Author: slquinlan

Phytopathology. 2025 Oct 17. doi: 10.1094/PHYTO-04-25-0142-R. Online ahead of print.

ABSTRACT

Globally, tomato spotted wilt virus (TSWV) is a serious pest causing tomato spotted wilt disease (TSWD) on a wide range of plant hosts. Integrated pest management (IPM) strategies are crucial for mitigating TSWD incidence in horticultural and row crops. To assess the impact of various IPM approaches on TSWV, we studied four different TSWV isolates collected from peanut (TSWV peanut), tobacco (TSWV tobacco), and tomato (TSWV tomato-1 and tomato-2) crops commonly grown in southeast Georgia, USA. All four isolates were phenotypically assessed based on disease incidence (DI), disease severity (DS), and serially passaged in Nicotiana tabacum cv NC196. In addition, viral genomic molecules were measured in the newly emerged leaves of the inoculated tobacco plants. Nucleocapsid (NP), non-structural movement (NSm), and non-structural silencing suppressor (NSs) gene sequences were analyzed from passages zero, two, and four. Our findings suggested 80-100% of DI in mechanically inoculated plants by all the isolates at 21 days post inoculation (DPI). Based on the expression of symptoms in inoculated plants, high DS was observed in plants inoculated with the TSWV peanut isolate. The difference between viral titer at 7, 14, and 21 DPI was not observed for any of the isolates. On successive passages, virulence decreased for all the isolates (except TSWV tomato-2 isolate). Our study indicated the difference in virulence between TSWV isolates from peanut, tobacco, and tomato crops on N. tabacum.

PMID:41105392 | DOI:10.1094/PHYTO-04-25-0142-R

Animals (Basel). 2025 Sep 26;15(19):2813. doi: 10.3390/ani15192813.

ABSTRACT

Natural areas near farmland can provide refuge for birds that contribute to natural pest control. However, birds can endanger food safety by defecating on or near produce. Work in the western US suggests that Campylobacter spp. are the potential foodborne pathogens most commonly associated with wild birds and that pathogen prevalence is higher in landscapes dominated by animal agriculture. However, relatively little is known about other fresh-market-produce growing regions. Working on produce farms in the Southeastern US, we characterized bird communities, tested bird feces deposited on crop foliage for Campylobacter and Salmonella, and searched for landscape features associated with heightened bird-associated food safety risks. We found that bird communities on farms were generally similar across ecoregions. Campylobacter was never detected from bird feces deposited on crop foliage, but Salmonella was detected in 8.6% of fecal samples. Salmonella prevalence in crop-surface-collected bird feces was highest when farms also produced livestock and when wetland cover was prevalent in the landscape. Overall, our results suggest that on-farm livestock production may be an indicator of bird-associated food safety risks in the Southeast, as in the West. We suggest there may be some similarities, but important differences, in food safety risks posed by birds in different US produce growing regions.

PMID:41096407 | DOI:10.3390/ani15192813

BMC Genomics. 2025 Oct 16;26(1):925. doi: 10.1186/s12864-025-11945-8.

ABSTRACT

BACKGROUND: Photoperiodic changes in diel cycles of gene expression are pervasive in plants. The timing of circadian regulators, together with light signals, regulate multiple photoperiod-dependent responses such as growth, flowering or tuber formation. However, for most genes, the importance of cyclic mRNA levels is less clear. We analyzed the diel transcriptome of modern cultivated potato, a highly heterozygous autotetraploid. Clonal propagation and limited meiosis have led to the accumulation of deleterious alleles, making tetraploid potato an ideal model system to investigate the conservation of cyclic expression and cyclic genes during artificial selection and clonal propagation.

RESULTS: Our results indicate that rhythmic alleles of cultivated potato are more highly expressed than non-rhythmic genes and are highly co-expressed not only under diel cycles but also across tissues, developmental stages, and stress conditions. Moreover, the smaller ratio of non-synonymous to synonymous differences within rhythmic versus non-rhythmic allelic groups indicates that cyclic genes, in general, have more conserved core functions than non-cyclic genes. In accordance with this observation, fully rhythmic allelic groups are highly enriched in photosynthesis and ribosome biogenesis genes, which have core functions in plants. Furthermore, we investigated differences in cyclic expression patterns between photoperiods identifying potential regulators for the strong changes in phase of expression of ribosome biogenesis and pathogen response genes. Finally, analyses of genes involved in tuber formation suggests that the regulation of CO gene transcription is not the only factor enabling tuberization under long days in modern cultivated potato.

CONCLUSIONS: This study not only provides high quality diel transcriptomic datasets of cultivated potato but also provides important insight on the role of allelic diversity in rhythmic expression in plants.

PMID:41102621 | DOI:10.1186/s12864-025-11945-8

Plant J. 2025 Oct;124(1):e70527. doi: 10.1111/tpj.70527.

