Author: slquinlan

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

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

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

PLoS Genet. 2025 Jun 2;21(6):e1011735. doi: 10.1371/journal.pgen.1011735. Online ahead of print.

ABSTRACT

In ciliates, cortical organelles, including ciliary arrays, are positioned at precise locations along two polarity axes: anterior-posterior and circumferential (lateral). We explored the poorly understood mechanism of circumferential patterning, which generates left-right asymmetry. The model ciliate Tetrahymena has a single anteriorly-located oral apparatus. During cell division, a single new oral apparatus forms near the equator of the parental cell and along the longitude of the parental organelle. Cells homozygous for hypoangular 1 (hpo1) alleles, assemble multiple oral apparatuses positioned either to the left or right flanking the normal oral longitude. Using comparative next-generation sequencing, we identified HPO1 as a gene encoding an ARMC9-like protein. Hpo1 colocalizes with the ciliary basal bodies, forming a bilateral concentration gradient, with the high point on the cell’s right side and a sharp drop-off that marks the longitude at which oral development initiates on the ventral side. A second Hpo1 concentration drop-off is present on the dorsal surface, where it marks the position for development of a cryptic oral apparatus that forms in the janus mutants. Hpo1 acts bilaterally to exclude oral development from the cell’s right side. Hpo1 interacts with the Beige-Beach domain protein Bcd1, a cell’s left side-enriched factor, whose loss also confers multiple oral apparatuses on the ventral surface. A loss of both Hpo1 and Bcd1 is lethal and profoundly disrupts the positioning, organization and size of the forming oral apparatus (including its internal left-right polarity). We conclude that in ciliates, the circumferential patterning involves gradient-forming factors that are concentrated on either the cell’s right or left side and that the two sides of the cortex interact to create boundary effects that induce, position and shape developing cortical organelles.

PMID:40455876 | DOI:10.1371/journal.pgen.1011735

Plant Dis. 2025 May 22. doi: 10.1094/PDIS-01-25-0117-SR. Online ahead of print.

ABSTRACT

Alternaria brassicicola is the causal agent typically associated with Alternaria leaf blight and head rot (ABHR) disease in broccoli and related crops in the Eastern United States. Recently a new species, A. japonica, has been reported as causing disease in broccoli and other vegetables in this region. We conducted a multi-state pathogen survey during the growing seasons of 2022 and 2023 to assess the distribution and occurrence of A. japonica in relation to A. brassicicola in five broccoli-producing states. Our approach specifically targeted collection of broccoli leaves with lesions typical of ABHR within commercially grown fields managed using either organic or conventional approaches in Connecticut, Massachusetts, New York, Virginia, and Georgia. Only typical ABHR leaf lesions were selected for pathogen isolation and, subsequently, sequencing of the Alternaria major allergen a1 gene was used to identify Alternaria species. The predominant species isolated was A. brassicicola (88% in 2022 and 94% in 2023) and the second most common was A. alternata (12% in 2022 and 6% in 2023), which was obtained from fields in Connecticut and Massachusetts in 2022, and in Virginia in both years. Alternaria japonica was not found in either year. Symptoms of A. alternata were indistinguishable from A. brassicicola, as were colony morphologies. While A. alternata is considered a generalist and of little consequence for broccoli, it is considered a pathogen of significance on multiple crops (blueberry, citrus, pistachios), but there remains scant information on the disease etiology on broccoli. Therefore, we inoculated broccoli with A. alternata in controlled conditions in order to shed light on possible differences in infectivity of these species on broccoli. Results of our study showed that A. alternata is pathogenic on broccoli, capable of initiating infection and causing lesions typical of ABHR. This indicates that future disease surveys of ABHR should conclusively identify species of Alternaria that are causing disease. Additional research is needed to determine the significance of this finding in relation to yield impacts, epidemiology, fungicide resistance, and management recommendations.

PMID:40403277 | DOI:10.1094/PDIS-01-25-0117-SR

Sci Adv. 2025 May 23;11(21):eadw3433. doi: 10.1126/sciadv.adw3433. Epub 2025 May 21.

