Author: slquinlan

Hortic Res. 2026 Jun 11;13(11):uhag223. doi: 10.1093/hr/uhag223. eCollection 2026 Nov.

ABSTRACT

Whether plant life form influences the long-term persistence of polyploid lineages remains an important unresolved question in plant evolution. Previous studies have suggested that perennial herbaceous plants harbor higher proportions of neo-polyploids, yet comprehensive phylogenetic validation across paleopolyploid lineages using genomic data remains limited. The rapid accumulation of plant genome sequences, particularly from horticultural and agricultural species, provides an unprecedented opportunity to investigate the evolutionary relationships among polyploidization, plant growth form, and plant stature across seed plants. Here, we analyzed 351 seed plant genomes, including major cereals, vegetables, fruits, and their wild relatives, to investigate the long-term evolutionary associations between paleopolyploidization and plant phenotypic diversity. Phylogenetically informed comparative analyses showed that lineages experiencing more paleopolyploidization events were significantly more likely to exhibit herbaceous rather than woody growth forms. We further found that paleopolyploidization frequency was negatively associated with plant height across seed plants after accounting for phylogenetic relatedness. In addition, evolutionary rates, estimated using synonymous substitution rates (Ks), were associated with paleopolyploidization, plant growth form, and species richness. Herbaceous species exhibited higher Ks values than woody and vine species, and plant families with higher evolutionary rates tended to contain more species. Together, these findings provide a phylogenetically informed evidence that paleopolyploidization is closely associated with plant growth form, plant stature, and evolutionary rate, offering new insights into the long-term evolutionary consequences of genome duplication in seed plants.

PMID:42967069 | PMC:PMC13722872 | DOI:10.1093/hr/uhag223

Ecol Evol. 2026 Oct 30;16(11):e74574. doi: 10.1002/ece3.74574. eCollection 2026 Nov.

ABSTRACT

Understanding the spatial dynamics of genetic ancestry is essential for elucidating historical and contemporary patterns of gene flow among populations. Honey bees in the United States have a 400-year history of importation, management, and adaptation to diverse environments. Genetic diversity is a key factor for colony health and resilience. Notably, the most genetically diverse populations in the country originate from the invasive A-lineage (Africanized or ‘Killer’ honey bees). In this study, we leveraged a nationwide community-science platform to assemble an extensive genomic dataset of U.S. honey bee populations and used it to ask how this invasive lineage is spreading across the country and how its spread has impacted honey bee genetic diversity nationwide. Using RFMix, we assigned local ancestry across the genome to capture fine-scale ancestry patterns and applied TreeMix to genome-wide allele frequency data to infer directional gene flow among U.S. populations. Our analyses revealed patterns consistent with a strong northward migration, with major source populations in southern states such as Texas (TX), Arizona (AZ), and Florida (FL), and primary targets in northern states including Michigan (MI), New York (NY), and Vermont (VT). Covariance estimates indicated strong genetic connectivity, particularly from TX and AZ. Spatial visualization of migration edges highlighted key routes of A-lineage expansion. Together, these results provide the first genome-wide evidence for a nationwide spread of A-lineage ancestry in the U.S., offering insights to guide breeding strategies and predict the future dynamics of honey bee genetic diversity.

PMID:42967103 | PMC:PMC13722957 | DOI:10.1002/ece3.74574

Plant Dis. 2026 Oct 30. doi: 10.1094/PDIS-04-26-0745-RE. Online ahead of print.

ABSTRACT

Early leaf spot (ELS), caused by Passalora arachidicola, remains one of the most economically important foliar diseases of peanut (Arachis hypogaea), and resistance within the cultivated germplasm is limited. Fungicide applications are commonly used to manage this disease, but this practice increases production costs, the risk of fungicide resistance, and environmental concerns. Wild Arachis species harbor diverse resistance alleles, but their direct use in breeding is constrained by ploidy barriers. In this study, eight induced allotetraploids derived from nine wild Arachis species were produced. Along with their diploid parents, they were evaluated for ELS resistance using in vitro detached leaf bioassays. Disease resistance was quantified using multiple components, including incubation period, lesion number, sporulation, and diseased leaf area. Several allotetraploids-particularly MagDio1, MagKuhl1, MagHoeh1, and ValMicro1-exhibited significantly reduced lesion development, limited sporulation, and slower disease progression compared with cultivated controls. In all cases, induced allotetraploids displayed resistance levels equal to or greater than those of both diploid parents, indicating enhanced resistance following allotetraploidization. Notably, Arachis hoehnei and its derived allotetraploid consistently exhibited strong resistance across disease components, identifying this phylogenetically distinct species as a novel resistance source. These results demonstrate that induced allotetraploids represent peanut-compatible reservoirs of diverse ELS resistance alleles and provide practical resources for breeding programs aimed at developing cultivars with more durable and diversified resistance to early leaf spot.

