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Category: Pub Med

MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and Helitrons 

MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and Helitrons  Kaitlin Higgins

Plant J. 2025 Jul;123(1):e70304. doi: 10.1111/tpj.70304.

ABSTRACT

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm transcripts, the mdr1 targets are enriched for TEs (particularly Helitrons), and DE genes are depleted for both core genes and GO term assignments, suggesting that the majority of DE transcripts are TEs and pseudo-genes. By comparing DE genes to imprinting calls from prior studies, we find that the majority of DE genes have maternally biased expression, and approximately half of all maternally expressed genes (MEGs) are DE in this study. In contrast, no paternally expressed genes (PEGs) are DE. DNG-dependent imprinted genes are distinguished by maternal demethylation and expression primarily in the endosperm, so we also performed Enzymatic Methyl-seq on hybrids to identify maternal demethylation and utilized a W22 gene expression atlas to identify genes expressed primarily in the endosperm. Overall, approximately ⅔ of all MEGs show evidence of regulation by DNGs. Taken together, this study solidifies the role of MDR1 in the regulation of maternally expressed, imprinted genes and TEs and identifies subsets of genes with DNG-independent imprinting regulation.

PMID:40587880 | DOI:10.1111/tpj.70304

Targeted demethylation by DNA glycosylases (DNGs) results in differential methylation between parental alleles in the endosperm, which drives imprinted expression. Here, we performed RNA sequencing on endosperm derived from DNG mutant mdr1 and wild-type (WT) endosperm. Consistent with the role of DNA methylation in gene silencing, we find 108 genes and 96 TEs differentially expressed (DE) transcripts that lost expression in the hypermethylated mdr1 mutant. Compared with other endosperm… [#item_author]

Leaf Organogenesis Improves Recovery of Solid Polyploid Shoots from Chimeric Southern Highbush Blueberry 

Leaf Organogenesis Improves Recovery of Solid Polyploid Shoots from Chimeric Southern Highbush Blueberry  Emily Walter

BioTech (Basel). 2025 Jun 12;14(2):48. doi: 10.3390/biotech14020048.

ABSTRACT

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species is challenging. Polyploid induction through tissue culture has been useful in bridging ploidy barriers. Mixoploid or chimeric shoots often are produced, along with solid polyploid mutants. These chimeras are mostly discarded because of their genome instability and the difficulty in identifying periclinal mutants carrying germline mutations. Since induced polyploidy in blueberries often results in a low frequency of solid mutant lines, it is important to recover solid polyploids through chimera dissociation. In this study, two vegetative propagation methods, i.e., axillary and adventitious shoot induction, were evaluated for their efficiency in chimera dissociation. Significantly higher rates of chimera dissociation were found in adventitious shoot induction compared to axillary shoot induction. Approximately 89% and 82% of the adventitious shoots induced from mixoploid lines 145.11 and 169.40 were solid polyploids, respectively, whereas only 25% and 53% of solid polyploids were recovered through axillary shoot induction in these lines. Effective chimera dissociation provides useful and stable genetic materials to enhance blueberry breeding.

PMID:40558397 | DOI:10.3390/biotech14020048

Interspecific and intersectional crosses have introduced valuable genetic traits for blueberry (Vaccinium sect. Cyanococcus) cultivar improvement. Introgression from Vaccinium species at the diploid, tetraploid, and hexaploid levels has been found in cultivated blueberries. Continued efforts to integrate wild blueberry genetic resources into blueberry breeding are essential to broaden the genetic diversity of cultivated blueberries. However, performing heteroploid crosses among Vaccinium species… [#item_author]

Evaporative cooling signals for wound healing in plants 

Evaporative cooling signals for wound healing in plants  Joseph Balem

bioRxiv [Preprint]. 2025 May 28:2025.05.23.655667. doi: 10.1101/2025.05.23.655667.

ABSTRACT

Repairing a damaged body part is critical for the survival of any organism. In plants, tissue damage induces rapid responses that activate defense, regeneration and wound healing. While early wound signaling mediated by phytohormones, electrical signals and reactive oxygen species is well-characterized, the mechanisms governing the final stages of wound healing remain poorly understood. Here, we show that wounding in Arabidopsis leaves induces localized cooling, likely due to evaporative water loss, accompanied by the activation of cold-responsive genes. The subsequent disappearance of localized cooling and deactivation of cold-responsive genes serve as a quantitative marker of wound healing. Based on these observations, we developed a workflow by leveraging computer vision and deep learning to monitor the dynamics of wound healing. We found that CBFs transcription factors relay injury-induced cooling signal to wound healing. Thus, our work advances our understanding of tissue repair and provides a tool to quantify wound healing in plants.

