Phenotypic expression of the gene‐for‐gene interaction in plant pathogenic bacteria: An implication for resistance to bacterial diseases by plants

Host-pathogen interaction in bacterial leaf blight of rice: Mechanisms of infection, colonisation and symptom development

This review examines the defence strategies of rice and provides key insights into host-pathogen interactions that inform the development of durable resistance and improved disease management strategies, including integrating molecular breeding with sustainable agricultural practices to mitigate yield losses caused by BLB.

Adaptation to Plant Defence in an Agricultural Insect Pest: Integrating Genome Scans and Gene Expression in the Soybean Aphid Reveals Multi-Genic Pathways.

In agroecosystems, intense selection pressures cause species to adapt and spread, often leading to the evolution and persistence of pests. Understanding how pests rapidly adapt can help develop sustainable strategies for their management and improve agroecosystem health. Pest adaptation involves stable variations in DNA sequence, as well as dynamic shifts in gene expression, often mediated by non-coding regulatory elements. We examined adaptation to plant defences in the soybean aphid, Aphis glycines, in which virulent aphids have overcome plant defences and avirulent aphids have not. Previous data with laboratory colonies suggested that virulent aphids have higher overall gene expression, including transposable elements, some of which influence gene regulation. However, we lack information on how genetic variation in natural populations impacts adaptation and potentially gene regulation. We integrated population genome scans of field-collected, soybean aphid populations with gene expression profiles of virulent and avirulent laboratory colonies to uncover connections between genetic differentiation and gene regulation for virulence. Genome scan methods found 2144 single nucleotide polymorphisms (SNPs) with significant genetic differentiation (i.e., outliers) in field-collected populations. These SNPs were near 1004 genes, representing 5.16% of the effective number of genes. Based on previous RNA-Seq data with laboratory colonies, we found 3160 genes and 147 long non-coding RNAs (lncRNAs) with differential expression among virulent and avirulent biotypes. By integrating both data sets, we identified 16 genes and 5 long non-coding RNAs with differential expression and that were associated with an outlier SNP (within 10 kbp). We validated SNPs with additional field collected aphids and found an aphid clone with stronger virulence than our laboratory virulent colony, surviving on 2 different aphid-resistant soybean varieties. This new virulent clone had fixed allele differences at 9 SNPs compared to our avirulent and other virulent colony. Field collected soybean aphids matching the phenotype of this new virulent clone had significant genetic differentiation with 3 outlier SNPs near genes related to zinc transport and lachesin compared to field collected avirulent aphids. Our entire data reinforced the importance of a potential multi-genetic response to overcome plant defence and generates new insights into complex genetic and regulatory mechanisms involved in insect-plant interactions.

Resistance induced in tomato plants with pathogenic and non-pathogenic agents: plasticity and differentiation

Atypical immunity induced by extracellular water in plants

Microbial pathogens require nutrients and water to support their growth and proliferation. Pathogen-mediated resource acquisition is orchestrated by the secretion of virulence factors that have evolved a diversity of forms (from effector proteins to small toxins), but which have converged in function (resource acquisition). A key observable virulence mechanism employed by a large number of microbial pathogens to cause disease is to induce a water-rich niche in the extracellular space (i.e. the apoplast) of their host, known as ‘water-soaked lesions’. Given the ubiquity of this virulence mechanism, we asked whether plants respond to pathogen-induced extracellular water to activate immune programs. We find that inducing a water-soaked apoplast induces an atypical transcriptional response, yet results in a functional immune response that restricts pathogen growth as effectively as canonical pattern-triggered immunity. Genetic and functional analyses reveal a role for the immune phytohormone salicylic acid (SA) in mediating apoplastic water-induced immunity (AWII). These results indicate that plants engage in an immune-priming program in response to apoplastic water accumulation and suggest that the pathogenic niches induced during infection may be perceived as danger signals.

Harnessing Natural Diversity and Rational Design for Enhanced Plant Immunity.

Plant pathogens cause crop loss. Genetic resistance, through natural genetic diversity or engineered resistance, can be highly effective in protecting plants from infection. Genetic resistance from wild relatives of crops has been successfully introduced into crops to control pathogen infection. Natural genetic diversity has also been used to dissect the molecular mechanisms of immunity. Pathogen recognition can be engineered due to advances in structural and computational biology, which have accelerated rational design approaches. We specifically focus on natural and engineered diversity in indirect recognition of pathogens, where the pathogen modifies a host protein and the modification is detected by a plant immune receptor, as these recognition systems are particularly common in bacterial pathogen resistance. We explore natural genetic diversity for indirect recognition at three scales (1) across species (2) within species and (3) within individuals. Finally, we extend these insights to approaches for rational engineering of plant-pathogen recognition.

Virus-induced gene silencing as a tool for functional genomics in weeds: Challenges and future directions

Virus-induced gene silencing provides a tractable approach to investigate genes associated with herbicide resistance, metabolic adaptation, and stress tolerance and highlights VIGS as a versatile biotechnology for elucidating gene function and supporting next-generation strategies in plant improvement and integrated pest management.