Areca palm velarivirus 1 (APV1) is the causative agent of yellow leaf disease (YLD), leading to severe yield losses in areca palms. However, how APV1 counteracts host immunity remains largely underexplored, and the underlying mechanisms are still poorly understood. RNA silencing is an evolutionarily conserved antiviral defense mechanism in eukaryotes. In this study, we identify the APV1-encoded capsid protein (CP) as a viral suppressor of RNA silencing (VSR) that inhibits both local and systemic silencing triggered by single-stranded RNA (ssRNA). Mechanistically, CP interacts with host Suppressor of Gene Silencing 3 (AcSGS3), a key component of the RNA silencing pathway, and promotes its degradation via autophagy. Additionally, CP disrupts the SGS3–AcRDR6 (RNA-dependent RNA polymerase 6) interaction, impairing the RNAi signaling cascade. Our findings reveal a novel dual mechanism to counteract host RNA silencing in which APV1 CP disrupts the SGS3–AcRDR6 complex and exploits the autophagic pathway to degrade AcSGS3, thereby undermining host antiviral defenses.
Starch is a principal storage component in plants, significantly influencing the yield and quality traits of major crops. Climate change, particularly drought and high temperatures, severely affects starch biosynthesis in crops, leading to reduced starch yield and quality. The composition and properties of native starch, such as its low amylose content, substantially affect its nutritional value and industrial applications. To tackle these issues, genes coding for starch synthetic enzymes or those involved in the regulation of starch biosynthesis could be targeted for site-directed mutation to improve starch traits in crops. The application of gene editing technology in crops, notably CRISPR/Cas9, has facilitated the precise manipulation of starch biosynthesis. This review summarizes current knowledge on the biosynthesis and regulation of starch and the influence of climate change on these processes. It highlights advancements in modifying starch biosynthesis in food crops using CRISPR/Cas9. We discuss the strategy of improving starch traits and stress tolerance in response to climate change challenges and propose future directions for research on starch modification in food crops. Developing climate resilient crops capable of stable starch production is crucial for ensuring food security in the face of a changing global climate and an increasing world population.
As the global warming intensifies, along with increased planting density and straw retention practices, stalk rot (SR) has become one of major diseases that negatively impacts crop yield and quality. The distribution of SR pathogens, encompassing both fungal and bacterial agents, is significantly influenced by climate and agricultural factors. Although significant researches have been conducted on identifying fungal SR in different crop plants, there remains a lack of comprehensive reviews focused on the genetic and molecular mechanisms that contribute to crop resistance against fungal and bacterial SR. This review provides a comprehensive comparison of the pathogenic mechanisms associated with fungal and bacterial SR. It emphasized recently cloned genes and molecular regulations linked to resistance against SR, highlighted the pivotal role of several smart strategies in advancing gene discovery and functional research. Furthermore, it summarized the potential molecular regulatory pathways involved in SR resistance. Ultimately, the article presents insights into several critical areas that warrant further investigation in the study of SR-resistant mechanisms and crop breeding.
Cold stress is a major environmental challenge limiting the survival and productivity of tropical aquaculture species such as Nile tilapia (Oreochromis niloticus). The brain and gill represent two key organs that orchestrate systemic and environmental responses: the brain serves as the central thermosensory integrator and neuroendocrine control center, while the gill serves as the primary interface for respiration, ion regulation, and immune defense. However, the molecular mechanisms underlying their tissue-specific and potentially coordinated responses to cold remain unclear. Here, we applied integrative ATAC-seq and RNA-seq analyses to systematically investigate chromatin accessibility and gene expression dynamics in tilapia brain and gill tissues under cold stress. We identified thousands of differentially expressed genes and accessible regions, with significant correlations between transcriptional changes. Transcription factor footprinting revealed that Fra1 and Nrf act as key tissue-specific regulators, governing immune, apoptotic, and metabolic reprogramming in the brain and gill, respectively. Notably, the Fra1 module in the brain activated signaling pathways associated with stress response, neurodevelopment, and metabolic regulation which may influence peripheral responses by coordinating systemic physiological adjustments under cold stress, while Nrf-mediated regulation in the gill supported local homeostasis through redox and transport-related mechanisms. These findings highlight the hierarchical and organ-specific transcriptional control underlying cold adaptation in ectotherms. Our study provides the first chromatin accessibility atlas of cold-responsive regulatory networks across central and peripheral organs in fish, offering mechanistic insight and molecular targets for breeding cold-tolerant aquaculture strains.
