Microbiome-Assisted Breeding: Engineering the Holobiont in Horticultural Crops

Abstract

Horticultural crop improvement is moving from a plant-centred model toward a soil-plant-microbiome framework in which host genotype, root-zone biology and the production environment are considered together. Microbiome-assisted breeding (MAB) aims to select plant genotypes that recruit, accommodate or respond to microbial communities capable of improving nutrient acquisition, soil fertility, disease suppression, abiotic-stress resilience, fruit quality and post-harvest performance. This review synthesizes the current basis of holobiont engineering with a primary focus on soil and plant-associated microbes of horticultural crops. The rhizosphere, rhizoplane, root endosphere, seed, flower and fruit compartments are considered as connected but functionally distinct microbial habitats. Important microbial groups include arbuscular mycorrhizal fungi, plant-growth-promoting rhizobacteria, diazotrophs, phosphate-solubilizing bacteria and fungi, actinobacteria, Trichoderma, endophytes, yeasts and defined synthetic communities. Recent literature highlights three developments: regulation of rhizosphere microbiomes by host traits and management, microbiome-interactive traits as potential breeding targets, and rhizosphere hybridization or microbiome engineering to build climate-smart and disease-suppressive soils. However, microbial abundance alone is not evidence of function, and inoculants frequently perform inconsistently when they cannot establish within a compatible native community. A practical MAB pipeline should combine host genotyping, soil physicochemical analysis, 16S/ITS or shotgun sequencing, culturomics, metabolomics, causal inoculation, synthetic-community testing and multi-environment validation. The review proposes priority research pathways for fruit, vegetable, spice, ornamental and underutilized crops and emphasizes that plant genotype × microbiome × soil management interactions must be measured explicitly. MAB should therefore complement—not replace—conventional breeding, crop management, conservation and farmer knowledge.