Author: slquinlan

Plant Physiol. 2026 May 22:kiag293. doi: 10.1093/plphys/kiag293. Online ahead of print.

ABSTRACT

Cytosolic ascorbate peroxidases (APXs) have been proposed to have bifunctional 4-coumarate 3-hydroxylase (C3H) activity, linking redox regulation to lignin biosynthesis in plants. Although this dual role has been shown in vitro, in vivo validation remains limited. Here, we used CRISPR/Cas9 gene editing to knock out cytosolic 4-coumarate 3-hydroxylase/ascorbate peroxidase (C3H/APX) genes in Brachypodium distachyon and poplar (Populus tremula × P. alba). In Brachypodium, BdC3H/APX1 catalyzed the ascorbate-dependent hydroxylation of 4-coumarate to caffeate in vitro. Loss of BdC3H/APX1 function led to reduced lignin content, altered monomer composition, elevated H2O2 levels, and impaired growth, while double monoallelic knockouts of BdC3H/APX1 combined with a biallelic BdC3H/APX2 mutation (Bdc3h/apx1&2) exhibited severe developmental defects. Exogenous caffeate and ferulate rescued the growth and lignin phenotype of the Bdc3h/apx1 knockout mutants, whereas catalase reduced H2O2 without restoring plant growth. Similarly, CRISPR/Cas9-mediated PtC3H/APX1 knockout in poplar resulted in stunted growth and altered lignin composition, while the double Ptc3h/apx1&2 mutants were unable to regenerate from tissue culture. These results provide in vivo evidence of C3H/APX bifunctionality, suggesting that perturbed lignin biosynthesis is the primary cause of the growth defects typically observed in C3H/APX-deficient plants.

PMID:42175571 | DOI:10.1093/plphys/kiag293

Phytopathology. 2026 May 22. doi: 10.1094/PHYTO-01-26-0028-R. Online ahead of print.

ABSTRACT

Glomerella leaf spot (GLS) and bitter rot, caused by Colletotrichum species, are two of the most economically damaging diseases of apple (Malus domestica) in the southeastern USA. However, the causal species and their resistance to fungicides have not been well established in Georgia. We surveyed nine orchards in the Georgia apple-growing region in 2023 to identify the Colletotrichum species responsible for these two diseases and to assess their resistance to QoI fungicides. A total of 252 isolates were identified to species, revealing that bitter rot was caused by C. chrysophilum, C. fioriniae, C. fructicola, and C. siamense, with frequencies varying by orchard. In contrast, GLS was dominated by C. fructicola (86%) and, in some orchards, by C. chrysophilum. Sequencing of the cytochrome b (cytb) gene showed that the G143A mutation, which confers complete QoI resistance, was present in all species, but was especially common in C. fructicola (96%) and C. siamense (63%). Several isolates were heteroplasmic for cytb intron variants as well as for G143A, which could only be detected using multiple, genotype-specific primer sets for each isolate, emphasizing that careful detection is required in future studies. Mycelium inhibition assays confirmed that G143A conferred resistance in vitro, as most G143A isolates (98.8%) were classified as resistant using a discriminatory dose of pyraclostrobin while most wild-type isolates (97.7%) remained sensitive. Overall, these findings indicate that QoI fungicides are unlikely to control GLS in Georgia and will be ineffective for bitter rot at many locations.

PMID:42171591 | DOI:10.1094/PHYTO-01-26-0028-R

Cell. 2026 May 20:S0092-8674(26)00506-4. doi: 10.1016/j.cell.2026.04.039. Online ahead of print.

ABSTRACT

Species occupying broad geographic regions have evolved multiple mechanisms to regulate phenological characteristics, enabling adaptations to diverse native habitats. By developing computer vision AI to process citizen science observations across native habitats over North America, we uncovered a consistent latitudinal trend of earlier flowering at higher latitudes in warm-season perennial grasses. To explore the underlying mechanisms of adaptation, we conducted common garden experiments with one species (switchgrass) and discovered the opposite latitudinal flowering-time trend. Integration of differential plasticity of GI-Hd1-FTL1 haplotypes of flowering time regulatory genes, haplotype range, and local environmental profiles found that observations from native habitats capture only part of the genotype-environment-phenotype spectrum established in common garden experiments, therefore reconciling the discrepancy. Two mechanisms emerged as key forces shaping current haplotype ranges and influencing future shifts. Our study highlights the power of combining citizen science observations with designed experiments to uncover mechanisms of adaptation across spatiotemporal scales.

PMID:42167250 | DOI:10.1016/j.cell.2026.04.039

Plant Genome. 2026 Jun;19(2):e70256. doi: 10.1002/tpg2.70256.

