Marker-assisted selection (MAS) and marker-accelerated breeding (MAB) require reliable identification and application of simply inherited markers that are in close proximity to genetic factors affecting simple, oligogenic and polygenic traits of interest to stakeholders. This can proceed through a mapping-population-based or an association mapping approach, the latter typically based on a sample of unrelated individuals.

The mapping-population-based approaches, with or without a linkage map, are popular in plants, relatively well-developed, and practical nuances of their application well understood. The use of association mapping in plants, on the other hand, has only recently started. Association mapping is likely to provide a reduced level of redundancy during the transition from marker identification to application in diverse breeding populations and germplasm. It may be of a particularly useful route to follow where the creation of a large enough mapping population and a good linkage map is not feasible due to constraints in the development of these populations or non-availability of sufficient polymorphic markers. In either approach, the journey from the phenotyping-and-genotyping of individuals to the identification and application of markers in molecular breeding involves the sequential use of a number of different software – each with its own input data format requirement and many alternative choices for data analysis.

The use of appropriate experimental design and data analysis is a critical component for successful development and application of marker-assisted breeding systems strategies. Making these choices rightly is a highly specialized function. There is a lack of proper and simple-to-use guidelines for non-specialists, which makes it difficult for them to confidently choose the appropriate design and analysis methods offered by various software. Having a centralized and evolving resource offering biometric inputs required for molecular breeding would be a tremendously valuable asset to the research and breeding community.

The Integrated Marker-Assisted Selection System (iMAS) is an integrated molecular breeding analysis platform to facilitate an integrated system, based on freely available software. Support for developing and testing iMAS has been provided by the Generation Challenge Program (GCP). The system is specifically designed to be used with only a minimal hardware configuration that can usually be found in most can be used in marker molecular research laboratories and breeding programs of national programs and breeders in developing countries. It also utilizes open-source software packages or we have obtained no-cost licenses to distribute the software to all users.

The iMAS provide s simple-to-follow guidelines embedded into the a common front-end of the system to help users choose the most appropriate experimental design and data analysis methods, and provide them with a regularly updated selection of the currently most appropriate options. Since converting the format of datasets to meet the differing requirements of various software is also an extremely time-consuming process fraught with errors, the iMAS performs the required data formatting for all included software.

It is envisaged that the availability of this system iMAS will foster further necessary developments of freely available tools to be integrated into it in future. Also, it is hoped that other parallel GCP competitive projects will support the development of solutions to any fundamental gaps in computational support for molecular breeding for which there are no alternative suppliers of freely available software.

For further details contact :Subhash Chandra