ABSTRACT

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene-free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High-throughput sequencing technologies, including long-read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements-often missed by standard genotyping-when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user-friendly, synthetic biology-compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue-specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next-generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

PMID:41092254 | DOI:10.1111/tpj.70527

J Hered. 2025 Oct 15:esaf081. doi: 10.1093/jhered/esaf081. Online ahead of print.

ABSTRACT

A central goal of evolutionary biology is to understand the mechanisms conferring adaptation. Gene expression is sensitive to environmental variability; thus, investigating gene expression differentiation among populations may reveal signatures of selection from predictable environmental conditions. Environmental pressures that covary with elevation gain (e.g., temperature) result in stark environmental differences along short distances. The phenological and life history traits of plants inhabiting elevational gradients might track these variables, providing an opportunity for testing hypotheses. Boechera stricta occupies a steep elevation gradient in the Rocky Mountains. Here, we grew F3 seeds from at least two genotypes each from five populations of B. stricta in a greenhouse. Analysis of leaf RNAseq data permitted tests of these hypotheses: 1) populations exhibit significant among population genetic variation in gene expression; 2) differentiation in gene expression (QST) exceeds neutral expectations (FST); and 3) the putative functions of differentially expressed genes are predicable based on a priori knowledge of environmental pressures that vary with elevation. Differentiation in gene expression (average QST = 0.53) significantly exceeded neutral differentiation (average FST = 0.17), implicating selection as a potential cause of genetically divergent patterns of gene expression. The putative functions of differentially expressed genes covarying with elevation were enriched for biological processes related to conditions that vary with elevation (circadian rhythm, response to light, chloroplast organization, and vegetative to reproductive meristem transitions). This study reveals considerable differentiation in gene expression, which may provide a mechanism for rapid adaptation to local environmental conditions in this and other species.

PMID:41092278 | DOI:10.1093/jhered/esaf081

Mol Hortic. 2025 Oct 10;5(1):55. doi: 10.1186/s43897-025-00177-9.

ABSTRACT

Citrate is critical to the flavor of horticultural fruit and governed by ACO. However, the specific ACO and its upstream regulators involved in citrate metabolism during pear (Pyrus spp.) fruit development remained uncharacterized. This study identified and characterized six PbrACOs from the Pyrus bretschneideri Rehd. genome. Comprehensive analyses of citrate levels, cyt/mitACO activities, and PbrACOs expression profiles in the pericarp and cortex tissues of developing ‘Yali’ and ‘Dangshansuli’ fruits revealed PbrACO2 as a candidate gene. Subsequently, PbrACO2 was confirmed as a mitochondrial aconitase catalyzing citrate-to-isocitrate conversion in vitro and in vivo. Analysis of differentially expressed transcription factors (TFs) and cis-acting elements in the PbrACO2 promoter identified nuclear PbrMYB3 and PbrMYB65, derived from whole genome duplication/segmental duplication, as candidate upstream regulators. These MYB TFs, without direct relationship, bound, as monomers, to the same two MYB-binding sites in the PbrACO2 promoter to activate its transcription, thereby promoting citrate isomerization in pear and tomato. Further investigation revealed that PbrMYB3 and PbrMYB65 are transcriptionally regulated by PbrNAC34a. Given their tissue-dependent expression profiles, the PbrNAC34a-PbrMYB3/65-PbrACO2 cascade partially accounts for citrate differences between pear fruit pericarp and cortex tissues. These findings enhance understanding of citrate accumulation in Rosaceae fruit and provide genetic resources for pear breeding.

PMID:41068843 | DOI:10.1186/s43897-025-00177-9

Physiol Plant. 2025 Sep-Oct;177(5):e70568. doi: 10.1111/ppl.70568.

ABSTRACT

One of the major disfunctions in heat-stressed plants is enhanced protein damage. Creeping bentgrass (Agrositis stolonifera L.) is an economically important perennial grass species but it is sensitive to high temperatures. Several experimental lines of creeping bentgrass varied in response for physiological traits, total protein content, and protein degradation rates in response to heat stress. The ubiquitin-proteasome system plays a crucial role in the removal of damaged proteins, and there is a critical need to better understand the changes in proteins that occur during heat stress. Hence, we aimed to estimate change in global protein accumulations by performing gel-free proteomics, and polyubiquitin-omics to identify proteins that have been polyubiquitinated and targeted to the ubiquitin-proteasome system with Tandem Ubiquitin Binding Entities in contrasting lines exposed to heat. We found that metabolic processes, like photosynthesis, antioxidant defense and protein refolding could be regulating heat tolerance in creeping bentgrass. Heat-tolerant line S11 729-10 was able to maintain proteins involved in the light reactions of photosynthesis, while enhancing antioxidant proteins, particularly during the later phase of heat stress. This contributed to its improved performance, including greater cell membrane integrity as well as healthier light harvesting components. Additionally, the faster turnover of key polyubiquitinated antioxidant proteins in S11 729-10 likely represents a critical mechanism for protecting against oxidative damage. This is the first time that polyubiquitin-omics has been utilized in turfgrass. These findings provide insights into protein metabolism during heat stress that could be utilized to help develop new cultivars with enhanced tolerance to heat.