ABSTRACT

Cotton (Gossypium hirsutum L.) breeding has primarily emphasized fiber yield and quality, yet plant architectural, developmental, and seed morphological traits also play key roles in productivity and management. Here, we dissect the genetic basis of four such traits: plant height (HT), number of nodes with one branch (N1B), days to flowering (DTF), and average surface area per seed (ASAS) using exotic × elite Upland cotton populations. Both population-specific and joint analyses of the populations identified 17 QTLs collectively, with ASAS having the largest number of detected QTLs. The exotic line T326 showed the highest potential for the improvement of ASAS. While HT, N1B, and DTF displayed limited genetic variance in these populations, gene ontology enrichment highlighted the CCR4-NOT complex as a potential shared regulatory hub connecting ASAS and DTF. In addition, ASAS showed a highly significant positive correlation and overlapping QTL regions with fiber strength and upper half mean length described in a companion paper, suggesting the possibility of strong linkage or pleiotropic effects of these genomic regions, which could be beneficial commercially. Overall, the data suggested no prevalence of negative allelic trade-offs or linkage drag from these secondary traits for the improvement of fiber quality traits, underscoring the value of exotic germplasm for simultaneous enhancement of fiber quality and seed morphology in Upland cotton breeding.

PMID:42159171 | DOI:10.1002/tpg2.70256

J Exp Bot. 2026 May 20:erag234. doi: 10.1093/jxb/erag234. Online ahead of print.

ABSTRACT

Crassulacean Acid Metabolism (CAM) is an adaptation that temporally separates carbon uptake at night from photosynthesis during the day. CAM has evolved repeatedly across vascular plants, as its emergence may depend on simple regulatory changes to deeply conserved metabolic pathways. Modern CAM research relies heavily on interpretation of transcriptomic data, though regulation occurs at multiple levels following transcription. Additionally, while most research to date has focused on a handful of genes and metabolites in the core CAM pathway, the co-option of conserved regulatory and functional genes is bound to have wide ranging effects on other aspects of primary metabolism. In this study, we integrate transcriptomic, proteomic, and metabolomic data to compare primary metabolism between the CAM species Yucca aloifolia and closely related C3 species, Y. filamentosa. We observe minimal correlation between protein abundance and mRNA expression, suggesting significant post-transcriptional regulation in CAM species. We also find evidence of shifts in gene expression and metabolite accumulation outside of the central CAM pathway suggesting that the shift to CAM has cascading effects across primary metabolism, especially nitrogen metabolism. Our findings provide insights into the metabolic shifts associated with CAM evolution and highlight the complexity of its regulation at multiple biological levels.

PMID:42157619 | DOI:10.1093/jxb/erag234

Front Plant Sci. 2026 May 1;17:1799510. doi: 10.3389/fpls.2026.1799510. eCollection 2026.

ABSTRACT

Cultivated peanut is susceptible to several highly damaging pests, pathogens and abiotic stressors, largely due to its very narrow genetic base. However, a ploidy barrier exists between cultivated and highly resistant wild peanuts, which makes the process of interspecific hybridization relatively laborious and beyond the scope of many peanut breeding programs. Thus, the peanut breeding community would greatly benefit from a germplasm collection that captures the diversity represented by wild peanut species in a format that is compatible with cultivated peanut and easily introduced into breeding programs. To this end, we report the construction of a structured introgression line (IL) population bearing introgressions from the wild species A. stenosperma and A. batizocoi. The IL population, which has 32 lines in total, has been constructed to maximize genome coverage across the cultivated peanut allotetraploid genome with complementary introgressed segments of a mean size of 34.7 Mbp. Nine of 10 chromosomes in the A subgenome and six of 10 in the B subgenome have at least one introgression. 60.1% of polymorphic markers from A. stenosperma and 34.8% from A. batizocoi are covered by introgressions. The phenotypic diversity of the population is demonstrated through several traits, including disease resistance and plant height. This IL population will be released for public use to the broader peanut research and breeding community. The open-ended nature of this resource will allow researchers and breeders to exploit the genetic value of these two wild peanut relatives for a number of traits without themselves needing to take on the task of interspecific hybridization.

PMID:42147300 | PMC:PMC13176233 | DOI:10.3389/fpls.2026.1799510

Plant Direct. 2026 May 6;10:e70170. doi: 10.1002/pld3.70170. eCollection 2026 May.

ABSTRACT

Peanut reproduction is foundational for crop yield, breeding, and evolution. However, gene regulation underlying peanut flowering pattern and timing has received limited attention. Cultivated peanut (Arachis hypogaea L.) shows two distinct flowering patterns between two subspecies, with ssp. hypogaea lacking flowers on the main stem and ssp. fastigiata having them. Understanding the gene regulatory networks that control peanut flowering will inform the genetic pathways impacting peanut reproduction, phenology, and yield. To this end, we measured whole-transcriptome gene expression of leaves and shoot tips (meristem) at six plant growth stages from Tifrunner, a peanut cultivar belonging to ssp. hypogaea, and GT-C20, a peanut germplasm belonging to ssp. fastigiata. Overall gene expression was distinct between the two genotypes in both tissue types. Flowering regulators including AhFT, AhSOC1, AhAGL42, and AhSPL3 were differentially expressed in both the main and lateral stem at the time of flowering initiation (T3-first bloom). This indicates that positive regulation of these flowering regulators drives the distinct pattern of flowering on the main stem in GT-C20. Meanwhile, the differential expression of two RING-finger E3 ubiquitin ligases was identified between the two genotypes, indicating that the PAF1-complex (PAF1C) may contribute to the lack of flowering on the main stem of Tifrunner. Gene co-expression network analysis indicates that gibberellic acid (GA) and jasmonic acid (JA) pathways are involved in reproductive regulation. These results provide insight into how flowering physiology is differentially controlled between the two peanut subspecies and provide a launching point for additional research in peanut floral development.