PMID:40502075 | PMC:PMC12154623 | DOI:10.1101/2025.05.23.655667

Repairing a damaged body part is critical for the survival of any organism. In plants, tissue damage induces rapid responses that activate defense, regeneration and wound healing. While early wound signaling mediated by phytohormones, electrical signals and reactive oxygen species is well-characterized, the mechanisms governing the final stages of wound healing remain poorly understood. Here, we show that wounding in Arabidopsis leaves induces localized cooling, likely due to evaporative water… [#item_author]

A Case Study for Visual Detection of a Systemic Disease: Optimizing Identification of Phony Peach Disease Based on Statistical and Machine Learning Models 

A Case Study for Visual Detection of a Systemic Disease: Optimizing Identification of Phony Peach Disease Based on Statistical and Machine Learning Models  Weiqi Luo

Phytopathology. 2025 Jun 22. doi: 10.1094/PHYTO-03-25-0093-R. Online ahead of print.

ABSTRACT

Phony peach disease (PPD), caused by Xylella fastidiosa subsp. multiplex (Xfm), poses a significant threat to commercial peach orchards in Georgia. Early and accurate detection is essential for effective disease management, yet visual assessment remains the primary approach for diagnosing PPD symptoms due to the high cost and logistical challenges of qPCR-based detection of Xfm. We evaluated the accuracy of visual PPD assessment and examined the factors influencing rater performance, symptom reliability, and optimal survey deployment strategies with CART/Random Forest analyses and simulations. Internode length was the most reliable symptom for PPD identification in two peach cultivars, consistently outperforming other physical traits such as canopy flatness and shape. Primer pair C06Xf-bamA had the greatest relative sensitivity, making it the preferred choice for qPCR confirmation. Principal component analysis suggested that rater experience significantly improved agreement with qPCR results and repeated assessments of the same orchards further enhanced consistency for raters. Simulations results suggested that deploying two experienced raters may provide the highest detection diagnostic accuracy for survey purposes, particularly when qPCR-based pathogen detection is unavailable. Last, PPD-affected trees, through PCR verification and visual identification, exhibited higher mortality rates than Xfm-negative trees, reinforcing the need for early detection and removal to limit disease spread. These findings underscore the importance of strategic rater deployment, targeted symptom selection, and integrating molecular diagnostics when feasible.

PMID:40544457 | DOI:10.1094/PHYTO-03-25-0093-R

Phony peach disease (PPD), caused by Xylella fastidiosa subsp. multiplex (Xfm), poses a significant threat to commercial peach orchards in Georgia. Early and accurate detection is essential for effective disease management, yet visual assessment remains the primary approach for diagnosing PPD symptoms due to the high cost and logistical challenges of qPCR-based detection of Xfm. We evaluated the accuracy of visual PPD assessment and examined the factors influencing rater performance, symptom… [#item_author]

Genetic and environmental influences on the distributions of three chromosomal drive haplotypes in maize 

Genetic and environmental influences on the distributions of three chromosomal drive haplotypes in maize  Meghan J Brady

bioRxiv [Preprint]. 2025 May 27:2025.05.22.655462. doi: 10.1101/2025.05.22.655462.

ABSTRACT

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used genotype-by-sequencing data to score more than 10,000 maize and teosinte lines for the presence or absence of each driver. Less than ~0.5% of modern inbred lines carry chromosomal drivers. Among individuals from 5331 open-pollinated landraces, 6.32% carried Ab10, 5.16% carried K10L2, and 12.28% carried at least one B chromosome. Using a GWAS approach we identified unlinked loci that associate with the presence or absence of the selfish genetic elements. Many genetic modifiers are positively associated with the drivers, suggesting that there may have been selection for alleles that ameliorate their negative fitness consequences. We then assessed the contributions of population structure, associated loci, and the environment on the distribution of each chromosomal driver. There was no significant relationship between any chromosomal driver and altitude, contrary to conclusions based on smaller studies. Our data suggest that the distribution of the major chromosomal drivers is primarily influenced by neutral processes and the deleterious fitness consequences of the drivers themselves. While each driver has a unique relationship to genetic background and the environment, they are largely unconstrained by either.

