Author: slquinlan

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

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

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 OmpR_Ac/EnvZ_Ac was upregulated in response to elevated osmotic pressure, low and high pH conditions, and host environment. Deletions of envZ_Ac, ompR_Ac, or both envZ_Ac and ompR_Ac in A. citrulli attenuated virulence to melon seedlings and mature leaf tissues, and delayed HR in N. benthamiana. OmpR_Ac was activated by EnvZ_Ac 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 OmpR_Ac/EnvZ_Ac mutants of A. citrulli displayed reduced swimming motility due to impaired flagella formation, but also had enhanced biofilm formation and exopolysaccharide production. OmpR_Ac/EnvZ_Ac 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

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

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

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

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

BMC Plant Biol. 2025 Jun 5;25(1):766. doi: 10.1186/s12870-025-06799-x.

ABSTRACT

BACKGROUND: Fruit ripening is a coordinated process that leads to an increase in sugars, decrease in acids and accumulation of pigments. Blueberry fruit exhibit an atypical climacteric ripening behavior. These fruit display an increase in respiration and ethylene production during ripening, however ethylene synthesis is developmentally regulated. In this study, the effect of ethylene on blueberry fruit ripening was investigated via preharvest applications of ethylene-releasing plant growth regulators (PGRs), ethephon and 1-aminocyclopropane 1-carboxylic acid (ACC), in one southern highbush cultivar, Miss Lilly in 2019, and two rabbiteye cultivars, Premier and Powderblue in 2019 and 2020. Further, the effects of these two PGRs on fruit metabolism during ripening in the two rabbiteye cultivars, and postharvest fruit quality in all three cultivars were evaluated.

RESULTS: Both PGRs increased ethylene evolution within 1-3 days after treatment (DAT). Ethephon and ACC applications increased the rate of ripening within 5 DAT in all cultivars, and increased ripe (blue) fruit by up to 35% and 29%, respectively between 7 to 10 DAT compared to the control. Metabolite analysis revealed that PGR treatments resulted in an immediate, but transient increase in sucrose, glucose and fructose, in ‘Premier’ at 3 DAT. Malate decreased at 3 DAT in response to both PGR treatments in ‘Premier’, and at 5 DAT in ethephon treatment in both cultivars. A rapid increase in the concentration of multiple anthocyanins was noted at 3 DAT in response to both PGRs in ‘Premier’ and ‘Powderblue’. Gene expression analysis revealed an increase in transcript abundance of VACUOLAR INVERTASE (vINV) and multiple anthocyanin biosynthesis genes between 1 and 3 DAT after PGR treatments in both cultivars, supporting the metabolite changes. However, the alteration in fruit metabolite concentrations were not sustained, and similar in PGR-treated fruit compared to the control in ripe fruit harvested at 10 DAT. Postharvest fruit quality attributes, such as firmness, total soluble solids, titratable acidity, and visual quality, were not consistently affected by the PGR applications compared to control treatments across all cultivars. A decrease in fruit weight was noted, although not consistently, in response to PGR treatments.

CONCLUSIONS: Overall, this study demonstrates that ethylene plays a crucial role in promoting ripening via rapid and transient stimulation of sugar, acid and anthocyanin metabolism. The promotion of fruit ripening by ethylene-releasing PGRs can lead to minimal but inconsistent changes in fruit quality attributes during postharvest storage.

PMID:40474063 | DOI:10.1186/s12870-025-06799-x

Plant Commun. 2025 Jun 3:101393. doi: 10.1016/j.xplc.2025.101393. Online ahead of print.

ABSTRACT

Teucrium chamaedrys, also called wall germander, is a small woody shrub native to the Mediterranean region. Its name is derived from the Greek words meaning ‘ground oak’, since its tiny leaves resemble those of an oak tree. Teucrium species are proliferative producers of diterpenes, which afford them valuable properties widely co-opted in traditional and western medicines. Sequence and assembly of the 3 Gbp tetraploid T. chamaedrys revealed 74 diterpene synthase genes, with the vast representation of these diterpene synthases clustered along four genomic loci. Comparative genomics revealed that this cluster is mirrored in the closely related species, Teucrium marum. Along with the presence of several cytochrome p450 sequences, this region is the one of largest biosynthetic gene clusters identified. Teucrium is well known for accumulating clerodane-type diterpenoids which are produced from a kolavanyl diphosphate precursor. To elucidate the complex biosynthetic pathways of these medicinal compounds, we identified and functionally characterized several kolavanyl diphosphate synthases from T. chamaedrys. Its remarkable chemistry and tetraploidy make T. chamaedrys an interesting and unique model for studying genomic evolution and adaptation in plants.

PMID:40468595 | DOI:10.1016/j.xplc.2025.101393

Annu Rev Phytopathol. 2025 Jun 4. doi: 10.1146/annurev-phyto-121823-080201. Online ahead of print.

ABSTRACT

Necrotrophic bacteria within the order Enterobacterales cause significant agricultural losses, with few effective management options available for producers. These pathogens have evolved at least two distinct strategies for infecting plants. Soft rot pathogens in the family Pectobacteriaceae, such as Dickeya and Pectobacterium, rely on secreting plant cell wall-degrading enzymes. In contrast, Pantoea necrotrophs depend on the production of phosphonate phytotoxins, a type of secondary metabolite, for their pathogenicity. This review summarizes recent discoveries on the virulence mechanisms of bacterial necrotrophs and current knowledge of factors that influence their host range and interactions with plant immune defenses. A deeper understanding of bacterial necrotroph host range determinants could inform the development and deployment of enhanced genetic resistance strategies.

PMID:40465659 | DOI:10.1146/annurev-phyto-121823-080201