Author: slquinlan

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

mBio. 2025 Sep 30:e0150525. doi: 10.1128/mbio.01505-25. Online ahead of print.

ABSTRACT

In most branches of the fungal kingdom, sexual development marks a dramatic shift from simple multicellular hyphae to complex fruiting bodies composed of multiple tissues and cell types. It is essential to tightly regulate development to prevent unnecessary energy investment into building these structures. Polycomb repressive complex 2 (PRC2) is a highly conserved regulator of development in multicellular organisms. In plants, animals, and some fungi, PRC2 tri-methylates histone H3 lysine 27 in promoters and gene bodies to repress gene expression. In Neurospora crassa, H3K27me3-associated genes are poorly conserved and stably repressed in standard lab conditions. Through analysis of publicly available RNA-seq experiments, we found that PRC2-methylated genes are specifically activated during sexual development. PRC2-methylated genes comprise a distinct subset of developmentally induced genes (DIGs) characterized by an exceptionally high degree of cell-type specificity. Loss of PRC2 activity results in the precocious formation of perithecia-like structures (dubbed false perithecia), even in the absence of a compatible mating-type partner. These structures show a unique gene expression profile with the activation of both PRC2-methylated and unmethylated DIGs, suggesting that loss of PRC2 leads to a major transcriptional reprogramming event. Together, these data suggest that PRC2 is part of a developmental checkpoint that restricts fruiting body development to the appropriate conditions.IMPORTANCEDevelopment of multicellular eukaryotes involves transcriptional reprogramming to drive cell fate transitions. This study identified PRC2 as a critical regulator of cell fate in the model filamentous fungus Neurospora crassa, where it silences a subset of sexual development genes. Loss of regulation by PRC2 triggers a major reprogramming event in which genes specifying sexual tissues cannot be repressed, causing a homeotic transition. These results provide novel insights into the role of PRC2-mediated regulation in the fungal kingdom and uncover a critical checkpoint regulating complex multicellular development.

PMID:41025791 | DOI:10.1128/mbio.01505-25

Proc Natl Acad Sci U S A. 2025 Oct 7;122(40):e2503876122. doi: 10.1073/pnas.2503876122. Epub 2025 Sep 29.

ABSTRACT

Polycomb group (PcG) proteins form chromatin modifying complexes that stably repress lineage- or context-specific genes in animals, plants, and some fungi. Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) to assemble repressive chromatin. In the model fungus Neurospora crassa, H3K27me3 deposition is regulated by the H3K36 methyltransferase ASH1 and components of constitutive heterochromatin including the H3K9me3-binding protein HETEROCHROMATIN PROTEIN 1 (HP1). Hypoacetylated histones are a defining feature of both constitutive heterochromatin and PcG-repressed chromatin, but how histone deacetylases (HDACs) contribute to normal H3K27me3 and transcriptional repression within PcG-repressed chromatin is poorly understood. We performed a genetic screen to identify HDACs required for repression of PRC2-methylated genes. In the absence of HISTONE DEACETYLASE-1 (HDA-1), PRC2-methylated genes were activated and H3K27me3 was depleted from typical PRC2-targeted regions. At constitutive heterochromatin, HDA-1 deficient cells displayed reduced H3K9me3, hyperacetylation, and aberrant enrichment of H3K27me3 and H3K36me3. CHROMODOMAIN PROTEIN-2 (CDP-2) is required to target HDA-1 to constitutive heterochromatin and is also required for normal H3K27me3 patterns. Patterns of aberrant H3K27me3 were distinct in isogenic ∆hda-1 strains, suggesting that loss of HDA-1 causes stochastic or progressive epigenome dysfunction. To test this, we constructed a new Δhda-1 strain and performed a laboratory “aging” experiment. Deletion of hda-1 led to progressive epigenome decay over hundreds of nuclear divisions. Together, our data indicate that HDA-1 is a critical regulator of epigenome stability in N. crassa.

PMID:41021810 | DOI:10.1073/pnas.2503876122

Theor Appl Genet. 2025 Sep 27;138(10):260. doi: 10.1007/s00122-025-05043-2.

ABSTRACT

Exotic Gossypium accessions still harbor QTL‑validated alleles that, combined with CRISPR pyramiding and genomic selection, can break the entrenched fiber length-strength trade‑off. Cotton’s four independent domestications twice in diploids and twice in allotetraploids offer a natural experiment in fiber improvement. Synthesizing three decades of data, we chart how polyploidy, selection and modern breeding have repeatedly reshaped the Gossypium genome. More than 15,000 quantitative trait locus (QTL) and genome wide association mapping studies (GWAS) hits converge on a handful of chromosomal “hotspots”; new MAGIC, NAM, NIL and long-read resources now narrow these peaks to < 200 kb, resolving causal genes such as GhHOX3, GhZF14 and GhMYB7. Multi-omics evidence links auxin, ethylene, gibberellin, brassinosteroid and strigolactone signaling to HDZIP IV, MYB, bHLH/HLH and ERF networks that drive fiber initiation, extreme cell elongation and cellulose deposition. Population genomics shows that ~ 40% of favorable fiber alleles are fixed in elite Gossypium hirsutum, yet wild diploids and landraces still harbor variants that could break the length strength trade-off. We propose a three-step roadmap genomic selection, CRISPR gene pyramiding and accelerated introgression to expand cotton’s genetic base and deliver fibers suited to sustainable textile demands.

PMID:41014362 | DOI:10.1007/s00122-025-05043-2