Genetic effects of plant plant interactions depend on neighbor identity and environmental context

Abstract

Plant-plant interactions shape community productivity and resilience, yet how genetic variation influences these interactions remains poorly understood. We conducted multi-environment field phenotyping of 200 common bean (Phaseolus vulgaris) lines grown in association with three maize (Zea mays ssp. mays) landraces to characterize the determinants of interspecific interactions. Our results reveal that maize landraces constitute distinct biotic environments, and interactions were strongly asymmetric, with maize acting as the dominant competitor. Bean responses to the identity of the maize partner involved phenology, vegetative development, productivity, and root architecture, and varied across field environments, with no evidence of bean local adaptation. We used genome-wide association to link variation across the bean genome to variation in bean and maize traits, thereby capturing both direct and indirect genetic effects, and tested for maize bean interactions. We identified six genomic regions with indirect effects: three with stable effects across maize partners and three whose effects varied with maize partner identity, including candidate genes involved in neighbor perception and facilitative interactions. Our findings demonstrate that the phenotypic effects of genetic variation extend beyond individual plants, with competitive tolerance modulated by the genetic identity of neighboring plants and the environment.