PMID:40501570 | PMC:PMC12154789 | DOI:10.1101/2025.05.22.655462

Meiotic drive elements are regions of the genome that are transmitted to progeny at frequencies that exceed Mendelian expectations, often to the detriment of the organism. In maize there are three prevalent chromosomal drive elements known as Abnormal chromosome 10 (Ab10), K10L2, and the B chromosome. There has been much speculation about how these drivers might interact with each other and the environment in traditional maize landraces and their teosinte ancestors. Here we used… [#item_author]

Osmotic and pH Stress-Responsive Two-Component System, OmpR/EnvZ, Modulates Type III Secretion, Biofilm Formation, Swimming Motility and Virulence in Acidovorax citrulli xjL12 

Osmotic and pH Stress-Responsive Two-Component System, OmpR/EnvZ, Modulates Type III Secretion, Biofilm Formation, Swimming Motility and Virulence in Acidovorax citrulli xjL12  Yuanjie Wang

Mol Plant Pathol. 2025 Jun;26(6):e70107. doi: 10.1111/mpp.70107.

ABSTRACT

Acidovorax citrulli, the causal pathogen of bacterial fruit blotch of cucurbits, relies on a functional type III secretion system (T3SS) for pathogenicity. Two-component systems (TCSs) are primary signal transduction mechanisms for bacteria to detect and adapt to various environmental conditions. However, the role of TCS on regulating T3SS and other virulence factors in response to environmental stimuli is still poorly understood in A. citrulli. Here, we report the identification of a conserved TCS, OmpR/EnvZ, involved in hypersensitive response (HR) induction in Nicotiana benthamiana by screening a transposon-insertion library in the group II strain xjL12 of A. citrulli. Transcription analysis confirmed that OmpRAc/EnvZAc was upregulated in response to elevated osmotic pressure, low and high pH conditions, and host environment. Deletions of envZAc, ompRAc, or both envZAc and ompRAc in A. citrulli attenuated virulence to melon seedlings and mature leaf tissues, and delayed HR in N. benthamiana. OmpRAc was activated by EnvZAc and directly bound to the promoter region of hrpG, a major regulator of T3SS. This binding activated hrpG transcription and promoted T3SS assembly in T3SS-inducing medium, XVM2. Additionally, the OmpRAc/EnvZAc mutants of A. citrulli displayed reduced swimming motility due to impaired flagella formation, but also had enhanced biofilm formation and exopolysaccharide production. OmpRAc/EnvZAc regulation of these virulence factors in A. citrulli depended on its own conserved phosphorylation sites. This work illuminates a signalling pathway for regulating the T3SS and provides insights into the OmpR/EnvZ-mediated virulence regulatory network in A. citrulli.

PMID:40524436 | DOI:10.1111/mpp.70107

Acidovorax citrulli, the causal pathogen of bacterial fruit blotch of cucurbits, relies on a functional type III secretion system (T3SS) for pathogenicity. Two-component systems (TCSs) are primary signal transduction mechanisms for bacteria to detect and adapt to various environmental conditions. However, the role of TCS on regulating T3SS and other virulence factors in response to environmental stimuli is still poorly understood in A. citrulli. Here, we report the identification of a conserved… [#item_author]

NLP-like deep learning aided in identification and validation of thiosulfinate tolerance clusters in diverse bacteria 

NLP-like deep learning aided in identification and validation of thiosulfinate tolerance clusters in diverse bacteria  Brendon K Myers

mSphere. 2025 Jun 17:e0002325. doi: 10.1128/msphere.00023-25. Online ahead of print.

ABSTRACT

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP), like techniques such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validated alt-like clusters in Pantoea ananatis 97-1R, Burkholderia gladioli pv. gladioli FDAARGOS 389, and Pseudomonas syringae pv. tomato DC3000. Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novel alt-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility of alt-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios.IMPORTANCEThiosulfinates, like allicin, are potent antifeedants and antimicrobials produced by Allium species and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (alt) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novel alt-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.

PMID:40525872 | DOI:10.1128/msphere.00023-25

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP), like techniques such as those used in DeepBGC, offers a… [#item_author]

Integration of plant-soil feedbacks with resilience theory for climate change 

Integration of plant-soil feedbacks with resilience theory for climate change  Jennifer A Rudgers

Trends Ecol Evol. 2025 Jun 13:S0169-5347(25)00132-6. doi: 10.1016/j.tree.2025.05.001. Online ahead of print.

