Author: slquinlan

ACS ES T Eng. 2026 Feb 24;6(3):1089-1105. doi: 10.1021/acsestengg.5c00635. eCollection 2026 Mar 13.

ABSTRACT

Efficient nutrient management is critical for crop growth and sustainable resource consumption (e.g., nitrogen and energy). Current approaches require lengthy analyses, preventing real-time optimization; similarly, imaging facilitates rapid phenotyping but can be computationally intensive, preventing deployment under resource constraints. This study proposes a flexible, tiered pipeline for anomaly detection and status estimation (fresh weight, dry mass, and tissue nutrients), including a comprehensive energy analysis of approaches that span the efficiency-accuracy spectrum. Using a nutrient depletion experiment with three treatments (T1-100%, T2-50%, and T3-25% fertilizer strength) and multispectral imaging, we developed a hierarchical pipeline using an autoencoder for early warning. Further, we compared two status estimation modules of different complexity for more detailed analysis: vegetation index features with machine learning (random forest, RF) and raw whole-image deep learning (vision transformer, ViT). Results demonstrated high-efficiency anomaly detection (73% net detection of T3 samples 9 days after transplanting) at substantially lower energy than embodied energy in wasted nitrogen. The state estimation modules show trade-offs, with ViT outperforming RF on phosphorus and calcium estimation (R ² 0.61 vs 0.58, 0.48 vs 0.35) at higher energy cost. With our modular pipeline, this work opens up opportunities for edge diagnostics and practical opportunities for agricultural sustainability.

PMID:41853757 | PMC:PMC12993859 | DOI:10.1021/acsestengg.5c00635

Nature. 2026 Mar 18. doi: 10.1038/s41586-026-10227-x. Online ahead of print.

ABSTRACT

Cinchona alkaloids, which have been studied for more than 250 years, are plant-derived natural products that have collectively had a substantial impact in medicine and basic science^1-5. Examples of cinchona alkaloids include quinine, a historically important antimalarial drug, and cinchonidine, a chiral catalyst widely used in process chemistry. However, it is still largely unknown how plants synthesize these well-known compounds. Here we report the discovery of genes responsible for the biosynthesis of the distinctive quinoline-quinuclidine scaffold of cinchona alkaloids. A combination of isotopic labelling, gene silencing, single-nucleus RNA sequencing and comparative transcriptomics revealed the involvement of several unexpected biosynthetic transformations. We also describe a previously unreported quaternary amine intermediate that is generated through an unusual enzymatic cyclization. We show that dihydroquini(di)none, dihydrocinchoni(di)none and cinchoni(di)none can be produced when these genes are heterologously expressed in Nicotiana benthamiana. Furthermore, we demonstrate that this N. benthamiana expression platform can convert non-native fluorinated and chlorinated tryptamine substrates into dihydrocinchoni(di)none analogues, which suggests that these biosynthetic enzymes can be leveraged to produce halogenated cinchona alkaloid derivatives. These discoveries uncover the long-standing mystery of how the cinchona alkaloid scaffold is biosynthesized and highlight prospects for access to these compounds through metabolic engineering approaches.

PMID:41851462 | DOI:10.1038/s41586-026-10227-x

Phytopathology. 2026 Mar 17. doi: 10.1094/PHYTO-01-26-0021-SA. Online ahead of print.

ABSTRACT

The cosmopolitan bacterium Pantoea agglomerans is renowned for its dual nature, with some strains promoting plant growth and aiding in the suppression of pests and phytopathogens, while others have been linked to plant disease and opportunistic human infections. This duality hampers the biotechnological application of this bacterium and underpins the necessity for taxonomic refinement. The genomes of 295 P. agglomerans strains were subjected to phylogenomic analyses (core genome phylogeny, ANI and dDDH), with strains consistently resolving as two coherent clades supported by proteome content analysis. Average interclade dDDH values (79.1%) fall near the proposed subspecies threshold. Comparative genomic analysis identified clade-specific orthologues and phenotypic assays demonstrate that citrate utilisation distinguishes the two clades. Based on these genotypic and phenotypic markers, we propose delineation of two subspecies of P. agglomerans, subspecies agglomerans (which includes the P. agglomerans type strain) and subsp. jekyllhydei, to reflect the dual nature of this versatile bacterial species.

PMID:41842656 | DOI:10.1094/PHYTO-01-26-0021-SA

Plant J. 2026 Mar;125(6):e70777. doi: 10.1111/tpj.70777.

ABSTRACT

Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia and Latin America. However, as a typical ‘orphan crop’, cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

PMID:41830563 | DOI:10.1111/tpj.70777

Phytopathology. 2026 Mar 11. doi: 10.1094/PHYTO-09-25-0307-SA. Online ahead of print.

