Breeder's Delight

The Generation Challenge Programme's new Molecular Marker Toolkit is a Swiss Army knife for breeders of 19 crops essential to maintaining global food security.

A woman farmer and her child in a cowpea field at Pobe, Burkina Faso. Marker-assisted selection is helping speed up the incorporation into this and other crops of traits that are essential for food security. Photo: GCP.

Over the past 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 by growing out and examining the phenotype. As such, marker-assisted selection (MAS) helps to speed up the incorporation of these valuable traits. The increase in genomics research has produced massive publications and databases that make the search for user-ready molecular markers for a particular trait a real odyssey. Driven by demand from agricultural researchers and plant breeders, particularly those in developing countries who face difficulties in accessing up-to-date scientific information on useful molecular markers, the Generation Challenge Programme (GCP) of the Consultative Group on International Agricultural Research designed a rapid-access tool for validated markers currently available for 19 crops essential to food security, including GCP's 18 mandate crops. The 19 crops currently covered are Musa spp. (banana and plantain), barley, bean, cassava, chickpea, coconut, cowpea, faba bean, groundnut, lentil, maize, millet, pigeonpea, potato, rice, sorghum, sweet potato, wheat and yam.

The first draft of GCP's Molecular Marker Toolkit is limited to the highly reproducible simple sequence repeat (SSR), sequence tagged site (STS) and sequence characterized amplified region (SCAR) markers. For each of the 19 crops, the toolkit summarizes the current status of MAS and offers useful tips on further reading. For each marker in the toolkit, the available information is divided into four easily navigable windows. Window 1 provides general information on a given marker, such as its name and type, the trait to which it is linked, and the name of the crop expert. Window 2 describes the corresponding laboratory protocol (primers, polymerase chain reaction conditions, etc.). Window 3 gives more information on the validation process of the marker, including the donor, recurrent parent, and population type and size. And window 4 displays references to key papers and/or websites consulted.

Preparatory work for the project was extensive and meticulously done. An early phase of the Molecular Marker Toolkit's development saw the compilation of information accessible via internet sources, public databases and papers on the available markers useful in MAS for each of the 19 crops. At a subsequent stage, the findings were analyzed and published in the form of a preliminary list of markers, which was then presented to several crop experts who checked if the markers were effectively used in MAS. In light of both breeders' access to the most up-to-date information and their essential hands-on experience in the use of markers, the collaboration of the breeder community was vital to the analysis. After this revision by experts, the updated information was entered into the toolkit.

For Musa spp., coconut, lentil, millet, pigeonpea, sweet potato and yam, either MAS is not yet applied or the markers that are used do not comply with the conditions for inclusion in the toolkit. For these crops the information provided is limited to the actual status of use of molecular markers in the crops. There are currently 200 entries in the toolkit, of which 172 refer to SSR, single nucleotide polymorphism, SCAR or STS markers that are linked to 65 traits. The remaining 28 entries refer to other marker types or to traits that are known only to have had MAS applied but for which there is no further information thus far. The toolkit complements GCP's Genotyping Support Service, which aims to facilitate national agricultural research systems' access to genotyping technologies.

As an easily accessible global public good paving the way to the latest advances in molecular plant breeding, the GCP Molecular Marker Toolkit is a key contribution to ensuring that modern agricultural science benefits the poor in developing countries, and one that is already causing a stir among the most critical audience of all - the breeders themselves.

"The database is a good idea and very useful," comments Sigrid Heuer, a molecular biologist at the International Rice Research Institute (IRRI).

"I think it's a great idea," concurs IRRI colleague and breeder Mike Thomson. "I hope we can support the toolkit more in the future."

Feedback from cassava breeders in Africa has been equally positive.

"I appreciate initiatives that make information easily accessible to breeders worldwide," says Emmanuel Okogbenin of the National Root Crops Research Institute in Nigeria. "This toolkit is excellent. It's a breeder's delight."

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