Diurnal plant and Rhizophagus irregularis transcriptional patterns are linked to shifts in cassava tissue partitioning in the field

O_LICassava is a globally-important crop whose yields can radically increase with arbuscular mycorrhizal fungi (AMF) inoculation. However, extensive background noise in field environments makes it very challenging to understand how the cassava-AMF symbiosis confers benefits, which is especially important for future applications of AMF treatments. C_LIO_LIIn two field experiments, we combined transcriptomics and allometric analyses to investigate functional variation in cassava-AMF interactions using sterile, single isolates of Rhizophagus irregularis. We developed a novel Index of Symbiotic Transcriptional Activity (ISTA) and accounted for sampling times to reduce transcriptomic noise and improve links to biomass traits. C_LIO_LIISTA significantly correlated with cassava shoot biomass in an isolate-dependent manner, and allometric analyses revealed that R. irregularis isolates can either reinforce or uncouple cassava shoot-root relationships to maximize root yields. Differential expression and co-expression network analyses uncovered isolate-specific plant and fungal gene module responses. Including ISTA and sampling time as random effects enhanced detection of gene candidates, including down-regulated genes linked to higher yield. C_LIO_LIOur study uses novel and translatable transcriptomic tools to readily dissect variably field data, allowing new links to be found between AMF symbiotic functions and cassava yields. C_LI