ABSTRACT

Center rot of onion is caused by diverse Pantoea species, including P. ananatis, P. agglomerans, P. allii, and P. stewartii ssp. indologenes. While the roles of swimming motility, exopolysaccharide (EPS) production, and quorum sensing (QS) have been explored in P. ananatis in the context of onion disease, those strains were not onion-derived; similar studies in onion-derived Pantoea strains, particularly in P. agglomerans and P. stewartii ssp. indologenes are lacking. In this study, we examined the roles of QS (luxI, luxR), EPS production (epsG), and swimming motility (motB) genes on the virulence of strains from three Pantoea species: P. ananatis PNA 97-1^R, P. agglomerans AR1a^R, and P. stewartii subsp. indologenes PNA 03-3^R, through gene deletions and virulence assays. Mutant characterization confirmed that motB was required for swimming motility, epsG for EPS production, and luxI for acyl-homoserine lactone production in strains from all three Pantoea species. Deletion of motB or epsG did not affect symptom development by any strains, indicating that motility and EPS production were dispensable for onion infection, whereas luxI was essential for virulence in P. ananatis PNA 97-1^R and P. stewartii subsp. indologenes PNA 03-3^R, but not in P. agglomerans AR1a^R, which retained complete virulence despite the luxI deletion. In P. ananatis, while ΔluxI produced no symptoms in onion, ΔluxR and ΔluxIR were virulent, suggesting a regulatory role of luxR as well. These findings indicate that QS-mediated regulation of virulence varies among onion-associated Pantoea strains, whereas motility and EPS production were dispensable for pathogenicity in the strains evaluated.

PMID:41812264 | DOI:10.1094/PHYTO-09-25-0307-SA

Plant J. 2026 Mar;125(5):e70754. doi: 10.1111/tpj.70754.

ABSTRACT

Glycosyltransferases (GTs) are the primary enzymes responsible for the biosynthesis of the complex polysaccharides in plant cell walls. Given the important role of GTs in plants, it is necessary to undertake their functional characterization to better understand plant cell wall synthesis pathways to develop improved feedstocks for efficient conversion into fuels and products to support the emerging bioeconomy. The GT47 family in plants represents a unique target for characterization due to the substantial diversity of donor and acceptor substrates observed within a single family. Here, we have carried out the biochemical characterization of MUR3 and XLT2 orthologs from the aquatic monocot Spirodela polyrhiza. Our findings support existing genetic and phylogenetic data classifying these enzymes as regio-specific galactosyltransferases involved in xyloglucan (XyG) sidechain biosynthesis. In addition, we have identified novel characteristics for both enzymes, such as in vitro arabinopyranosyltransferase activity and distinctiveness in xyloglucan reducing end specificity.

PMID:41784714 | DOI:10.1111/tpj.70754

Theor Appl Genet. 2026 Mar 5;139(3):87. doi: 10.1007/s00122-026-05177-x.

ABSTRACT

A paralog of Cell Size Regulator (CSR), CSR-like1, underlies the novel fw6.2 QTL in tomato. The gene and locus regulate fruit weight by increasing pericarp cell size and its function on fruit weight appears to be conserved in other crops. Fruit weight is a quantitative trait that was under strong selection during the domestication of fruit and vegetable crops such as tomato (Solanum lycopersicum). While numerous fruit weight QTLs have been identified, only three tomato fruit weight genes have been cloned. In this study, we utilized a genetically diverse tomato panel, the Varitome collection, to identify additional genetic loci that control fruit weight. We mapped and fine mapped two fruit weight QTLs on chromosome 6, fw6.1 and fw6.2, by using Genome Wide Association studies (GWAS) and linkage mapping in bi-parental populations. We identified a member of the Cell Size Regulator family, CSR-like1, as the likely candidate underlying fw6.2. The near isogenic lines (NILs) carrying the derived allele of fw6.2 produced heavier fruits with larger fruit pericarp cells than lines with wildtype (WT) allele. Transgenic downregulation of CSR-like1 led to a decrease in fruit weight and pericarp cells, supporting the role of this gene at the fw6.2 locus. The haplotype analysis implied that the CSR-like1-Derived (CSR-like1-D) allele was selected in the transition from the fully wild S. pimpinellifolium to the earliest S. lycopersicum cerasiforme accessions. Four single nucleotide polymorphisms (SNPs) were identified in the regulatory region of CSR-like1 that were conserved in the accessions carrying CSR-like1-WT and were significantly associated with lower fruit weight and pericarp cell size at the locus. Moreover, a pepper GWAS identified a CSR-like1 ortholog that was associated with fruit weight. Together, our findings established CSR-like1 as a novel fruit weight gene likely conserved in other crops in the Solanaceae family.

PMID:41784692 | DOI:10.1007/s00122-026-05177-x

New Phytol. 2026 Mar 3. doi: 10.1111/nph.71037. Online ahead of print.

