The Potential of Ultrahigh Throughput Genomic Technologies in Crop Improvement

THE PLANT GENOME ■ MARCH 2009 ■ VOL. 2, NO. 1 T HERE IS NO DOUBT this unlimited sequencing and genotyping capacity will signifi cantly aff ect plant breeding, functional genomics, systems biology, and many other related fi elds. But its eff ect is probably analogous to that of the Internet, World Wide Web, Web browsing, and e-mail on globalization in the mid-1990s. In the book Th e World is Flat, author Th omas Friedman identifi ed this “new” age of connectivity as one of 10 forces that fl attened the world. Investment, or overinvestment, in sequencing and genotyping will likely drive the cost of these technologies down further, mirroring how fi ber optics enabled virtually free data transmission. It is almost certain, however, that several other “fl atteners” need to be in place for the fi nal, grand-scale revolution in plant breeding. A second fl attener, methods of establishing genotype-phenotype relationship, requires further research. Continued eff orts in fi ne-tuning available tools (e.g., mutational library, reverse genetics, QTL mapping, cloning and tagging, association mapping, comparative mapping, introgression library, etc.) and identifying new tools are warranted. Although more “-omics” will be added to our toolbox, we should never underestimate the complexity of biological processes for complex traits. Essential genetic manipulation, physiological screening, and phenotyping processes that facilitate the breeding process, a third fl attener, also need to be in place. Effi cient protocols for double haploid and transformation do not exist for many crop species, and random mating cannot be conducted eff ectively in many self-pollinated crop species. Physiological screening methods for vari-