Back to the future: implications of genetic complexity for the structure of hybrid breeding programs

Commercial hybrid breeding operations can be described as decentralized networks of smaller, more or less isolated breeding programs. There is further a tendency for the disproportionate use of successful inbred lines for generating the next generation of recombinants, which has led to a series of significant bottlenecks, particularly in the history of the North American and European maize germplasm. Both the decentralization and the disproportionate contribution of inbred lines reduce effective population size and constrain the accessible genetic space. Under these conditions, long-term response to selection is not expected to be optimal under the classical infinitesimal model of quantitative genetics. In this study, we therefore aim to propose a rationale for the success of large breeding operations in the context of genetic complexity arising from the structure and properties of interactive genetic networks. For this, we use simulations based on the NK model of genetic architecture. We indeed found that constraining genetic space through program decentralization and disproportionate contribution of parental inbred lines, is required to expose additive genetic variation and thus facilitate heritable genetic gains under high levels of genetic complexity. These results introduce new insights into why the historically grown structure of hybrid breeding programs was successful in improving the yield potential of hybrid crops over the last century. We also hope that a renewed appreciation for "why things worked" in the past can guide the adoption of novel technologies and the design of future breeding strategies for navigating biological complexity.