Author: slquinlan

Ecology. 2026 Sep;107(9):e70478. doi: 10.1002/ecy.70478.

ABSTRACT

The frequency and severity of droughts are increasing in grasslands globally. Forecasting changes in community composition is challenging due to the direct and indirect effects of drought as well as varied species ecologies. Rare species are predicted to be more susceptible to perturbations, but extreme drought may also disproportionately reduce common species that are well adapted to modal environmental conditions. Resolving these contrasting effects is key to predicting species reordering in response to extreme drought. We explored how species drought responses varied by their spatial and temporal rarity, defined by their local abundances relative to co-occurring species, at six sites across a gradient of mean annual precipitation (MAP) in the Central USA. We found that in general, both spatially sparse and temporally intermittent species increased during and after drought, while common and persistent species declined. Responses were similar at four of the six sites across a gradient of MAP, but did not align with the precipitation gradient as expected. Instead, patterns depended on the characteristics of common species, where rarity was not related to drought responses at sites with many common, early-season, C₃ annual grasses that likely avoided the effects of the summer drought. Finally, the increase in rare species persisted for 4 years after the experimental drought was lifted, suggesting that this extreme drought resulted in lasting shifts to community composition. These findings highlight that rare species can be favored under non-modal environmental conditions like extreme drought and underscore the importance of assessing species recovery to periodic environmental disturbances.

PMID:42710502 | DOI:10.1002/ecy.70478

Tree Physiol. 2026 Sep 8:tpag128. doi: 10.1093/treephys/tpag128. Online ahead of print.

ABSTRACT

In hybrid plants, phenotypic outcomes are governed by interactions between the two parental genomes. However, the mechanisms underlying the interplay of divergent regulatory networks from these genomes remain poorly understood. In this study, we compared gene-level and allele-specific expression patterns, as well as differentially enriched pathways between F₁ and complex backcross (CBC) lines derived from a natural interspecific hybrid population of Populus fremontii (Pf) and P. angustifolia (Pa). Metabolic differences between Pf and Pa which exhibit low and high levels respectively of phenylpropanoid-derived condensed tannins were leveraged. Using individualized transcriptome references, differential expression and clustering analyses revealed CBC-biased and F₁-biased expression for genes involved in phenylpropanoid metabolism and photosynthesis, respectively. Biased expression of these genes at the allele level was also observed in F1. At the whole-transcriptome level, Pa-biased genes predominated in F₁ hybrids, and Pa alleles displayed more conserved expression patterns than Pf alleles across examined samples. Further analyses indicated that allelic expression bias was significantly associated with parental origin, which could be driven by sequence variations in cis-regulatory elements and differences in CpG island length. Our findings demonstrate strong parent-of-origin effects on divergent regulatory networks governing gene expression in poplar hybrids and provide clues for strategic parental selection tailored to specific metabolic pathways of interest.

PMID:42708896 | DOI:10.1093/treephys/tpag128

Theor Appl Genet. 2026 Sep 5;139(9):259. doi: 10.1007/s00122-026-05326-2.

ABSTRACT

Tomato fruit weight is primarily controlled by stable genetic effects and domestication-/improvement-associated loci, including prominent chromosome 5 signals, and integrating SNP, INDEL, and SV diversity improves candidate-locus discovery, biological interpretation, and genomic prediction across environments. Tomato fruit weight (fw) is a major breeding target shaped by domestication, crop improvement, and environmental variation. We investigated the genetic architecture and genomic predictability of fw in the Varitome population representing the tomato domestication continuum, including Solanum pimpinellifolium (SP), S. lycopersicum var. cerasiforme (SLC), and cultivated S. lycopersicum (SLL). Genome-wide SNPs, insertions and deletions (INDELs), and structural variants (SVs) were analyzed individually and in combination to assess their contributions to association mapping, candidate locus discovery, and genomic prediction. Population structure based on all three variant classes clearly separated the domestication groups. Genome-wide association analyses identified 15 SNP, 10 INDEL, and 10 SV loci significantly associated with fw across environments. Several associations co-localized with known fw genes, including fw2.2/CNR, fw3.2/KLUH, fw11.3/CSR, lc/WUSCHEL, and fas/CLAVA3 supporting the biological relevance of the detected signals. Chromosome (Chr) 5 was particularly notable, with a 390-bp deletion at chr5_45,551,023 detected across all four environments and an INDEL at chr5_55,361,233 detected across three environments, suggesting stable improvement-associated candidate loci for fw variation validation. Multiple loci exhibited clear allele-frequency shifts from SP through SLC to SLL, consistent with selection during domestication and improvement, whereas others were detected almost exclusively in cultivated germplasm, suggesting more recent breeding-associated origins. Fw displayed strong genetic control, with genotype explaining more than 92% of the phenotypic variance and only minor contributions from environment and genotype-by-environment interactions. Five genomic prediction models based on SNPs, INDELs, SVs, their combinations, and genotype-by-environment interaction kernels were evaluated using four cross-validation scenarios (CV1, CV2, CV0, and CV00). Prediction accuracy was influenced more strongly by validation scenario and prediction algorithm choice than by marker class. Partial Least Squares (PLS) and Bayesian Genomic Linear Regression (BGLR) consistently outperformed Random Forest (RF) and Deep Learning (DL) models, particularly under scenarios involving untested genotypes and environments. INDEL-based models frequently achieved the highest accuracies under the most stringent prediction scenarios, although differences among marker classes were generally modest. Integrating multiple classes of genomic variation improved biological interpretation, enabled the identification of domestication- and improvement-associated loci, and provided accurate prediction across environments and genetic backgrounds. Together, these results demonstrate that tomato fw is governed primarily by stable additive genetic effects and highlight the value of multi-variant genomic approaches for both genetic dissection and genomic-assisted breeding.

