Lagardere, B. | bioRxiv Science

bioRxiv2026

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

O_LICereal-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. C_LIO_LIWe 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 x E interactions tested using contrasts among maize landraces. C_LIO_LICompetitive 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. C_LIO_LIThese 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. C_LI

genetics↗

bioRxiv2024

A multidisciplinary on-farm survey of maize-bean intercropping shows that revival of traditionalagricultural systems requires careful consideration of partner varieties and agronomic practices.

O_LICereal-legume intercropping is a promising strategy for sustainable agroecosystems. The traditional intercropping of maize and bean is experiencing a revival in some modern agricultural settings, such as in southwestern France, where maize hybrids are intercropped with the commercialized Tarbais bean. We conducted on-farm surveys and a field assay to address the following questions: How does the cropping system impact yield, nutrient uptake, and rhizosphere bacterial assemblages? Do positive or negative interactions between maize and beans dominate in intercropping? What is the effect of intercropping on plant transcriptomics? C_LIO_LIWe recorded farming practices, conducted yield and nutrient measurements, and characterized soil bacterial assemblages to compare sole-cropped maize and beans with intercropped plants. A controlled field assay was also established to extend this comparison to plant gene expression differences. C_LIO_LIIntercropping was associated with a trend towards increased bacterial diversity. The cropping system significantly influenced agronomic traits, with frequent farm-by-cropping system interactions underscoring the critical role of farming practices. Competition dominated maize-bean intercropping, with 34 negative correlations among the 47 significant ones between maize and bean traits. This competition affected yield and nutrition, but primarily impacted beans, which produced fewer but bigger/heavier seeds. Transcriptomic results concurred with these findings, revealing no differentially expressed genes in maize but 5,070 in beans under competition. C_LIO_LIOverall, our findings suggest that beneficial interactions between the two crops are hindered under current field conditions, underscoring the importance of carefully considering partner varieties and farming practices to revive traditional agricultural systems. C_LI Societal Impact StatementCereal-legume intercropping is a promising strategy for sustainable agroecosystems that leverages the biological complementarities between plant species, reducing the need for chemical inputs while enhancing field biodiversity. Here, we focused on maize-bean intercropping, which is experiencing a revival in modern conventional agricultural settings. We found a trend towards an increased soil bacterial diversity in intercropping. However, competition between the two crops dominated and primarily impacted yield and gene expression in beans. Despite lower yield, bean seeds exhibited greater size. Our study indicates that implementing variety selection of both species and adapting farming practices is essential to fully harness the potential of intercropping.

plant biology↗