Microbiome-assisted plant breeding: integrating host-microbiome interactions into crop improvement

Conventional breeding and domestication have boosted crop productivity but have also narrowed plant genomic diversity and reduced the diversity of associated microbiota, contributing to domestication syndrome and limiting resilience under increasingly variable environments. Thus, genetic improvement remains essential for developing low-input, high-yielding, enhanced nutrient content and stress-tolerant crops. However, traditional breeding has largely focused on plant genomes, overlooking the microbial partners that influence plant performance. Plants function as holobionts where integrated units composed of the host and its microbiome. These microbial communities colonize all plant tissues and regulate nutrient acquisition, immunity, physiology, and yield, often generating novel phenotypes without altering the plant genome. Some beneficial microbial taxa can even restore plant traits lost during domestication, ascertaining their potential as heritable contributors to crop performance. Seeds play a major role in transmitting plant genes and vertically inherited microbiota, making them a strategic entry point for microbiome integration in breeding. Recent advances include seed microbiome inheritance, root-exudate-mediated microbial recruitment, microbiome-associated QTLs and synthetic microbial communities (SynComs) which can be harnessed to enhance crop traits. These insights provide the foundation for Microbiome-Assisted Plant Breeding (MAPB), a complementary breeding paradigm targeting both plant genomes and microbial partners. Hence, incorporating microbial inheritance, recruitment traits and holobiont performance into breeding pipelines positions MAPB as a promising path toward climate-resilient, resource-efficient, and sustainable crop varieties.