PMID:42700247 | PMC:PMC13546169 | DOI:10.1007/s00122-026-05326-2

J Invertebr Pathol. 2026 Sep 6:108742. doi: 10.1016/j.jip.2026.108742. Online ahead of print.

ABSTRACT

Oil-in-water Pickering emulsions stabilized by titania (TiO2) nanoparticles have shown potential to increase ultraviolet (UV) protection in the entomopathogenic fungus Metarhizium brunneum. In this study, we expand the findings by comparing several nanoparticle-based formulations for UV tolerance, and investigating the impact of protective formulations in a biocontrol setting. The fungal viability in colony forming units (CFUs) and virulence to the 2nd instar tobacco thrips, Frankliniella fusca, were assessed. Under UV-A (380-nm), a titania-based formulation was effective in protecting the fungal viability at 6-h exposure but not at 12-h; silica (SiO2) did not provide any UV protection. UV-A radiation for up to 12 h did not reduce the fungal virulence in any treatment; then a stronger UV treatment was warranted. Under UV-C (254-nm), silica was ineffective in improving the viability or virulence of M. brunneum. The titania-based emulsion showed partial protection for up to 10-min exposure, with 51-56% reduction in CFU counts compared to nearly 100% reduction in the control, while it only exhibited marginal effect in assessing fungal virulence. Two titania-based formulations (titania-MO-1 and titania-PO-2) were further explored for enhanced UV tolerance. Titania- MO-1 had fewer CFUs at 10-min UV compared to control; titania- PO-2 showed no reduction in fungal viability. The two titania formulations were equally effective in maintaining fungal virulence to F. fusca regardless of UV exposure. Overall, titania nanoparticles (particularly titania- PO-2) protected M. brunneum conidia against UV radiation, suggesting the potential use of titania nanoparticles in formulating M. brunneum for improved UV tolerance and biocontrol potential.

PMID:42702346 | DOI:10.1016/j.jip.2026.108742

Theor Appl Genet. 2026 Sep 5;139(9):260. doi: 10.1007/s00122-026-05348-w.

ABSTRACT

We mapped key regions of the maize genome that influence the formation of aboveground (aerial) roots, which in some varieties have been associated with symbiosis with nitrogen-fixing bacteria. Modern agriculture relies heavily on chemically synthesized nitrogen fertilizers, which ensure high yields but also carry high economic and environmental costs. Biological nitrogen fixation (BNF) supplies high amounts of nitrogen to legumes, and several avenues of research are underway to extend it to cereal crops. In maize, aerial roots formed in Sierra Mixe landraces have been associated with BNF. However, much of the genetics underlying aerial root morphology remains unknown. Here, we evaluate aerial root morphology traits associated with BNF in three segregating populations derived from crosses between two Midwest-adapted inbred lines and three landraces. Inclusive composite interval mapping (iCIM) with flowering time as a covariate identified 37 quantitative trait loci (QTL) for three aerial root traits (nodes with roots, root size, and roots per node) which exhibit moderately high heritability (H² = 0.65 to 0.83). The combined proportion of phenotypic variance explained by the detected QTL ranged from 23 to 51%, depending on the trait and population, and potential candidate genes were identified through literature searches, macrosynteny, and gene expression analyses. Introgressing the most relevant aerial root-associated QTL into elite genotypes may provide a path toward achieving meaningful levels of BNF-associated traits in maize, but further work is needed to assess this approach’s viability under field conditions.

PMID:42700241 | DOI:10.1007/s00122-026-05348-w

Phys Rev Lett. 2026 Aug 14;137(7):071801. doi: 10.1103/vbxg-71c2.