PMID:42963873 | DOI:10.1094/PDIS-04-26-0745-RE

Plant Physiol. 2026 Oct 30:kiag803. doi: 10.1093/plphys/kiag803. Online ahead of print.

ABSTRACT

Soil boron deficiency is a global abiotic stress, negatively impacting on crop yield. In the dicot model species Arabidopsis thaliana, inhibition of root elongation is one of the earliest symptoms of boron deficiency. In the monocot model maize (Zea mays L.), boron deficiency-induced root defects are widely unexplored. In this study, we assessed boron deficiency-induced defects in the primary root system of maize and tested the suitability of phenylboronic acid (PBA) as boron deficiency mimic by performing phenotypic, histological, molecular, and biochemical analyses. Our analyses showed that boron deficiency and PBA resulted in similar defects in primary root elongation and lateral root density. The PBA-induced defects, however, were much stronger than those induced by boron deficiency, particularly regarding lateral root development. We provide evidence that the PBA-induced defects were caused by the boric acid moiety and show that both boron deficiency and PBA altered the levels of auxin and reactive oxygen species. Strikingly, PBA did not affect rhamnogalacturonan-II (RG-II) dimerization. Interference of boron-mediated RG-II crosslinking, however, was previously proposed to be the mode of action of PBA in planta. Our study shows that PBA is particularly suited for the molecular dissection of lateral root development in maize and suggests that PBA does not mimic known molecular boron deficiency responses.

PMID:42960663 | DOI:10.1093/plphys/kiag803

Plant Physiol Biochem. 2026 Oct 26;240:111896. doi: 10.1016/j.plaphy.2026.111896. Online ahead of print.

ABSTRACT

The soybean gene Glyma.20G085100 (Gm20P), contributing to the cqSeed protein-003 QTL, and its paralog Glyma.10G134400 (Gm10P), were edited using the CRISPR/Cas9-based genome editing reagents. Two mutants, a gm20p single mutant and a gm10p gm20p double mutant devoid of editing reagents, were identified. Additional gm10p and gm20p single mutants were isolated from F2 population of the cross between the gm10p gm20p double mutant and the wild-type Thorne. The above mutants were characterized in different growing conditions. Seed protein content of the gm10p single and the gm10p gm20p double mutant were significantly reduced relative to the gm20p single mutant and Thorne, with a concomitant increase in oil and starch content. A delayed maturity phenotype was observed in the gm20p single, the gm10p single, and gm10p gm20p double mutants under field conditions across multiple environments. Under controlled conditions in a growth chamber, prominent delayed maturity was only observed under short-day conditions, while long-day conditions induced phenotypic changes in growth in the gm10p gm20p double mutant, but slight delay in maturity. Transcriptomic analysis revealed that the gm10p gm20p double mutant exhibited repression of genes involved in light signaling, enhanced expression of JAZs in JA signaling, suppression of ABA-responsive and senescence-related genes, and elevation of genes that inhibit IAA signaling. Furthermore, the gm10p gm20p double mutant displayed higher sensitivity to salt and ABA during germination. Collectively, these results suggest that both Gm10P and Gm20P modulate light signaling and impact soybean development, maturity and seed reserve content.

PMID:42945731 | DOI:10.1016/j.plaphy.2026.111896

Am J Bot. 2026 Oct 27:e70282. doi: 10.1002/ajb2.70282. Online ahead of print.

ABSTRACT

PREMISE: Gynodioecy is maintained through female advantage in seed fitness that depends on the sex ratio of a population. We hypothesized that females of Silene acaulis would exhibit floral traits associated with elevated outcross pollination and that sex ratio would impact pollen limitation and inbreeding depression such that female advantage is greatest at high hermaphrodite frequency.

METHODS: We examined how sex ratio affects female advantage by pairing observations of floral morphology and natural pollination with a pollination experiment in two sites that differed in sex ratio. We described the population structure of sex ratio by comparing site sex ratio to local scale sex ratio within 1 m of focal plants.

