K. Murugan, M. Vengadesan, L. Soukoumar, P. Adhimoolam Abiotic stress, biotic Stress, microbiome, nutrient acquisition, plant breeding 39-46 10 (1) January, 2026 Conventional plant breeding primarily focuses on genotype × environment (G × E) interactions to select superior cultivars for commercial cultivation. However, plant–microbe interactions have remained largely underexplored despite their critical role in regulating plant growth, development and environmental adaptation. Plant-associated microbiomes enhance tolerance to biotic and abiotic stresses by modulating plant metabolism, nutrient acquisition, signaling pathways, and antimicrobial defense mechanisms. Host-specificity of beneficial microbes remains a major challenge limiting their successful application under field conditions. Therefore, further research is required to overcome these constraints and facilitate the effective integration of microbiomes into plant breeding programs. This review summarizes recent advances in microbiome-assisted crop improvement, discusses mechanisms underlying stress resilience and breeding applications, and outlines future directions for integrating beneficial microbiomes into sustainable plant breeding programs.