Use of optimal contribution selection and optimal cross selection in various plant breeding settings

This contribution demonstrates the use of optimal contribution selection and optimal cross selection in plant breeding with a focus on different plant reproductive systems and stages of a breeding programme. Optimal contribution selection is a method that enables breeders to ensure long-term sustainability of a breeding programme. This is achieved by optimizing selection and use of selected individuals such that short-term genetic gain is maximized for a given loss in genetic diversity. While optimal contribution selection achieves the aim by assuming random crossing, including selfing, the cross selection expands the utility by optimising a crossing plan. These two methods are well known in animal breeding and have been recently advocated also for plant breeding. However, plant breeding involves a range of species with diverse biological and operational characteristics that have to be accounted for when deploying these methods. Here we demonstrate the use of optimal contribution selection and optimal cross selection in three specific scenarios: (i) a dioecious species, such as hemp, araucaria, and kiwi; (ii) a monoecious or bisexual species in settings with an unlimited amount of seed per selection candidate, for example in advanced stages of a breeding programme; and (iii) a monoecious or bisexual species in settings with a limited amount of seed per selection candidate, for example in early stages of a breeding programme. We demonstrate each scenario with a small simulation, including scenario-specific formulation of the optimisation problem and implementation of the optimisation with the AlphaMate software. These examples will help breeders to evaluate optimal contribution selection and optimal cross selection in specific settings.