RESULTS: We found evidence for frequency dependence of female advantage through pollination. As local hermaphrodite abundance increased, females were more likely to receive pollen and set fruit. Sex ratio was spatially structured, and only local sex ratio had significant effects on reproductive processes. Both sexes were similarly severely pollen limited, but longer stigmas on female flowers increased chances of pollen deposition. Hermaphrodites experienced inbreeding depression expressed during seed germination, but inbreeding did not fully explain female advantage.

CONCLUSIONS: We confirm female reproductive advantage in a gynodioecious species and show that it is partly facilitated by superior pollination-mediated seed production due to longer stigmas which maximizes pollen receipt. Female advantage exhibits negative frequency dependence locally, such that female advantage is greatest when nearby hermaphrodites are abundant. These results advance our understanding of links between population reproductive processes and sexual selection.

PMID:42947368 | DOI:10.1002/ajb2.70282

Biochem J. 2026 Oct 28:BCJ20260401. doi: 10.1042/BCJ20260401. Online ahead of print.

ABSTRACT

Plant cell walls are made of complex polymeric networks of diverse polysaccharides, proteins, polyphenolics, and glycoproteins called hydroxyproline-rich glycoproteins (HRGPs), like arabinogalactan proteins or AGPs. Approximately 90 to 98% of the mass of AGPs is composed of polysaccharide components, which are synthesized by a group of enzymes known as glycosyltransferases (GTs). One subset of these enzymes comprises a family of fucosyltransferases (FUTs) that transfer fucose (Fuc) residues to the arabinose (Ara) moiety of AGP. Ten FUTs involved in plant cell wall polymer synthesis have been identified in Arabidopsis thaliana, three of which have been characterized: AtFUT1, a xyloglucan-specific FUT, and AtFUT4 and AtFUT6, which are AGP-specific FUTs. In this study, we determined the crystal structure of AtFUT4 to gain insights into its substrate specificity toward GDP-Fuc (donor substrate) and AGP-based oligo- and polysaccharides (acceptor substrates). Through integrated bioinformatics and biochemical analyses, we identified key features that define acceptor- and donor-specificities. We tested two acceptors, AGPs and the pseudo-substrate arabinotetrose, and identified critical residues that contribute to acceptor recognition. In addition to identifying residue-level interactions, our analysis highlights the importance of structural flexibility: tighter binding of GDP-fucose by AtFUT4 likely enables broader acceptor specificity compared with AtFUT1, while also increasing donor hydrolysis in the absence of acceptor. Overall, the study advances understanding of the structure-function relationship of AtFUT4 in AGP fucosylation and provides a foundation for rational engineering of GTs, particularly FUTs, development of inhibitors, studies of cell wall polysaccharide interactions, and exploration of the roles of AtFUT4 in plant physiology.

PMID:42949158 | DOI:10.1042/BCJ20260401

Plant Biotechnol J. 2026 Oct 28. doi: 10.1111/pbi.70779. Online ahead of print.

ABSTRACT

Plant cell walls are polysaccharide-rich extracellular matrices composed of multiple complex carbohydrate polymer networks, including cellulose, hemicelluloses, pectins, and glycosylated proteins. Polysaccharide deposition critically impacts cell wall structure, and structural microheterogeneity within cell wall glycans also influences polymer rigidity and polymer-polymer interactions. Collections of monoclonal antibodies (mAbs) have been developed to target unique carbohydrate epitopes within cell wall polysaccharides and to investigate how these structural changes impact cellular and plant development. Here, we implement generalizable methods to attach unique DNA barcodes to mAbs that recognize major cell wall polysaccharide classes. By applying these mAbs individually to polysaccharide standards, we demonstrate that bound DNA barcoded antibody abundance can be measured via quantitative PCR. Additionally, we demonstrate that DNA-conjugated antibodies can be pooled to quantitatively analyze polysaccharide epitope composition of polysaccharide standards and fractionated cell wall material by amplifying their unique barcodes via qPCR. These results demonstrate that barcoded polysaccharide-directed mAbs offer sensitive, quantitative insights into cell wall polysaccharide composition and facilitate multiplexed profiling of cell wall polysaccharide abundance. This approach will also enable multiple future high-throughput applications, such as glycome profiling, spatial glycomics, and glycan interaction measurements, that will further our understanding of cell wall compositional impacts on plant physiology.

