Progress and Challenges in the Use of High-Density Genetic Markers by CGIAR Breeding Programs to Increase Genetic Gains for Major Food Crops in the Developing World.

The breeding programs of Consultative Group on International Agricultural Research (CGIAR) centers are beginning to use high-density genotyping (HDG) technology, ranging from relatively small SNP arrays to very large chips and genotyping-by-sequencing (GBS) technologies that detect hundreds of thousands of polymorphisms.  Low cost HDG will permit the integration of genotypic information across multiple populations, allowing faster localization of useful QTL alleles and generating very large datasets for training of genomic selection (GS) models. Most use to date has been for association mapping and diversity studies, but HDG is not yet used routinely for genomic selection in CGIAR centers.  The CIMMYT Global Maize Program is piloting the implementation of HDG in its breeding to support GS, which has the potential to reduce breeding cycle time and increase rates of gain.  Initial results in maize indicate that GS accuracy will be sufficient for identifying parents with high breeding value for rapid-cycle marker-based recurrent selection, but may not be  for predicting phenotypic value. The situation may be different in other crops.  Delivering useful genomic predictions to breeders to support selection decisions will require substantial improvements in the integration of genotypic, phenotypic, and pedigree data in all the major CGIAR breeding programs, and the costs of DNA extraction and genotyping will need to be reduced. Large investments in breeding informatics capacity and DNA extraction systems will be required that may be beyond the capacity of most public and private sector breeding programs in the developing world.  Centralized genotyping and breeding informatics services may be the most effective approach for delivering the benefits of HDG technology to CGIAR breeding programs and partners.  Networked, “open-source” genomic selection programs integrating CGIAR breeding programs with those of national programs and small regional breeding programs are likely to be needed to deliver the promise of the technology to smallholder farmers.