PMID:41070926 | DOI:10.1111/ppl.70568

Commun Psychol. 2025 Oct 7;3(1):145. doi: 10.1038/s44271-025-00324-4.

ABSTRACT

Every social situation that people encounter in their daily lives comes with a set of unwritten rules about what behavior is considered appropriate or inappropriate. These everyday norms can vary across societies: some societies may have more permissive norms in general or for certain behaviors, or for certain behaviors in specific situations. In a preregistered survey of 25,422 participants across 90 societies, we map societal differences in 150 everyday norms and show that they can be explained by how societies prioritize individualizing moral foundations such as care and liberty versus binding moral foundations such as purity. Specifically, societies with more individualistic morality tend to have more permissive norms in general (greater liberty) and especially for behaviors deemed vulgar (less purity), but they exhibit less permissive norms for behaviors perceived to have negative consequences in specific situations (greater care). By comparing our data with available data collected twenty years ago, we find a global pattern of change toward more permissive norms overall but less permissive norms for the most vulgar and inconsiderate behaviors. This study explains how social norms vary across behaviors, situations, societies, and time.

PMID:41057696 | DOI:10.1038/s44271-025-00324-4

Nat Plants. 2025 Oct 3. doi: 10.1038/s41477-025-02122-6. Online ahead of print.

ABSTRACT

Iridoids are specialized monoterpenes ancestral to asterid flowering plants^1,2 that play key roles in defence and are also essential precursors for pharmacologically important alkaloids^3,4. The biosynthesis of all iridoids involves the cyclization of the reactive biosynthetic intermediate 8-oxocitronellyl enol. Here, using a variety of approaches including single-nuclei sequencing, we report the discovery of iridoid cyclases from a phylogenetically broad sample of asterid species that synthesize iridoids. We show that these enzymes catalyse formation of 7S-cis-trans and 7R-cis-cis nepetalactol, the two major iridoid stereoisomers found in plants. Our work uncovers a key missing step in the otherwise well-characterized early iridoid biosynthesis pathway in asterids. This discovery unlocks the possibility to generate previously inaccessible iridoid stereoisomers, which will enable metabolic engineering for the sustainable production of valuable iridoid and iridoid-derived compounds.

PMID:41044409 | DOI:10.1038/s41477-025-02122-6

Front Plant Sci. 2025 Sep 16;16:1657140. doi: 10.3389/fpls.2025.1657140. eCollection 2025.

ABSTRACT

In reciprocal interspecific near-isogenic lines developed by crossing elite cultivars Acala Maxxa (Gossypium hirsutum) and Pima S6 (G. barbadense) representing the two major domesticated species of cotton, we identified genomic locations underpinning an important fiber quality trait – fiber elongation (ELO). Phenotypic evaluation of these lines in three environments revealed a total of 36 QTLs, including 14 (38.89%) on the D subgenome, from a progenitor that does not produce spinnable fiber. Nearly half (16, 44.4%) of the 36 QTLs identified in the study explained less than 6% of phenotypic variation, and two (EL07.1 and EL25.1) were new, justifying the use of near-isogenic lines for analysis. Significantly larger additive effects of these QTLs in comparison to those reported using early generation backcrosses, F₂ and F₂ derived populations as well as recombinant inbred lines (RILs) show that NILs offer an advantage in estimating more precise QTL effects by removing background noise due to segregating genomic regions. Seven genomic regions on chromosomes 2, 6, 9, 12, 15 and 18 were consistently associated with ELO in two of the three environments tested. A total of 11 (30.56% of) QTLs had transgressive allele effects, i.e. which were opposite of what would be predicted from the parental phenotypes, indicating opportunities to breed superior interspecific lines; and three QTLs (8.33%) had heterotic alleles that may contribute to the striking fiber quality of F₁ hybrids between these species. Limited reciprocity of QTLs in the two backgrounds is attributed to the combined consequences of epistasis, small phenotypic effects and imperfect coverage of donor chromatin in the recipient background. The availability of DNA markers linked to both G. barbadense and G. hirsutum QTLs identified in this and other studies promise to assist breeders in transferring and maintaining valuable traits from exotic sources during cultivar development.

PMID:41036399 | PMC:PMC12479486 | DOI:10.3389/fpls.2025.1657140