ABSTRACT

Activation of synthetic centromeres on chromosome 4 in maize leads to its breakage and formation of trisomic fragments called neochromosomes. A limitation of neochromosomes is their low and unpredictable transmission rates due to trisomy. Here, we report that selecting for dicentric recombinants through male crosses uncovers stabilized chromosome 4 fission events, which split it into 4a-4b complementary chromosome pairs, where 4a carries a native centromere and 4b carries a synthetic one. The cells rapidly stabilized chromosome ends by de novo telomere formation, and the new centromeres spread among genes without altering their expression. When both 4a and 4b chromosomes were made homozygous, they segregated through meiosis indistinguishably from wild type and gave rise to healthy plants with normal seed set, indicating that the synthetic centromere was fully functional. This work leverages synthetic centromeres to engineer chromosome fission, raising the diploid chromosome number of maize from 20 to 22.

PMID:40397737 | PMC:PMC12094224 | DOI:10.1126/sciadv.adw3433

Plant Methods. 2025 May 20;21(1):66. doi: 10.1186/s13007-025-01375-8.

ABSTRACT

High resolution three-dimensional (3D) point clouds enable the mapping of cotton boll spatial distribution, aiding breeders in better understanding the correlation between boll positions on branches and overall yield and fiber quality. This study developed a segmentation workflow for point clouds of 18 cotton genotypes to map the spatial distribution of bolls on the plants. The data processing workflow includes two independent approaches to map the vertical and horizontal distribution of cotton bolls. The vertical distribution was mapped by segmenting bolls using PointNet++ and identifying individual instances through Euclidean clustering. For horizontal distribution, TreeQSM segmented the plant into the main stem and individual branches. PointNet++ and Euclidean clustering were then used to achieve cotton boll instance segmentation. The horizontal distribution was determined by calculating the Euclidean distance of each cotton boll relative to the main stem. Additionally, branch types were classified using point cloud meshing completion and the Dijkstra shortest path algorithm. The results highlight that the accuracy and mean intersection over union (mIoU) of the 2-class segmentation based on PointNet++ reached 0.954 and 0.896 on the whole plant dataset, and 0.968 and 0.897 on the branch dataset, respectively. The coefficient of determination (R²) for the boll counting was 0.99 with a root mean squared error (RMSE) of 5.4. For the first time, this study accomplished high-granularity spatial mapping of cotton bolls and branches, but directly predicting fiber quality from 3D point clouds remains a challenge. This method provides a promising tool for 3D cotton plant mapping of different genotypes, which potentially could accelerate plant physiological studies and breeding programs.

PMID:40394606 | DOI:10.1186/s13007-025-01375-8

Mol Plant Pathol. 2025 May;26(5):e70096. doi: 10.1111/mpp.70096.

ABSTRACT

Harpins are proteins secreted by many gram-negative, plant-pathogenic bacteria that stimulate the hypersensitive reaction (HR), a host cell death defence response, when infiltrated into plant leaves as purified proteins. This activity of harpins was first discovered in Nicotiana tabacum (tobacco), which manifests an especially strong and rapid harpin-activated HR that becomes evident within 12-24 h after infiltration. HrpN is the major harpin of the fire blight pathogen Erwinia amylovora. We discovered natural variation in the HrpN-induced HR among tobacco accessions and identified candidate genes using genetic mapping and bulked-segregant analysis with whole genome sequencing. Virus-induced gene silencing of candidate gene Wall-Associated Kinase 2 (WAK2) abrogated the HR in response to HrpN and HpaG, a harpin from the soybean bacterial pustule pathogen Xanthomonas citri pv. glycines. WAK2 silencing also compromised the avirulence activity of harpin HrpZ in the tobacco wildfire pathogen Pseudomonas syringae pv. tabaci. A natural, disruptive mutation in WAK2 correlated with the inability of tobacco accessions to mount the harpin-mediated HR. We conclude that the predicted receptor-like kinase WAK2 is required for the strong HR induced in tobacco leaves by harpin protein infiltration and can potentially mediate resistance to bacterial pathogens based on harpin recognition.

PMID:40391583 | DOI:10.1111/mpp.70096