PMID:42949253 | DOI:10.1111/pbi.70779

Curr Issues Mol Biol. 2026 Sep 22;48(10):973. doi: 10.3390/cimb48100973.

ABSTRACT

The use of wheat as forage remains underutilized, particularly in the southeastern U.S., despite its potential to fill seasonal forage gaps when warm-season forages are dormant. Genetic improvement of forage yield traits in wheat has been limited. A genome-wide association study on 182 soft red winter wheat lines was conducted to identify quantitative trait loci for five forage yield traits. The panel was evaluated across four environmental-year combinations in Georgia (2023-2025). ANOVA revealed significant phenotypic variation, with heritability ranging from low to moderate in combined locations and from low to high within individual locations. Correlation analysis revealed significant positive associations between growth stages (GS), forage height (FHt), fresh forage weight (FWt), and dry forage weight (DWt). Using 47,339 SNP markers, we identified 192 marker-trait associations. Twenty-two major-effect QTLs explained 10% of the phenotypic variance, of which six were multi-trait. Chromosomes 7A, 1B, and 6B harbor key regions for FHt, FWt, and DWt. Accumulating favorable alleles showed significant increases in FHt (7 cm), FWt (1611.2 kg/ha), DWt (58.6 kg/ha), and germination counts (G) (4.5%), while reducing GS (0.81 units). QTLs (QFht.uga-7A, QFht.uga-4A) were possibly allelic with known loci, and the remaining 20 QTLs appeared novel. Candidate genes were identified for 10 of 22 QTLs related to plant growth and development. This study provides promising candidates for forage yield improvement in wheat under forage-production systems, supporting marker-assisted selection. Upon further validation, these results can be used in breeding for desirable plant architecture to improve wheat potential for forage yield.

PMID:42939511 | DOI:10.3390/cimb48100973

Appl Environ Microbiol. 2026 Oct 26:e0125626. doi: 10.1128/aem.01256-26. Online ahead of print.

ABSTRACT

Oak wilt, caused by Bretziella fagacearum, is a destructive disease of Quercus species. Symptoms consist of leaf scorch, dieback, defoliation, vascular discoloration, and eventual death. Prompt diagnosis is crucial for timely management that involves laborious and expensive practices such as sanitation, cutting of infected trees, and proactive tree removal to create a buffer zone, root trenching, and/or fungicide injections. Due to these resource-intensive management tactics, laboratory test accuracy and speed are paramount. Diagnoses of oak wilt currently rely on culturing, nested PCR, or qPCR, but all these methods have limitations, ranging from ambiguous results to high barriers to application. We developed a rapid, robust, and sensitive loop-mediated isothermal amplification (LAMP) diagnostic test using primers and probes that target a section of the internal transcribed spacer region of the rDNA of the oak wilt pathogen, B. fagacearum. This assay can detect B. fagacearum from pure isolates and environmental samples, including branch sapwood, leaf petioles, nitidulid sap beetle vectors, and degraded fungal mats. The LAMP assay developed here is sensitive to a detection limit as low as 1 pg/μL and can detect the pathogen in under 20 min. This real-time LAMP-based diagnostic test is thoroughly validated to specifically detect the oak wilt pathogen, B. fagacearum, and is demonstrated to detect the fungus from a variety of routinely collected sample types. Our rapid molecular detection protocol can provide a useful tool for diagnostic labs, forest health practitioners, and researchers studying oak wilt.IMPORTANCEOak wilt is a deadly disease of oaks that represents a growing threat to natural and planted forests throughout eastern North America. To enhance the speed and accuracy of molecular diagnostics for this disease, we designed a molecular test using loop-mediated isothermal amplification (LAMP) to reliably and rapidly detect the oak wilt pathogen, Bretziella fagacearum. To optimize the practicality of this assay in real-world conditions, we developed a rigorous validation process that incorporated the known breadth of genetic diversity of the oak wilt pathogen, sample tissue range, and a panel of non-target fungi to assess the potential for false positives. The novel assay is demonstrated to be highly specific and can detect B. fagacearum from host sapwood, leaf petioles, and nitidulid sap beetles, serving as a versatile new tool for forest health surveillance. Our approach also represents a thorough framework for researchers interested in the development of rapid molecular methods for the detection of forest microbes more broadly.

PMID:42929542 | DOI:10.1128/aem.01256-26