PMID:42099581 | PMC:PMC13147162 | DOI:10.1002/pld3.70170

Nat Genet. 2026 May 5. doi: 10.1038/s41588-026-02598-8. Online ahead of print.

ABSTRACT

Pangenomes are increasingly important for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here we present a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated genomes representing all seven species. This super-pangenome captures approximately 1 million structural variants (SVs), enabling accurate variant genotyping across 914 accessions. Broader sampling within the pangenome provides insights into watermelon genome evolution and the origin of cultivated watermelon. Incorporating SVs into genome-wide association studies improves mapping resolution and reveals a copy number variant upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, these findings and genomic resources establish a foundation for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crops.

PMID:42086854 | DOI:10.1038/s41588-026-02598-8

PLoS Biol. 2026 May 5;24(5):e3003561. doi: 10.1371/journal.pbio.3003561. Online ahead of print.

ABSTRACT

Cryptococcus neoformans is an environmental pathogen that remodels its cellular physiology to survive within mammals and, in susceptible hosts, cause life-threatening meningoencephalitis. Of the many distinctions between the external environment and mammalian tissues, CO2 concentration in the host is two orders of magnitude higher than in the environment and represents a critical stress for C. neoformans. C. neoformans strains that do not replicate at host CO2 concentrations are less virulent in mouse models of infection, further supporting CO2 tolerance as a virulence trait. To further understand the genetic determinants of C. neoformans CO2 tolerance, we performed a near genome-wide screen for deletion mutants with altered CO2 fitness using a competitive growth assay. A total of 301 of 4,692 deletion mutants showed altered CO2 tolerance (245 reduced fitness; 56 increased fitness) demonstrating the global effect of host CO2 on C. neoformans physiology. Based on this data set as well as a metabolomic analysis of C. neoformans adaptation to host CO2, we show that remodeling of central carbon metabolism, oxidative stress buffering, and membrane homeostasis represent an integrated response to CO2 stress that is mediated in part by the TOR-Ypk1 signaling axis. We propose that CO2-induced capsule formation leads to reduced cellular glucose which, in turn, triggers remodeling of central carbon metabolism toward utilization of alternative carbon sources and increased mitochondrial respiration/reactive oxygen generation. Thus, these data provide a near genome-wide profile of the genetic determinants of C. neoformans CO2 tolerance as well as a model for how this important environmental human fungal pathogen alters its physiology to proliferate in the host.

PMID:42085498 | DOI:10.1371/journal.pbio.3003561

Theor Appl Genet. 2026 May 5;139(6):148. doi: 10.1007/s00122-026-05240-7.

ABSTRACT

Although herbicide resistance in Setaria is rampant and cosmopolitian across four herbicide families, we encountered little evidence of target-site resistance, indicating diverse non-target mechanisms of metabolizing, sequestering, and overwhelming herbicides. Setaria viridis is a cosmopolitan weed and model genetic system with increasing reports of resistance to multiple classes of herbicides. Our goal was to assess the herbicide resistance and allelic diversity in herbicide target genes in a collection of Setaria genotypes from North America and Eurasia, and identify the occurrence of novel and known target-site mutations that led to resistance. A total of 214 Setaria genotypes were exposed to commonly used herbicides that inhibit specific genes: herbicide action class (HRAC) group 1 herbicides targeting acetyl-CoA carboxylase (ACCase), HRAC 2 targeting acetolactate synthase (ALS), HRAC 9 targeting 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, and HRAC 10 targeting glutamine synthetase. ACCase and ALS genes in 53 accessions were PCR-amplified and sequenced. Whole-genome sequencing reads covering the target genes were analyzed for an additional 98 genotypes. Herbicide trials showed that 30% of our accessions set seed following application of at least one herbicide, and 13 accessions were resistant to multiple classes of herbicides. Although there were numerous SNPs, including some known to lead to resistance, in our target genes, SNPs found predominantly in herbicide-resistant genotypes were largely intronic or synonymous. A small number of amino acid substitutions in ALS and ACCase indicated potential and incomplete resistance to HRAC 1 and 2 herbicides, but no SNPs putatively associated with herbicide resistance were identified in the other 6 target-site genes. The broader pattern of herbicide resistance in S. viridis is likely driven by non-target mutations that detoxify or compartmentalize applied herbicides.

PMID:42084731 | DOI:10.1007/s00122-026-05240-7