Host Genetic Determinants of Plant–Microbiome Assembly and Function

Plants shape the structure, composition, and function of their associated microbial communities through genetically regulated traits, including physical barriers, root architecture, root exudation, immune signaling, habitat modification, metabolism, and nutrient homeostasis. Together, the host and its microbiome form an interconnected biological system in which interactions range from mutualism and commensalism to pathogenicity. Increasing evidence demonstrates that host genetic variation influences microbiome assembly, thereby affecting plant growth, nutrient acquisition, stress tolerance, and disease resistance. Recent advances in comparative genomics, microbiome profiling, and functional genomics have facilitated the identification of host loci (or genes) and regulatory networks involved in recruiting and maintaining beneficial microbial communities in both model and crop plants. However, the genetic and molecular mechanisms underlying host control of microbiome assembly remain incompletely understood across diverse crop species and environmental conditions. Integrating host genetics with microbial genomics and functional validation is essential for understanding plant–microbe co-adaptation and for developing microbiome-informed strategies, including the genetic improvement of crops to enhance the recruitment and persistence of beneficial microorganisms. This Research Topic aims to advance our understanding of the host genetic determinants that govern the assembly, composition, and functional attributes of the plant microbiome. We welcome studies that identify host genes, loci, regulatory pathways, and molecular mechanisms controlling microbial recruitment, colonization, persistence, and activity in the rhizosphere, endosphere, and phyllosphere. Contributions employing comparative microbial genomics, genome-wide association studies (GWAS), quantitative genetics, transcriptomics, metagenomics, metabolomics, transgenic approaches, and genome editing to elucidate host–microbiome interactions are particularly encouraged. We also seek studies investigating plant–microbe co-adaptation in natural and agricultural ecosystems, including responses to nutrient limitation, abiotic stress, and pathogen challenge. Studies integrating functional validation of candidate host genes with microbial community analyses, as well as those exploring how host genetic variation can be exploited to engineer or breed crops with improved microbiome recruitment and function, are especially welcome. By bringing together multidisciplinary research, this collection aims to provide mechanistic insights into the genetic basis of plant–microbiome interactions and support the development of crop improvement strategies that harness beneficial microbial partnerships for resilient and sustainable agricultural systemsThis Research Topic welcomes original research articles, reviews, perspectives, and methodological papers addressing the genetic basis of plant–microbiome interactions. Topics of interest include host genetic regulation of microbial recruitment and colonization, genotype-dependent microbiome variation, comparative microbial genomics, functional characterization of host genes and loci, plant–microbe co-evolution and co-adaptation, and host genetic influences on microbiome function under biotic and abiotic stresses. Studies integrating genomics, transcriptomics, metagenomics, metabolomics, proteomics, genome editing, quantitative genetics, or computational approaches are encouraged, particularly when supported by functional or experimental validation. Contributions involving model species, crop plants, and agriculturally important microbial communities are equally welcome. Manuscripts should provide novel mechanistic insights, methodological advances, or translational approaches that improve our understanding of host genetic control of microbiome assembly and function, with potential applications in crop breeding, microbiome engineering, and sustainable agricultural production. Topic editors: Jyotsana Tilgam, Murugan Kumar, Parthiban Subramanian, Hillol Chakdar Source: https://www.frontiersin.org/research-topics/86089/host-genetic-determinants-of-plant-microbiome-assembly-and-function