ABSTRACT

This Letter reports on the first evidence of inclusive Higgs-boson production at high transverse momentum in the bb[over ¯] final state, reconstructed in a single large-radius jet. The results are based on proton-proton collision data recorded by the ATLAS detector at the Large Hadron Collider at a center-of-mass energies of 13 and 13.6 TeV, corresponding to a total integrated luminosity of 301 fb^{-1}. The study profits from the large background suppression provided by the use of a new transformer-based algorithm for jet identification and the sharper mass and transverse momentum, p_{T}, resolution from a dedicated regression model. The yield relative to the standard model prediction for Higgs bosons produced at p_{T} larger than 450 GeV is measured to be 1.53±0.27)_{-0.27}^{+0.33}±0.17, where the first uncertainty is statistical, the second is experimental systematic, and the third accounts for theory systematic, corresponding to an observed (expected) significance of 3.8σ(2.5σ) relative to the background-only hypothesis. Results are also obtained in three Higgs boson p_{T} intervals and found to be compatible with standard model predictions, where the first uncertainty is statistical, the second is experimental systematic, and the third accounts for theory systematic.

PMID:42675441 | DOI:10.1103/vbxg-71c2

Theriogenology. 2026 Aug 25;266:118156. doi: 10.1016/j.theriogenology.2026.118156. Online ahead of print.

ABSTRACT

The aim of this study was to compare luteal blood perfusion (BP) estimated by subjective human evaluation, ImageJ pixel analysis, and a deep learning (DL)-based system. Color Doppler ultrasound (CDU) examinations utilized herein were from three independent studies where CDU videos were collected at embryo transfer (Day 7; early luteal phase; ELP; n = 129), or on Days 15 (mid luteal phase; MLP; n = 48) and 20 (late luteal phase; LLP; n = 47) of pregnancy. Each corpus luteum (CL) was classified as cavitated (CV; cavity ≥10% of luteal area) or non-cavitated (NC; <10%). Luteal BP was estimated using three methods: Human evaluation, ImageJ pixel counting, and a DL pipeline for frame selection, CL segmentation, and BP quantification. Positive linear relationships were observed among BP estimation methods in all datasets (r ≥ 0.52; P < 0.001) and within CL cavity classifications (r ≥ 0.62; P < 0.001). Strong relationships were consistently observed in the LLP dataset (r ≥ 0.79; P < 0.001). No relationship was detected between circulating progesterone (P4) and BP at ELP or MLP (P ≥ 0.14), regardless of the estimation method. Positive linear relationships (P ≤ 0.001) with P4 were observed for Human, ImageJ, and DL estimates at LLP. In conclusion, DL-derived BP estimates showed strong linear relationships, satisfactory agreement, and biological validity comparable to Human and ImageJ methods, supporting its use for automated assessment of luteal BP in cattle.

PMID:42664605 | DOI:10.1016/j.theriogenology.2026.118156

Appl Environ Microbiol. 2026 Sep 3:e0086526. doi: 10.1128/aem.00865-26. Online ahead of print.

ABSTRACT

Trichoderma reesei is known for its ability to secrete high amounts of cellulases, enzymes of fundamental importance in generating products from lignocellulosic biomass. Diverse signaling pathways and transcription factors (TFs) control the cellulolytic repertoire in T. reesei to ensure correct adaptation to the environment. Here, we analyzed RNA-Seq data and identified a new potential regulator of cellulase production in T. reesei: a novel TF named Nsd3, a homolog of NsdC from Aspergilli. Deletion of nsd3 reduced vegetative growth and conidiation on solid medium. Phenotypic characterization of the Δnsd3 strain showed that it is more sensitive to osmotic stress, but more resistant to cell wall and oxidative stresses. Our results showed that Nsd3 is a repressor of cellulase expression by directly regulating key genes in the cellulolytic pathway, an unreported role for this TF in fungi. Loss of nsd3 leads to a faster and more robust induction of cellulolytic genes, and higher cellulase and hemicellulase activities. Transcriptional profiling by RNA-Seq, chromatin accessibility profiling by ATAC-Seq, and protein-DNA interaction assays showed that sugar transporters are important targets of Nsd3 during cellulase expression regulation. Combined with microscopy and gene expression analyses, the ATAC-Seq data also highlighted Nsd3 as a central regulator of cell wall remodeling and organization. Furthermore, the transcriptomics also showed that Nsd3 regulates genes involved in secondary metabolism. These results showed that Nsd3 regulates several physiological processes and provide novel insights into the regulatory system of cellulases in T. reesei that can be used in the design of high-performance strains for biorefinery.IMPORTANCETrichoderma reesei is a key player in the production of hydrolytic enzymes for the degradation of lignocellulose biomass, and transcription factors are important targets for genetic engineering to construct cellulase-hyperproducing strains. Here, we identified the transcription factor Nsd3 and characterized its role as a regulator of cellulase production in T. reesei. We applied two powerful genomics methods (transcriptome sequencing and chromatin accessibility sequencing) to unravel the global role of Nsd3 and its regulatory mechanism. Nsd3 participates in various biological processes in T. reesei, including cell wall remodeling, calcium metabolism, and secondary metabolism, in addition to regulating the expression of sugar transporters. Protein-DNA interaction assays demonstrate that Nsd3 acts through important genes to regulate cellulase expression, including ace4, crt1, stp1, and cel1b. Our study provides mechanistic insights about how Nsd3 regulates diverse physiological processes in T. reesei. This work also applied ATAC-Seq for the first time to study chromatin accessibility in T. reesei.

