Dissecting the phenotypic and genetic determinants of maize-bean interactions in intercropping

Abstract

Cereal-legume intercropping is a cornerstone of agroecological systems because interactions between species can enhance agroecosystem resilience. Yet, the mechanisms underlying these interactions remain poorly understood. To address this gap, we investigated the maize-bean association under low-input conditions. We conducted a two-year intercropping experiment with 200 climbing bean lines grown alongside three maize landraces in France and Romania. We evaluated bean phenotypic responses above- and below-ground to 3 maize landraces, treated as distinct biotic environments (E). Direct and indirect genetic effects were assessed by mapping bean and maize phenotypic traits onto the bean genome (G), with G-by-E interactions tested using contrasts among maize landraces. Competitive interactions dominated, maize acting as the stronger competitor. Maize landraces created distinct biotic environments affecting bean traits. Best-performing partners varied across experimental fields, with no evidence of bean local adaptation. The most productive and balanced mixtures were obtained with the traditionally intercropped maize landrace. Genome-wide association analyses identified loci underlying direct and indirect genetic effects, including candidate genes associated with neighbor perception. These findings reveal the genetic complexity of maize-bean interactions and highlight competitive tolerance in bean and reduced aggressiveness in maize as key traits for improving cereal-legume intercrop performance.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 30 Jul 2026.

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