Shaping root system architecture: holobiont-based phenotyping for root traits

The root system is a critical component of plants, significantly influencing above-ground growth and development. Root traits determine critical aspects of water use efficiency (WUE) and nutrient use efficiency (NUE). Additionally, roots are the site of synthesis of certain metabolites in response to various internal and external signals, which can influence plant-microbe interactions. Recent findings highlight the crucial role of beneficial microorganisms in shaping root phenotype and function. Root-specific endo-symbionts (endophytes) can modify root system achitecture (RSA) and root activity by improving water uptake, nutrient acquisition, and phytohormone production, thereby boosting growth, development, and productivity of crops. Studies suggest that endophyte-mediated activation of root traits can enhance the resilience of host plants to abiotic stress. This review discusses findings related to RSA and the importance of hologenome (the host and endophytes genomes) in root trait activation. Exploring root trait-specific endophytes and evaluating hologenome combinations with high-throughput phenotyping offer an eco-friendly alternative to traditional breeding methods and other biotechnological approaches used for crop improvement.