ABSTRACT

The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is manipulated; and (iii) PSF must alter the resistance or recovery of ecosystem structure or function to disruption. Several case studies suggest that PSF may support (or degrade) resilience, but no study has yet met all criteria. Doing so could yield novel insights into how aboveground-belowground interactions shape ecosystem resilience to climate change.

PMID:40517042 | DOI:10.1016/j.tree.2025.05.001

The resilience of ecosystems to climate disruption requires internal feedbacks that support the stability of ecosystem structure and function. Such feedbacks may include sustained interactions between plants and soil [plant-soil feedback (PSF)]. Theoretically, PSF could either boost or degrade ecosystem resilience. Three criteria must be met to attribute resilience to PSF: (i) The presence or amount of PSF must be manipulated; (ii) the ecosystem must face climate disruption after PSF is… [#item_author]

Discovering leaf and stripe rust resistance in soft red winter wheat through genome-wide association studies 

Discovering leaf and stripe rust resistance in soft red winter wheat through genome-wide association studies  John W Bagwell

Plant Genome. 2025 Jun;18(2):e70055. doi: 10.1002/tpg2.70055.

ABSTRACT

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States. Genome-wide association study has emerged as a valuable tool to identify new LR and YR resistance loci. In this study, a panel of 263 soft red winter wheat genotypes was evaluated for LR and YR severity in Plains, GA, and Williamson, GA, in a randomized complete block design of two replicates during 2019 and 2021-2023. Also, LR and YR infection types were assessed on seedlings at the three leaf stage in three greenhouse trials. A total of 26 significant quantitative trait loci (QTL) explaining 0.6%-30.8% phenotypic variance (PV) was detected by at least two of the five GAPIT models (BLINK, CMLM, FarmCPU, GLM, and MLM) tested. Nine major QTL included QLrYr-2A.1 linked to single-nucleotide polymorphism S2A_20855466, which had the highest overall PV (30.8%) for response to both rust pathogens in the field. Using the Chinese Spring Reference Genome Version 1.0, we detected 16 candidate genes, and four known R genes and QTL overlapped two major QTL. Of these QTL, 16 are likely novel genetic loci with potential for marker-assisted selection.

PMID:40495572 | DOI:10.1002/tpg2.70055

Leaf rust (LR) and stripe rust (YR), which are caused by Puccinia triticina and Puccinia striiformis, respectively, are among the most devastating wheat rusts worldwide. These diseases can be managed by using genetically resistant cultivars, an economical and environmentally safer alternative to fungicides. Over 100 and 80 Lr and Yr resistance genes have been discovered, respectively; however, rust pathogens are overcoming introduced resistance genes in the southeastern United States…. [#item_author]

Comparative Transcriptomic Analysis of Soybean Recombinant Inbred Lines Differing at the Rmi1 Locus for Resistance to Meloidogyne incognita During Early Stages of Nematode Infection 

Comparative Transcriptomic Analysis of Soybean Recombinant Inbred Lines Differing at the Rmi1 Locus for Resistance to Meloidogyne incognita During Early Stages of Nematode Infection  Kelly Goode

Phytopathology. 2025 Jun 11. doi: 10.1094/PHYTO-04-25-0143-SC. Online ahead of print.

ABSTRACT

Root-knot nematodes (Meloidogyne spp.) are a continuing threat to soybean production, with M. incognita being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to M. incognita, Rmi1, was previously identified in soybean cv. Forrest and associated with the emigration of second-stage juveniles from the roots. To better understand the Rmi1-mediated resistance response, we used Forrest-derived F5 RILs differing for Rmi1 to analyze global changes in gene expression in response to M. incognita infection at 2- and 4-days post inoculation. We identified 1,471 differentially expressed (DE) genes in the compatible interaction and 1,037 DE genes in the incompatible interaction. Forty-five percent of DE genes were DE in both interactions, 42% (856) were unique to the compatible interaction, and 13% (261) were unique to the incompatible interaction. Genes uniquely DE in the incompatible interaction included genes involved in cell wall modification, hormone signaling, endomembrane trafficking, and redox reactions providing new insights into the resistance mechanism mediated by Rmi1 in soybean to root-knot nematodes.

PMID:40498525 | DOI:10.1094/PHYTO-04-25-0143-SC

Root-knot nematodes (Meloidogyne spp.) are a continuing threat to soybean production, with M. incognita being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown. A single, additive gene for resistance to M. incognita, Rmi1, was previously identified in soybean cv. Forrest and associated with the emigration of second-stage juveniles from the roots. To better… [#item_author]