Author: slquinlan

J Comput Chem. 2026 Jan 5;47(1):e70298. doi: 10.1002/jcc.70298.

ABSTRACT

Pectin, a major class of matrix polysaccharides present in plant cell walls (PCW), contains widespread anionic saccharides that cross-link in the presence of cations. It modulates important functions such as cell-cell adhesion and determines the PCW’s biomechanical properties. It is known that mono-, di-, and tri-valent cations facilitate cross-linking; however, significant knowledge gaps remain in understanding the structure and mechanism of pectin cross-linking. In this study, replica-exchange molecular dynamics (REMD) simulations were employed to elucidate the role of ionic charge, ionic radii, and functional groups on the cross-linking of homogalacturonan (HG), the most abundant pectin molecule. Our enhanced sampling approach in fully solvated environments suggests more effective cross-linking with higher-valent and smaller ions, and that the “zipper” conformation is more favorable than the prevalent “egg-box” conformation. These findings advance our fundamental understanding of pectin matrix structure in PCWs and provide a solid foundation to probe structure-property relationships in pectic polysaccharides.

PMID:41472421 | DOI:10.1002/jcc.70298

Plants (Basel). 2025 Dec 18;14(24):3860. doi: 10.3390/plants14243860.

ABSTRACT

Cold stress limits cucumber productivity, and grafting onto tolerant rootstocks offers a promising strategy for improving resilience. This study compared the responses of cucumber heterografts and self-grafts exposed to different cold temperatures, aiming to uncover the molecular basis of grafting-mediated tolerance. Morphological observations showed that grafting onto Cucurbita ficifolia and C. maxima X C. moschata cv. Tetsukabuto rootstocks improved plant growth under moderate cold, while extreme stress remained lethal. Transcriptome analysis revealed that heterografts displayed broader and more sustained differentially expressed genes than self-grafts. Gene ontology (GO) enrichment in heterografts indicated early activation of structural, regulatory, and metabolic processes, with continued enrichment at later stages. KEGG analysis highlighted plant hormone signaling as a central pathway modulated by heterografting, with selective regulation of auxin, ethylene, and ABA signaling. Heterografts activated key regulators, including MAPK3-like, TIFY5A, and CPK28, which were strongly expressed, alongside transcription factors from NAC, CAMTA, WRKY, and MYB families, suggesting coordinated regulation of cold-responsive networks. These results demonstrate that heterografting enhances cold tolerance by orchestrating multi-layered molecular responses, including hormone modulation, stress signaling, and transcriptional factors. This underscores the potential of grafting onto cold-tolerant rootstocks as a practical strategy for cucumber cultivation in cold-prone environments.

PMID:41470743 | PMC:PMC12736856 | DOI:10.3390/plants14243860

Toxins (Basel). 2025 Dec 15;17(12):596. doi: 10.3390/toxins17120596.

ABSTRACT

The year 2025 marks two significant milestones for aflatoxin research: 65 years since aflatoxin was first identified in 1960, and 50 years of focused research on preharvest aflatoxin contamination since it was first recognized in 1975. Studies in the 1970s revealed that A. flavus could infect crops like maize and produce aflatoxin in the field before harvest and made it possible to investigate the potential genetic resistance in crops to mitigate the issues. Tremendous efforts have been made to learn about the process and regulation of aflatoxin production along with interactions between A. flavus and host plants as influenced by environmental factors. This has allowed for the breeding of more resistant crops and investigations into the underlying genetic and genomic components of resistance mechanisms in crops like maize and peanut. However, despite decades of studies, many questions remain. One established “dogma” is that drought stress, especially when combined with high temperatures, is the single greatest contributing factor to preharvest aflatoxin contamination and is a perennial risk faced throughout the major agricultural production regions of the world. Although there are many reviews summarizing the decades’ long wealth of information about A. flavus, aflatoxin biosynthesis, management and host plant resistance, there are few reports that put the spotlight on why aflatoxin contamination is exacerbated by drought stress, which places plants under severe physiological stress and weakens immune systems. Therefore, here we will focus on three major areas of research in maize: the “living embryo” theory and host resistance mechanisms, the “Key Largo hypothesis” and the causes of drought-exacerbated aflatoxin contamination, and recent advancements in CRISPR-based genome editing for enhancing drought tolerance and increasing plant immune responses. This will highlight key breakthroughs and future prospects for the continuing development of superior crop germplasm and cultivars and for mitigating aflatoxin contamination in food and feed supply chains.

PMID:41441631 | DOI:10.3390/toxins17120596

Plant J. 2025 Dec;124(6):e70617. doi: 10.1111/tpj.70617.

ABSTRACT

This study, the third in a three-part series, investigates whether chromosomal instability persists in cultivated peanut. The allotetraploid peanut (Arachis hypogaea; genome type AABB) originated from the hybridization and polyploidization of A. duranensis (AA) and A. ipaënsis (BB). Our first study established that this was an extremely narrow genetic origin, likely from a single hybridization event. This raised a paradox: how did such narrow genetics give rise to the phenotypic diversity seen in cultivated peanut? The second study addressed this, showing that a single neoallotetraploid spontaneously generates striking diversity, and that homoeologous exchanges-abundant in early generations following polyploidy-are a key mechanism in creating this diversity. In contrast to this early-generation instability, cultivated peanut is generally considered to be genetically stable, presumably due to selection. This third study tests whether residual instability still occurs in modern peanut. From a single plant of the highly selfed ‘genome stock’ of the cultivar ‘Tifrunner’, we advanced lineages through seven generations in a pollinator-free greenhouse. Among 233 plants, we identified three new large-scale chromosomal instability events: a large deletion on chromosome B01, associated with reduced pod width and seed weight, and two ABBB compositions involving chromosomes A02/B02 and A05/B05. With these observations in hand, we reinterpreted previously published data from two recombinant inbred populations. Together, these results indicate that at least 1% of pure pedigree A. hypogaea plants exhibit spontaneous large-scale chromosomal changes-a surprising frequency of instability that likely contributes to peanut’s long-term adaptability and evolution.

