Molecular breeding of genes, pathways and genomes by DNA shuffling

Classical breeding is a gentle mutagenesis process that simply creates new combinations of a large number of DNA sequence polymorphisms that pre-exist in the population, thus allowing the evolutionary optimization of very complex genomes. We have developed and applied a wide variety of derivative processes called ‘molecular breeding’ to breed single genes, contiguous pathways, distributed pathways, and even whole microbial genomes. Libraries of clones that are created by breeding are phenotypically diverse because clones tend to differ by many amino acids due to the exchange of sequence blocks, yet an exceptionally high fraction of the library is functional because the natural sequence polymorphisms were preselected for compatibility with function. A wide variety of formats and applications of molecular breeding is described.