The GCP Molecular Marker Toolkit: Background information
- Home
- GCP’s mandate crops
- The GCP Molecular Marker Toolkit—What’s in it and how it works
- Recommendations when using MM Toolkit markers in own breeding material
- Acknowledging the use of the MM Toolkit
- Sources of accessions
- Further reading
- Your feedback
- Acknowledgements
Welcome to the Generation Challenge Programme’s Molecular Marker Toolkit.
GCP’s mandate crops
Of the crops identified by the Food and Agriculture Organization of the United Nations (FAO) as the basis for human food security, 18 of them are GCP’s mandate crops, and the toolkit contains information on markers linked to these 18 GCP mandate crops and more.
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The GCP MM Toolkit—What’s in it and how it works
For each of the 19 crops covered by the MM Toolkit, a summary outlining the current status of MAS, together with some useful tips on further reading can be found. MM Toolkit users should note that the references listed within these summaries are a selection intended for guidance only, and do not by any means represent a complete list of all papers and/or websites available on MAS for the crop in question. Users keen to find further sources of information on their markers of interest are strongly encouraged to carry out additional searches, external to the GCP MM Toolkit.
To give a clear overview of the available information per marker, toolkit data has been divided into four windows which can be activated separately:
- The first window shows general information on the given marker, such as marker name, marker type, trait to which it is linked, name of crop expert, etc).
- The second window describes the corresponding laboratory protocol (primers, PCR conditions, etc.)
- The third window gives more information on the process of the validation of the marker (donor and recurrent parent, population type and size, etc.)
- The fourth window displays key references of consulted papers and/or websites.
In addition to browsing the MM Toolkit, a simple search interface is available whereby fields such as crop species, trait and marker type can be defined to search for the requested markers.
This first draft of the toolkit is limited to SSR, STS and SCAR markers as they are highly reproducible. Newly available validated markers, as well as markers used to pursue GM trait introgression, will be included in a future, updated version of the toolkit.
The toolkit shows all markers that are currently, as of April 2009, being used in marker-assisted selection (MAS). The existence of a marker for a specific trait does not necessarily mean that phenotypic selection for that trait should be excluded. In fact phenotypic selection may at times be preferred to MAS, when considered more cost-efficient and because of the relative ease with which it can sometimes be applied. It is therefore up to the breeder to decide which of the two kinds of selection is the most appropriate in his/her particular case.
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Recommendations when using MM Toolkit markers in own breeding material
As all markers of the MM Toolkit are routinely applied in breeding programmes there is no need to validate the marker-trait correlation again within the given crop, i.e. the linkage between the marker and the gene has already been proven.
However, before using a marker in segregating populations, one needs to know the polymorphism of the parents with regard to the marker of interest. If the parental genotypes do not show polymorphism for the marker, it will be useless to identify the trait. Ideally, together with the parental genotypes, one should include 2 NILs, one with the donor segment and the other with the recurrent allele in order to compare the genotypes and confirm presence and absence of the band of interest. It is important to know if the parents are homozygous or heterozygous for the marker, as segregation ratios may differ accordingly.
In the ideal case, other lines involved in the related breeding programme would also be screened with several or nearly all markers, as this will help to make breeding decisions and might provide additional information on other segregating markers. This will obviously depend on the breeder’s previous knowledge of the parental genotypes and the available funds for screening.
In addition, before embarking in testing a large sample, it is recommended to assay the marker for reliability of the protocols. As laboratory conditions vary, as do, consequently, the results obtained, the protocol described in the MM Toolkit or in the corresponding publication should be tested and optimised on a set of parental or key lines of the breeding programme. Lines known to be a source of the target trait should be included as checks. Equally, controls should be included for a clear comparison of banding patterns. It can happen that a parent has a slightly different allele than the known allele. Without the positive control in the test this cannot be distinguished. It might be necessary to re-run markers in high-resolution platforms to be sure that the right allele is detected and reported.
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Acknowledging the use of the the GCP MM Toolkit
All the markers included in this version of the toolkit have open access. However, kindly note that toolkit users are requested to provide due acknowledgement to:
- The original source (publication/database, etc) of the markers used (as per common practice)
- The MM Toolkit itself, as a source of information. Correct citation: Generation Challenge Programme (2009). The GCP Molecular Marker Toolkit. Material developed by Veerle Van Damme for the Generation Challenge Programme and available online at http://www.generationcp.org/sp5_toolboxhomepage_april_09.
Sources of accessions
As a breeder, you most likely already know how to gain access to the required breeding material. For those who are less familiar with how to get access to this kind of information, we are pleased to provide useful links to some key databases on plant genetic resources (PGR), below. In addition, TB users may like to visit the Consultative Group on International Agricultural Research (CGIAR) website. The CGIAR comprises centres with a mandate for specific crops, as well as centres that work on thematic and/or ecoregional issues in the wider natural resource management arena.
The System-wide Information Network for Genetic Resources (SINGER)
A searchable database that provides access to information on the collections of genetic resources held by the centres of the CGIAR and its partners. Together, these collections comprise over half a million samples of crop, forage and tree germplasm of major importance for food and agriculture.
GCIAR System-wide Genetic Resources Programme (SGRP)
Crop Genebank Knowledge Base
European Plant Genetic Resources Information Infra-Structure (EPGRIS)
A number of European countries have established national Plant Genetic Resources inventories that are available on the web.
List of Germplasm databases can be found as well on the website of Bioversity International
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Further reading
Interactive Resource Center & Helpdesk
The Interactive Resource Center & Helpdesk, created by the Institute for Genomic Diversity, with support from the Syngenta Foundation and the Generation Challenge Programme, provides information (including protocols, publications etc.) and interactive support to the international community of scientists working on molecular genetics and molecular breeding.
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GCP Learning Materials
GCP’s SP5 learning materials span several subjects (eg, policies, genomics, etc), and are directly derived from workshops and/or commissioned work at programme (SP5) level. The three sets of Learning Materials currently available are:
- Genetic resource policies course
- The McClintock crop bioinformatics course
- Genomics and comparative genomics tutorial
They are offered for free public use.
Global Partnership Initiative for Plant Breeding Capacity Building (GIPB)
The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, Germany
The IPK’s genebank in Germany holds an ex situ collection of agricultural and horticultural plants.
The National Plant Germplasm System of USDA–ARS
Part of the Germplasm Resources Information Network (GRIN) web server, providing germplasm information on plants. This programme is held within the U.S. Department of Agriculture's Agricultural Research Service (USDA–ARS).
CGN Plant Genetic Resources, The Netherlands
The Plant Genetic Resources (PGR) is part of the Centre for Genetic Resources (CGN) at the University of Wageningen in the Netherlands. On this site you can find information on CGN's crop collections, related research and protocols.
Feedback
As the MM Toolkit is designed to be a practical tool for breeding programmes, we strive to give as complete and accurate information as possible in order to meet breeders’ needs. As such, your comments and suggestions on ways to update and improve the site would be greatly appreciated.