Editorial: Genetics and genomics of emerging and multifactorial stresses affecting plant survival and associated plant microbiomes

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Several contributions leverage powerful genomics tools to identify genes and markers associated with stress-related traits. Vutla et al. dissected the genetic basis of eight key traits in pearl millet (Cenchrus americanus) using a recombinant inbred line population and high-density SNP map, identifying 45 QTLs. The co-localization of multiple QTLs on LG3 and consistent detection across years emphasizes the robustness and breeding relevance for the yield-related traits and also suggesting linked improvement of traits like plant height and panicle size in pearl millet.The overlap of QTLs means breeders can potentially improve multiple traits with fewer selection cycles. This work helps secure millet's role as a hardy cereal for food and fodder in marginal lands. Sahu et al. conducted a comprehensive meta-analysis consolidating QTL data from 30 studies over 12 years, leading to the identification of 70 high-confidence meta-QTLs associated with yield, stress tolerance, and aflatoxin resistance in peanut (Arachis hypogaea). The discovery of candidate genes linked to aflatoxin resistance and fatty acid composition offers direct targets for marker-assisted programs. This sets the stage for peanuts that are safer, healthier, and more climate-resilient. Chandana et al. conducted a large-scale genome-wide association studies (GWAS) in chickpea (Cicer arietinum), identifying over 1,000 marker-trait associations, including 75 novel loci related to root nodulation. Their work provides critical genetic insights into enhancing biological nitrogen fixation, an essential trait for sustainable crop production. In wheat, Sharma et al. employed QTL meta-analysis to consolidate over 200 QTLs associated with powdery mildew resistance into 68 meta-QTLs and 13 high-confidence MQTLs, some colocalizing with known resistance genes in wheat. The refined loci enable fine mapping and functional studies to enhance durable resistance. Complementarily, Vishwakarma et al.performed GWAS to map SNPs linked to grain quality and agronomic traits in bread wheat (Triticum aestivum). Their identification of stable, environment-resilient SNPs informs breeding programs aimed for dual improvement in yield and quality. Suresh et al. screened 427 tropical maize lines and identified 14 lines with robust Gray Leaf Spot resistance, some carrying extra drought or viral resistance. The genetic markers found provide a toolkit for breeders to combine disease resistance with agronomic performance. Given GLS's yield impact in Africa, these donor lines could substantially reduce crop losses without heavy fungicide use. Together, these studies illustrate the power of modern genomic tools to untangle complex stress-related traits and move toward the development of crop varieties that are not only high-yielding but also resilient to multifactorial environmental stresses. Their collective contributions mark a critical step in incorporating multi-trait and environment-stable genomic regions into mainstream breeding programs. Collectively, these insights reveal the sophisticated regulatory frameworks plants employ to navigate environmental stress and emphasize untapped avenues for breeding resilient cultivars through the integration of molecular and evolutionary principles.Several studies bridged molecular discoveries with practical applications. Wambi et al. employed a multi-trait, principal component-based selection index on 192 maize hybrids to identify genotypes resistant to fall armyworm (FAW). The best index improved yield under infestation while cutting leaf damage significantly. This approach lets breeders target multiple traits at once, speeding development of pest-resilient hybrids. Such tools could be crucial for African farmers battling FAW without heavy pesticide reliance. This approach offers a robust and efficient tool for breeding high-yielding, FAW-resistant maize varieties. Kavai et al. investigated the genetic basis of resistance to maize lethal necrosis (MLN) in tropical maize by evaluating 182 hybrids from a 14-parent diallel across three years under artificial inoculation and rainfed conditions in Kenya. Identifying inbred lines with both resistance and yield potential allows for hybrid development without major trade-offs. In regions hit by MLN, these results offer a pathway to stable maize production in sub-Saharan Africa. Wang et al. offer a mechanistic foundation for hemiparasitic seedling development in Malania oleifera, an ecologically significant and oil-rich tree endemic to karst regions. Growth trials with nutrient-rich/poor soils and various hosts showed vigorous hosts greatly improved aboveground growth, with less effect on roots.Hormone metabolism, stress response, and antibiotic biosynthesis genes were upregulated in haustoria. Host association boosted nutrient synthesis and stress tolerance. Findings aid cultivation of hard-to-grow hemiparasites while optimizing propagation strategies for this economically valuable species.An essential component of this Research Topic is the examination of plant-microbiome interactions in stress contexts: Rhizosphere microbial communities are dynamic mediators of plant stress responses and disease resistance. Crop genotype, soil conditions, and biotic stresses co-influence microbial shifts, with strong implications for sustainable agriculture. One of the most forward-looking themes in this Research Topic is the plant holobiont conceptthe recognition that plant performance is co-determined by its microbiome:• Tyagi et al. reviewed microbial dysbiosis under waterlogging stress.• Ahmad et al. showed how P. indica inoculation enhances salt tolerance in date palm.These studies collectively advocate for "holobiont breeding", integrating host genetic traits with microbiome function-a paradigm shift from conventional plant-centric approaches to cooptimized plant-microbiome systems.The articles in this Research Topic signal a transformation in plant biology-from single-gene studies to systems-level, multidimensional investigations. Key future directions identified include:• Causal microbiome engineering uses synthetic communities and functional metagenomics.• Temporal and spatial gene expression resolution through high-resolution time-series and cell-type-specific profiling.• Pan-genome analysis and structural variant discovery beyond SNP-centric studies.• CRISPR/dCas9 epigenome editing and synthetic RNA technologies for precision trait modulation.• AI-driven phenotype prediction and climate-resilient variety design through integration of omics and environmental data.These trajectories call for transdisciplinary collaboration, uniting plant genetics, epigenomics, microbiology, data science, and field-based agronomy.The 17 articles published under this Research Topic represent a significant leap forward in our collective understanding of plant stress biology. These studies span a diverse array of plant systems, stress types, and methodological frameworks ranging from GWAS, meta-QTL analyses, transcriptomics, metabolomics, and epigenetics to field validation and microbiome profiling. these works signal a notable advancement toward designing crops not merely as standalone genetic entities, but as dynamic systems interacting continuously with their environment and associated biota. A compelling future direction emerging from these studies is the incorporation of microbiome-aware selection and breeding a concept gaining traction as "holobiont breeding" (Huitzil et al., 2023). This requires precise characterization of beneficial microbial consortia, their functions, and the plant traits that facilitate their recruitment and persistence under stress.The future of plant resilience research must integrate multi-omics with high-throughput phenotyping, environmental modeling, and artificial intelligence. Such convergence will enable the discovery of novel gene networks, predictive trait-microbe associations, and adaptive alleles suited to future climates (Wang

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