genotyping
Cassava IITA - Morag Ferguson, P. Rabinowicz 1740 Available for genotyping
Sorghum EMBRAPA - Jurandir Magalhaes
CIRAD - Jean-Francois Rami
1503 Available for genotyping
Common bean USDA - Perry Cregan
CIAT - Stephen Beebe
1497 Available for genotyping
Wheat CIMMYT - Susane Dreisigacker 2000 Available by end of 2011

Workflows

Work Order Documents

Genotyping Service Request Agreement (GSRA)

GSRA contains the terms and conditions under which the services are provided, it also authorizes CIMMYT to (at our own discretion) find suppliers of genotyping services and to hire them to fulfill the needs of the users of the IBP.

A GSRA is required from each scientist that applies for genotyping services. It has no due date, thus unless you are informed that there is a new version of GSRA, we can use it continuously. 

Material Transfer Agreement (MTA)

The germplasm that will be included in a Work Order needs to be covered by an MTA, it directly binds the requesting scientist and the Lab.  It is mandatory to have this document for a WO to be processed, that is why we need a copy of the fully executed MTA in each request.  With the MTA the lab and the requesting scientist accept their share of responsibility regarding the use of the genetic materials in which the work will take place and the resulting data. 

In paragraph 5 the MTA require that the Lab destroy all remaining specimens once the work is completed. This sentence can be removed by request of the supplier of the samples; we recognize that there are instances in which the same sample(s) may be used in different genotyping activities.

Work Order (WO)

The WO will document each genotyping work we request to the labs. It binds the lab and CIMMYT (CIMMYT acts in representation of the requesting scientist). The WO is at the same time the vehicle used within CIMMYT to make the financial and administrative execution of the genotyping activities.

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