Significant progress has been made over the past years in the development and exploratory application of genomic tools for marker-assisted breeding in most ICRISAT crops. Collaborations with advanced research institution (ARI) and national agricultural research systems (NARS) partners have helped ICRISAT to make the best use of existing resources, develop the expertise in different disciplines, and establish a strong interface between advanced genomics research and downstream applications in breeding. Despite these facts, we still need to develop molecular genetic maps, based on intra-specific mapping populations, with reasonable marker density for some of our species like pigeonpea, groundnut and chickpea. The establishment of the Centre of Excellence in Genomics (CEG) at ICRISAT through the funding of the Department of Biotechnology (DBT), Government of India, will help us to achieve our goals to develop the genomic tools in a cost-effective manner at a fast pace. For example, establishment of DArT facilities at ICRISAT will help generate a larger number of marker data points that will make the development of maps quicker and cheaper. Further advances in discovery and genotyping of SNPs will allow us to explore the possibility of using cost-effective SNP marker assays for our crops. For example, integration of SNP markers into genetic maps of pearl millet and sorghum is already underway at ICRISAT by using CISPs on SSCP gels. It is anticipated that with the reducing costs of SNP genotyping, we will be exploring the possibility of utilizing SNP markers for integrating them into genetic maps, marker-trait associations and eventually for marker-assisted breeding.

The information provided by genomics/marker technology strongly complements that provided by good quality phenotyping, so the greatest value to crop improvement research will come from the integration of good quality marker and phenotyping data sets. To exploit this synergy for SAT crop improvement, it is critical to have a strong collaboration or network among the genomics program, breeding, genetic resources, crop physiology, pathology and entomology (for phenotyping) that may be appropriately complemented with biometrics and bioinformatics research and support capabilities.

The applied genomics team focuses on a range of priority traits across ICRISAT's mandated crops. For some crops, such as chickpea, finger millet, groundnut, pearl millet and pigeonpea, efforts are focused on marker development, as there are severe limitations for mapping and MAS. As marker systems and segregating populations become available, markers linked to the genes/traits are identified, verified and used in marker-assisted selection. The current status in each of these areas is indicated in the following table.

For further information contact: Dave Hoisington, Rajeev Varshney, Tom Hash