PMID:42690075 | DOI:10.1128/aem.00865-26

mBio. 2026 Sep 1:e0183126. doi: 10.1128/mbio.01831-26. Online ahead of print.

ABSTRACT

Aspergillus fumigatus is a thermotolerant saprobe found in soils and plant debris worldwide and an important pathogen of humans, causing two million deaths annually. A. fumigatus makes abundant asexual spores (conidia), which are widely distributed by wind and can be inhaled from the environment. In susceptible individuals, inhaled conidia break dormancy, germinate, and grow in the lung, leading to serious disease. Recent work has shown that conidia made at 37°C and 50°C have different morphologies and germination kinetics. While the asexual cycle is well-characterized at 37°C, much less is known about the asexual cycle at 50°C. Here, we combine flow cytometry and transcriptomics to track morphology and gene expression in the hyphae, conidiophores, and conidia of A. fumigatus during asexual development at 37°C or 50°C. We show that the temperature during a narrow time window in late-stage conidiophore development dictates resulting conidial morphology, transcriptional program, and germination kinetics. As expected, conidiation at 37°C resulted in upregulation of brlA, encoding the master regulator of asexual development, and its downstream targets in conidiophores and conidia. Surprisingly, conidiation at 50°C resulted in upregulation of MAT1-1-1, encoding the master regulator of sexual development, and its downstream targets in conidiophores and conidia. Our findings suggest that temperature during late conidiophore development transcriptionally primes conidia for asexual, parasexual, or sexual development, enhancing chances of survival for progeny. Our findings are especially relevant for agricultural compost, where a wide gradient of temperatures exists, abundant A. fumigatus has been isolated, and resistance to antifungals is thought to evolve.IMPORTANCEThe human pathogen Aspergillus fumigatus has been found in natural and agricultural environments around the world. Disease is acquired when susceptible individuals inhale airborne asexual spores from the environment, which in agriculture generally includes proximity to compost and plant debris piles. This work shows that the environmental temperature when A. fumigatus spores are made determines the transcriptomes of those spores, priming them for future asexual or sexual development. The survival of asexual and sexual spores is very different at different temperatures, so these results are important for understanding how this pathogen survives in varied hostile environments. In addition, there are very few antifungal drugs with which to treat A. fumigatus infections, and resistance is increasing, driven in part by agricultural use of fungicides. These results suggest that higher temperatures during asexual spore formation can lead to increased sexual reproduction and greater chances to evolve antifungal resistance.

PMID:42678159 | DOI:10.1128/mbio.01831-26

J Evol Biol. 2026 Aug 26:voag075. doi: 10.1093/jeb/voag075. Online ahead of print.

ABSTRACT

Abiotic and biotic factors interact to shape the expression of traits and fitness. In contemporary environments, species must respond not only to novel climates but also to altered biotic interactions, and these pressures likely differ across the landscape, which affects population persistence and range limits. Here, we tested the interactive effects of soil microbial communities and temperature variation on plant traits and fitness. We predict that plants are locally adapted to their home soil communities and temperatures, and that local soil microbes could mitigate stresses associated with exposure to elevated temperatures. We conducted a growth chamber experiment using a perennial plant native to the southeastern U.S.A., Elephantopus tomentosus (Asteraceae, L.), in which we exposed accessions from populations in the center of the range and the northern range edge to a fully factorial combination of three soil communities and two temperature levels, reflecting the current average temperature in the central portion of the range vs. potential future climates (+ 4°C). To test whether plants are adapted to their local soil microbial community, we inoculated pots with field soils collected from the center of the range, the range-edge, or with a sterilized control. Plants experienced a greater reduction in reproductive fitness under elevated temperatures when exposed to sterile soil than when grown in live soil. Additionally, plants in central soils had greater fecundity at elevated temperatures than those in northern range-edge soils, which is congruent with expectations and with the finding that seeds sourced from northern populations exhibited a greater reduction in fecundity under elevated temperatures than those sourced from the warmer central populations. Central soil communities increased the growth rate of both accessions, likely due to central-range specific microbes. Our study revealed that plant fitness varied with both temperature and soil microbes, highlighting the importance of accounting for biotic interactions in studies of the biological evolution to climate change.

PMID:42642040 | DOI:10.1093/jeb/voag075