A hybrid optimal contribution approach to drive short-term gains while maintaining long-term sustainability in a modern plant breeding program

Abstract

1Plant breeding programs must adapt genomic selection to an already complex system. Inbred or hybrid plant breeding programs must make crosses, produce inbred individuals, and phenotype inbred lines or their hybrid test-crosses to select and validate superior material for product release. These products are few, and while it is clear that population improvement is necessary for continued genetic gain, it may not be sufficient to generate superior products. Rapid-cycle recurrent truncation genomic selection has been proposed to increase genetic gain by reducing generation time. This strategy has been shown to increase short-term gains, but can quickly lead to loss of genetic variance through inbreeding as relationships drive prediction. The optimal contribution of each individual can be determined to maximize gain in the following generation while limiting inbreeding. While optimal contribution strategies can maintain genetic variance in later generations, they suffer from a lack of short-term gains in doing so. We present a hybrid approach that branches out yearly to push the genetic value of potential varietal materials while maintaining genetic variance in the recurrent population, such that a breeding program can achieve short-term success without exhausting long-term potential. Because branching increases the genetic distance between the phenotyping pipeline and the recurrent population, this method requires sacrificing some trial plots to phenotype materials directly out of the recurrent population. We envision the phenotypic pipeline not only for selection and validation, but as an information generator to build predictive models and develop new products.