Distinguishing varying and carrying populations in holobiont breeding

Breeding for plant-microorganism interactions is challenging, and existing approaches remain conceptually fragmented. We distinguish the 'varying population', comprising organisms that harbor heritable variation, from the 'carrying population', comprising organisms that express the selected property. In traditional breeding, a single partner typically fulfills both roles. In novel plant-microorganism breeding, these two roles may be distributed between both partners, and selection may rely on 'indirect genetic effects'. Holobiont breeding can be defined as cases in which the varying population is the combination of both partners. By providing a community-level perspective on the causal roles of replicators and interactors, our framework offers an operational translation of evolutionary concepts, which is compatible with quantitative genetics and usable as a step-by-step guide for designing breeding programs.