The domestication and selective breeding of horses have profoundly influenced the emergence of adaptive traits and stress resistance mechanisms, shaping modern equine populations. This comprehensive review examines the genomic foundations of these traits, emphasizing recent advancements in high-throughput sequencing technologies and bioinformatics. These tools have elucidated the genetic underpinnings of key characteristics such as endurance, speed, metabolic efficiency, and disease resistance. Importantly, the review identifies and connects gene variants associated with thermoregulation, immune function, and cellular repair mechanisms, shedding light on their synergistic roles in enabling horses to adapt to diverse environmental challenges and physiological stressors. By establishing these causal links, this review enhances the coherence between genomic findings and their implications for equine biology. Furthermore, the integration of genomic insights provides a framework for addressing contemporary challenges in horse management and conservation. Issues such as climate change, disease outbreaks, and the preservation of genetic diversity demand innovative strategies grounded in genomics. By bridging the findings on equine adaptation and stress resistance mechanisms with practical applications in breeding and management, this review highlights the potential of genomics to ensure the sustainability and resilience of equine populations in the face of evolving environmental and societal pressures. This expanded perspective underscores the critical role of genomics in both understanding the evolutionary trajectory of horses and guiding future practices in equine health and conservation.
Cryptocaryon irritans is an obligate parasitic ciliate that significantly endangers marine fish. Hypoxia suppresses the development and hatchability of C. irritans during the tomont stage, which often develops on the seafloor under hypoxic conditions. Despite this knowledge, the underlying adaptation mechanisms of tomonts remain poorly understood. We aimed to determine how hypoxia reprograms tomont metabolism and whether ferroptosis contributes to hypoxia-induced vulnerability. Herein, metabolomic profiling revealed 2,964 differential metabolites under hypoxia. Notably, there were significantly elevated glucose levels, suggesting enhanced glycolytic activity. Enzymatic and qRT-PCR analyses further confirmed hypoxia-induced metabolic reprogramming, including increased hexokinase and pyruvate kinase activities and upregulation of glycolysis-related genes. Hypoxia also induced surface depressions, disrupted cell walls, mitochondrial deformation, reduced mitochondrial membrane potential, disrupted energy homeostasis, and increased NAD⁺/NADH ratio fluctuations and lactate accumulation. To probe ferroptotic susceptibility under hypoxia, hypoxic tomonts were exposed to the ferroptosis inducer erastin, resulting in a hatchability of 13% and promoting reactive oxygen species (ROS) accumulation, lipid peroxidation, and mitochondrial damage. Fluorescence staining revealed strong PI and ROS signals in hypoxic tomonts exposed to the ferroptosis inducer erastin. Notably, mitochondrial dysfunction was accompanied by Ca2⁺ and Fe2⁺ accumulation. Ferroptosis-related genes were upregulated at 24 h post-hypoxia induction. In contrast, gpx4 and mitochondrial electron transport chain components were downregulated at 48 h post-hypoxia induction. These findings demonstrate that hypoxia triggers glycolytic reprogramming and mitochondrial dysfunction in C. irritans, whereas erastin induces ferroptosis under hypoxic stress. This study provides new insights into protozoan hypoxia adaptation and highlights ferroptosis as a potential therapeutic target for controlling parasitic infections in marine aquaculture.
Advanced genotyping technologies for understanding the genetic intricacies of fungal pathogens have broad applications in crop protection. Here, we introduce a novel genotyping-by-target sequencing (GBTS) chip, a versatile tool designed for comprehensive genetic analysis of fungal populations. This technology overcomes key limitations of traditional molecular marker-based approaches by providing a more efficient, economic, and streamlined solution while bypassing the need for labor-intensive pathogen culturing. We demonstrate its utility by applying it to profile Pucciniastriiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. Our analysis involved 225 infected leaves collected from wheat fields in the northwest oversummering region for Pst in China. We delineated three genetic groups and revealed frequent gene flow, with closer connectivity between Qinghai and Gansu than either province with Ningxia, a pattern consistent with wind trajectory models. These findings illustrate a highly connected regional epidemic system and highlight the value of the GBTS chip for genomic epidemiology. The methodology established here provides a scalable framework for population genetic studies in other fungal pathogens, promising to enhance disease monitoring and management across agricultural systems.
Leaf shape plays a crucial role in plant growth and development. Among various leaf traits, marginal lobation serves as an ideal morphological marker for breeding programs. However, the genetic mechanism underlying leaf margin lobation in Brassica juncea L. remains unclear. Through RNA sequencing and map-based cloning, we identified an incompletely dominant gene, BjA10.LL, which encodes an HD-ZIP I protein and is responsible for the formation of leaf margin lobation in B. juncea. Sequence analysis of parental alleles revealed no critical variations in the coding region but identified substantial variations in regulatory regions. Heterologous expression of BjA10.LL in Arabidopsis thaliana confirmed its sufficiency to induce lobed leaves. To functionally link the regulatory variations to the phenotype, we analyzed promoter activity and developed a co-dominant molecular marker targeting key indels in a core enhancer. The promoter activity was significantly affected by these sequence variations, and the marker exhibited perfect co-segregation with the lobed-leaf phenotype in an F₂ population, collectively establishing these regulatory polymorphisms as the causal basis for divergent BjA10.LL expression and leaf morphology. These results demonstrate that BjA10.LL positively regulates marginal lobe formation, providing insights into leaf shape regulation in B. juncea and facilitating the genetic improvement of rapeseed.