Screenhouse-based shade-tolerance assessments of coffee and bean varieties, and cover crops, to optimize multi-strata intercropping in African smallholder systems

Introduction Intercropping annuals with perennials such as banana, coffee and trees is widespread in East and Central Africa, where farms are typically small and fragmented. Within such multi-strata production systems, shade is a critical constraint affecting crop productivity. This study aimed to identify crop species and varieties tolerant to varying shade levels. Methods Twenty common bush and climbing bean ( Phaseolus vulgaris ) varieties each, eight Arabica coffee ( Coffea arabica ) varieties, and three cover crops (velvet bean ( Mucuna pruriens ), rattle pod ( Crotalaria grahamiana ), and elephant grass ( Pennisetum purpureum )) were screened under four screenhouses transmitting photosynthetically active radiation (PAR) levels of 70%, 50%, 35% and 10% compared to open field light levels. Results Eight bush and four climbing bean varieties maintained grain yields comparable to open-field conditions at low (70% light transmission) shade conditions. High tolerance persisted for many beans at 50% and 35% transmission, though only two bush beans (HM21-7, CODMLB 499) remained unaffected at the deepest shade (10% light transmission). Bush beans consistently elongated under shade, whereas climbing beans showed mixed height responses. Arabica coffee seedlings exhibited stable height and stem diameter across all shade levels, with only a few varieties showing modest reductions. Cover crops showed no shade tolerance, with > 84% above-ground biomass loss across all shade levels for elephant grass. Meanwhile velvet bean and rattle-pod suffered 48–58% biomass losses even at 70% light transmission, though velvet bean retained a high root mass until the deepest shade. Discussion These findings suggest a high diversity in shade tolerance within existing bean and coffee varieties. They demonstrate that selecting shade-tolerant bean cultivars and stable coffee varieties can substantially improve productivity in multi-strata systems, while many common cover crops are unsuitable beneath canopy shade. Rapid phenotypic screening could offer a low-cost strategy for optimizing crop mixtures and guiding breeding efforts toward greater shade resilience in smallholder multi-strata agro-ecosystems.