Molecular Pathogens, 2025, Vol.16, No.6, 266-275 http://microbescipublisher.com/index.php/mp 269 4.3 Regulation of rhizosphere microbial composition through host genome selection Often, breeding focuses on "visible" traits such as disease resistance, drought tolerance, and well-developed root systems, but the plant's ability to recruit microorganisms is often indirectly "adjusted" as well. In some cases, this change is even conscious. For example, in legumes and strawberries, varieties resistant to soil-borne pathogenic bacteria recruited more Pseudomonas and Burkholderia, which themselves have inhibitory effects (Dwivedi et al., 2025). Not only these, GWAS analysis has also identified some genetic loci related to the characteristics of microbial communities (Yue et al., 2024), which makes "microbial selection" a realistic approach that can be integrated into crop breeding goals. From this perspective, regulating microbial recruitment through host genes is not an "added bonus", but could be a crucial step in promoting healthier and more sustainable agricultural systems. 5 Integrated Strategies Combining Rhizosphere microbiota and Disease-Resistance Breeding 5.1 Integrated analysis approaches for microbiome–plant interaction omics What exactly happens between plants and microorganisms? To clarify this matter, relying solely on a single data dimension is far from enough. Once metagenomics, metabolomics, transcriptomics, phenomics and other omics technologies are introduced, the research perspective becomes three-dimensional - what can be seen is not only "who is there", but also "what they are doing". For instance, metabolites released by the root system, the genetic background of the plant itself, and even changes in the external environment can all affect the structure and function of rhizosphere microorganisms (Mishra et al., 2022). The integrated data are not simply superimposed but help researchers identify the key microbial groups that may affect plant disease resistance and find the specific regulatory pathways or metabolic links behind them (Ferrarezi et al., 2023; Mmotla et al., 2025). Although data processing is complex, this systematic perspective is particularly valuable for the subsequent design of microbial intervention strategies or targeted breeding pathways (Vidal et al., 2022). 5.2 Utilizing core microbial resources to enhance crop resistance Not all microorganisms are worthy of focused research; some "core members" are the true protagonists. They are commonly found in the rhizosphere of healthy plants, such as the taxonomic groups of Helicobacter nitrifying, Monococcus, and Pseudomonas, and often hold important positions in the microbial network. They can both inhibit the expansion of pathogenic bacteria and enhance the stability and mutual assistance of the entire platform (Qiao et al., 2023). Sometimes, "transplanting" them into originally susceptible soil or crop root zones can also achieve a certain degree of disease resistance effect - synthetic microbial communities (SynCom), healthy soil mixtures, and even complete transplanting have all been used in such experiments (Badar et al., 2025; Liu et al., 2025). Although the transformation efficiency is limited by environmental factors, such operations at least provide another approach for disease-resistant breeding - not just modifying the plants, but also "changing the circle of friends". 5.3 Breeding models combining microbial screening and plant material selection In the past, breeding focused more on the plants themselves. Now, the attention has gradually expanded to the "microbiome" around the plants. Introducing microbiome information into the breeding process is no longer an attempt by a minority. For instance, some research studies first select some plant genotypes that can stably recruit beneficial microorganisms, while others use GWAS or molecular markers to lock onto those microbial-mediated sites related to disease resistance. Meanwhile, the use of microbial inoculants is no longer a simple addition but has entered the screening process to determine which plant-microbial combinations are the most reliable (Araujo et al., 2024). Of course, there are also more radical approaches, such as "mutual soil transplantation" or building artificial ecosystems to directly promote the co-breeding of plants and their microbial partners (Zhao et al., 2025). This kind of "cooperative breeding" may seem complicated, but in the face of a complex disease system, it might be a solution that better conforms to the logic of natural ecology.
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