Optimization of genetic gain and diversity in seed orchard crops considering variation in seed germination

Abstract Balancing genetic gain and diversity in seed orchard crops is of a major regeneration importance. Here we extend our earlier work on the development of an optimization protocol that maximizes crops' genetic gain at any predefined diversity level, considering parental reproductive output, co-ancestry, and inbreeding, by incorporating variation in seed germination as an input. Variation in seed germination capacity substantially affected seedlots' genetic diversity by either under- or overestimating their effective population size; however, genetic gains were robust and their differences were negligible. The contrasting results of gain and diversity support the inclusion of the germination capacity, when available, in the optimization protocol.