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Molecular Marker Toolkit

Welcome to the Generation Challenge Programme's Molecular Marker Toolkit.

Over the last decade genomics has become a key factor in biological research worldwide. It has helped in targeting, identifying and deploying useful genes. Molecular markers greatly facilitate the selection of traits that are often difficult and time-consuming to detect based on phenotype. As such, marker-assisted selection (MAS) helps to speed up the incorporation of these valuable traits. The pervasiveness of research programmes on genomics has led to both an overwhelming amount of publications and many databases, whereby searching for available molecular markers ready for use for MAS can become a real odyssey.

Driven by the demand of agricultural researchers and plant breeders, particularly those based in developing countries and who face difficulties in accessing up-to-date scientific information on useful molecular markers, GCP's Subprogramme 5 decided to address the need to establish a tool which will allow rapid access to currently available and validated markers. Our response to this growing knowledge gap is the GCP Molecular Marker Toolkit ('MM Toolkit'). This toolkit is a compilation of information available via internet sources, public databases and papers that has been verified against plant breeders' experiences. As an easily accessible global public good, it marks an important step towards supporting the adoption of modern agricultural technologies for the benefit of the poor in developing countries.

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Data templates

The help desk provides support to GCP researchers in the use of the GCP Templates. For help please contact This email address is being protected from spambots. You need JavaScript enabled to view it. and provide your full name, email address and institute details. Please provide a description of the problem you having with the templates or with details on the type of data you wish to put in a template.

At the Annual Research Meeting (ARM) this year we will be providing a physical help desk during the whole meeting. Please bring your data to the meeting if need help in getting it into one of the templates. For the help desk timetable and to register for the help desk please see the the registration form.

Quick Links

    Templates Main Page
    Templates Guidelines
    Templates Download Page
    Templates Software


The SP4 Helpdesk on Bioinformatics and Biometrics
    Here you will find information on the SP4 Bioinformatics and Biometrics helpdesk of the Generation Challenge Program. In september 2008 this new GCP helpdesk became available, to support GCP scientists on request.

    The SP4 Helpdesk on Bioinformatics and Biometrics is intended for the GCP scientists with questions regarding handling, storing, or analyzing their data. The helpdesk is aiming to create transparency in availlable resources and expertise in the field of biometry, bioinformatics, and software engineering relevant to GCP scientists, such that the expertise and products of SP4 will be used optimally. The helpdesk will match the question of the scientist with solutions or experts from SP4, or other helpdesks dedicated to a specific area.

    Both simple and more complicated questions are welcomed by the SP4 BB helpdesk. We will probably not give you the answer, but hope to point you to the one who can.

    Examples of questions for which an answer can be sougth:

    - how to upload my data to the GCP central registry?

    - what is the best approach to analyse the genotypic diversity in a collection?

    - who is analyzing microarray data in the GCP?

    The helpdesk is accessible by sending an email to This email address is being protected from spambots. You need JavaScript enabled to view it. , including your full name, email address and institute details, and a brief description of the problem. We will get back to you in two workingdays.

    Please provide feedback on the design, suggested features or problems and errors you might discover, to This email address is being protected from spambots. You need JavaScript enabled to view it. .


GCP Intellectual Property Helpdesk
For answers on GCP IP issues and general information on IP and access and benefit-sharing (ABS). The goal is to help GCP member institutions, scientists and staff fulfill GCP Consortium-related IP management requirements. More
GCP's Interactive Resource Center & Helpdesk now on Facebook! More

Interactive Resource Centre & Helpdesk
In association with the Cornell University’s Institute for Genomic Diversity (IGD). For personalised, interactive support to address specific research needs. More

GCP Data Templates Helpdesk
Support to GCP researchers on using GCP Templates. More

SP4 Bioinformatics and Biometrics Helpdesk
Coordinated by GCP’s Subprogramme 4 (SP4), this helpdesk provides personal support to GCP scientists on data handling, storage and analysis. The helpdesk makes available resources and expertise in the fields of biometry, bioinformatics and software engineering to optimise the use of SP4 expertise and products.

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