White paper on GCP research components: Informative molecular markers


A series of Position Papers have been drafted by the CGIAR Generation Challenge Programme (GCP) team in collaboration with external experts. The goals are to communicate the outputs and deliverables from each research component during 2004–2014, and to explore options for enabling and ensuring that the potential benefits of these components will be fully realised in the future.

This paper focuses on the outputs and options for GCP’s informative molecular marker component. Outputs have been achieved through (a) collaborative work among three sets of actors: a broad network of partners in regional and country research programmes, the CGIAR and academia; and (b) through capacity enhancement to assist developing-world researchers to tap into new genetic diversity and access modern breeding tools and services.

Recent developments in plant molecular genetics have provided plant breeders with powerful tools to identify and select Mendelian components underlying both simple and complex agronomic traits. DNA markers enable identification of genes and genomic regions (quantitative trait loci or QTLs) associated with the expression of numerous qualitative and quantitative traits important for crop breeding. Today, scientists are able to genetically dissect pathways that control important biochemical and physiological parameters, and thus better understand how they are regulated. As a natural extension of the ‘discovery phase’, molecular markers permit the pyramiding of favourable alleles in targeted genetic backgrounds through molecular breeding. The genetic dissection of a target trait starts with positioning neutral polymorphic markers along the crop genome to construct a genetic map to identify QTLs or to define haplotypes for association studies. Once a marker is identified as linked to a region of interest and explains a significant percentage of the phenotypic variance of the target trait, it is designated as an informative marker.


GCP Management Team. White paper on GCP research components: Informative molecular markers. Generation Challenge Programme, Mexico (2012) 21 pp.

White paper on GCP research components: Informative molecular markers

Published 1 January 2012