Breeding Informatics for Crop Improvement: Current Status and Prospects

Advances in modern biology have changed the whole profile of plant breeding. The increasing availability of breeding information, including pedigree, phenotypic and genotypic, coupled with environmental data, brings both opportunities and challenges in effectively managing and utilizing such information in breeding programs. Etyping, or environmental assay, is proposed (Xu et al. 2012. Mol Breed 29:833–854) to characterize all environmental factors associated with plant growth, development and crop productivity. Genotyping, phenotyping and etyping work together to provide three major sources of breeding information that becomes increasingly important in modern plant breeding. Some important platforms have been developed in recent years for collecting breeding information, including high-density genotyping, high-throughput and precision phenotyping and whole-profile etyping. The technology platforms to support projects that generate large amounts of data in multiple locations require highly adaptable and flexible system architecture and implementation. The architecture needs to be flexible enough to attend each of the anticipated problems whilst at the same time taking advantage of opportunities to improve standards, tools and processes related to the management of genetic resources, genotypic data, environmental data, germplasm information and phenotypic characterization. A comprehensive information system is required to integrate and manage all available information generated in genetics and breeding research activities such as gene discovery, functional marker development and precision environment profiling. With numerous tools available for curating, retrieving, integrating and mining of all breeding-related information, molecular breeding can be driven at the scale and depth that have never been possible. There are opportunities now to design and implement strong decision support systems, with appropriate tools and procedures, for enhancing the efficiency of crop breeding programs. Such a system will aid the breeders in selection of desirable recombinants through an optimum combination (in time and space) of phenotypic and genotypic information, as well as minimizing population sizes, number of generations and overall costs while maximizing genetic gain for traditional and novel target traits. Simultaneous with these developments, massive efforts are required to train human resources in relevant institutions, especially in the developing world, for taking advantage of the technological developments in breeding information management.