ABSTRACT

Soybean (Glycine max) plants counteract soybean cyst nematode (SCN, Heterodera glycines Ichinohe) infection through an impairment of soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (α-SNAP) – NSF interactions and vesicular trafficking leading to cellular toxicity in response to nematode feeding. Through the use of a bi-parental mapping population from a cross between the SCN-resistant soybean cultivars Pickett × Peking, a major QTL on chromosome 14 was mapped to a confidence interval containing the GmSNAP14 gene. SCN-resistant genotypes were found to carry one of two variant GmSNAP14 alleles harboring either a deletion or an insertion in GmSNAP14. Expression of full-length transcripts was absent or markedly lower in plants carrying these alleles when compared to susceptible plants. Additionally, the generation of deleted and/or alternatively spliced isoforms coding for GmSNAP14 C-terminal variant proteins was pronounced in resistant plants, suggesting that SCN resistance may result from a combination of diminished GmSNAP14 expression and GmSNAP14 protein variants. CRISPR/Cas9-mediated knockout of GmSNAP14 enhanced resistance to SCN, consistent with susceptibility gene behavior indicating GmSNAP14 as a potential nematode virulence target. Our findings can be leveraged through the use of genome editing and conventional breeding techniques utilizing native alleles to develop resistant soybean cultivars.

PMID:41776743 | DOI:10.1111/nph.71037

J Exp Bot. 2026 Mar 3:erag117. doi: 10.1093/jxb/erag117. Online ahead of print.

ABSTRACT

The plant cell wall hemicellulose xyloglucan in most dicot species consists of repeating units of three consecutive xylosylated Glc residues followed by an unsubstituted Glc (XXXG). Available evidence suggests that galactosylation of the second and the third Xyl side chains of XXXG is carried out regiospecifically by two xyloglucan galactosyltransferases XLT2 and MUR3, respectively, resulting in XLXG and XXLG units, but the mechanism underlying their regiospecificity remains elusive. In this report, we demonstrated that recombinant MUR3 and XLT2 proteins of Arabidopsis, poplar and duckweed were able to regiospecifically galactosylate not only XXXG, but also XLXG and XXLG, respectively, to generate XLLG. Interestingly, they were also able to galactosylate mono- and di-xylosylated xyloglucan oligomers. Protein structural modeling revealed that Arabidopsis and poplar MUR3 proteins contained an α-helical lid-like domain covering their active site clefts and its deletion led to increased galactosyltransferase activity. Molecular docking of the structural models of MUR3 and XLT2 identified amino acid residues interacting with UDP-Gal and XXXG in their active site clefts. Furthermore, site-directed mutagenesis uncovered critical roles of these substrate-interacting residues in the catalytic activity. Together, these findings provide biochemical insights into the molecular determinants of the regiospecificity of MUR3 and XLT2 in xyloglucan galactosylation.

PMID:41773316 | DOI:10.1093/jxb/erag117

Front Plant Sci. 2026 Feb 10;17:1733839. doi: 10.3389/fpls.2026.1733839. eCollection 2026.

ABSTRACT

Real-time monitoring of photosynthetic efficiency can improve our understanding of plant stress responses. In this study, we used a high-frequency chlorophyll fluorescence (CF) monitoring system to investigate the effects of combined temperature and light effects on lettuce. Plants were exposed to three temperatures (18, 25, and 32 °C) and two light intensities (150 and 500 μmol·m^-2·s^-1) for one week, and CF parameters were measured every 30 minutes. Gas exchange measurements were conducted at 2 and 7 days after treatment (DAT). High light combined with low temperature initially suppressed Φ_PSII but gradually improved via reductions in quantum yield of non-regulated energy dissipation (Φ_NO), indicating adjustments in the photosynthetic machinery. While the quantum yield of non-photochemical quenching (Φ_NPQ) decreased sharply only on the first day, Φ_NO continued to decline, highlighting its role in longer-term acclimation. In contrast, high temperatures enhanced CO₂ assimilation through elevated stomatal conductance; however, the maximum efficiency of PSII (F _v/F _m) remained suppressed (~0.81), suggesting sustained photoinhibition. The relationship between electron transport rate (ETR) and photosynthetic rate (A) varied with temperature and time, indicating that the efficiency of converting photochemical energy into carbon assimilation depended on stress conditions and the acclimation stage. However, cumulative ETR integrated over the experiment period was significantly associated with shoot dry weight independent of temperature conditions, indicating that temporally integrated CF metrics retain predictive value for growth, unlike instantaneous CF parameters. These findings demonstrate that high-resolution CF monitoring captures subtle and dynamic photosynthetic responses that are not detectable via single-point gas exchange measurements alone. The ability to interpret changes in CF parameters in real-time provides valuable insights into plant acclimation and stress physiology for the optimization of environmental conditions in controlled environment agriculture systems.

PMID:41743201 | PMC:PMC12929122 | DOI:10.3389/fpls.2026.1733839