PMID:41443178 | DOI:10.1111/tpj.70617

Plant J. 2025 Dec;124(6):e70618. doi: 10.1111/tpj.70618.

ABSTRACT

This study, the second in a three-part series, shows how peanut’s polyploid origin enabled rapid diversification and enhanced domestication potential. Building on the knowledge that cultivated peanut (Arachis hypogaea) originated from a narrow hybridization between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago, we are confronted with a paradox: how did such a narrow origin give rise to so much diversity-two subspecies, six botanical varieties, and thousands of landraces differing in growth habit, seed size, and pod morphology? Although several diploid Arachis species were cultivated earlier, only the allotetraploid became fully domesticated and widely adopted. The global success of peanut, despite its narrow genetic origin, suggests that polyploidization itself facilitated domestication. To test this hypothesis, we investigated how the two diploid progenitors and neoallotetraploids derived from a single hybridization and polyploidization event responded under artificial selection. In a pollinator-free greenhouse, we advanced lineages of the neoallotetraploid and its diploid parents over 6 years, selecting for divergent seed weights. The neoallotetraploid showed a much stronger response to artificial selection than its diploid parents, while also spontaneously generating diverse phenotypic variation-including flower color, pod reticulation, and chlorophyll content-traits that distinguish A. hypogaea subspecies and landraces. These traits mirrored directional shifts in parental genome dosage caused by homoeologous exchange, supporting a causal connection with phenotype. These findings offer a compelling rationale for a domestication advantage in polyploid peanut, and provide a living demonstration of how a single ancestral tetraploid, despite an extreme genetic bottleneck, generates a phenotypic boom.

PMID:41443173 | DOI:10.1111/tpj.70618

Plant J. 2025 Dec;124(6):e70619. doi: 10.1111/tpj.70619.

ABSTRACT

This study, the first in a three-part series, lays the foundation for understanding the origin of the peanut crop (Arachis hypogaea). Its subsequent evolution is explored in the two papers that follow. The evidence that A. hypogaea originated from a single hybridization event between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago was already very strong. Here, we extend this evidence using more than 1600 single-nucleotide polymorphisms to make an almost exhaustive comparison of wild Arachis section germplasm conserved ex situ with the A and B subgenomes of divergent, sequenced cultivated peanuts. The wild relatives of peanut are highly selfing and their geocarpy means they plant their own seeds, allowing them to persist as discrete populations for millennia. This unusual biology creates a rare opportunity for genetic archaeology: ancestral lineages can be identified with exceptional precision. Our results reaffirm a single origin for the cultigen, identifying A. duranensis from Río Seco and A. ipaënsis K 30076 as the closest known relatives of the A and B subgenomes of peanut. As a genomic resource, we generated a chromosome-scale assembly of the Río Seco A. duranensis K 30065 and confirmed that it is more closely related to the A subgenome of peanut than the current reference genome (V14167). Even if somewhat closer wild accessions were found through new field collections, they would still belong to the same ancestral lineage. With this level of evidence, the origin of peanut is now known in greater detail than that of any other ancient polyploid crop.

PMID:41442708 | DOI:10.1111/tpj.70619

Nat Commun. 2025 Dec 23. doi: 10.1038/s41467-025-67371-7. Online ahead of print.

ABSTRACT

Accumulating evidences have shown that the mid-oleic fatty acid phenotype in peanuts cannot be explained by the traditional two-gene model involving AhFAD2A and AhFAD2B, which are genes encoding fatty-acid desaturase 2. But the underlying genetic mechanism remains unclear. Here, we present a population-specific pangenome using the eight founder genomes of the PeanutMAGIC population. This graph-based pangenome serves as a comprehensive reference, capturing all segregating haplotypes within the population. We conduct whole genome sequencing for the MAGIC Core, a subset of 310 RILs, for genotyping. Using pangenome-based genotypes, we trace recombination for detailed genomic analysis and phenotypic association. This investigation identifies a unique third gene, named AhFAD2C, near AhFAD2B. When recombination occurs, AhFAD2C segregates from AhFAD2B. We reveal the genotype determining mid-oleic fatty acid phenotype. Our findings underscore the limitations of a single-reference genome, which leads to false association and marker discovery. In contrast, a population-specific pangenome provides a more reliable framework for genomic studies. This study reveals insights into the genetic mechanism of peanut oil quality and demonstrates the advantages of population-specific pangenomes.

PMID:41429781 | DOI:10.1038/s41467-025-67371-7

Plant Phenomics. 2025 Jun 6;7(3):100066. doi: 10.1016/j.plaphe.2025.100066. eCollection 2025 Sep.

ABSTRACT

Fusiform rust, caused by the pathogen Cronartium quercuum (Berk.) Miyabe ex Shirai f. sp. fusiforme, is the most important disease of loblolly pine (Pinus taeda L.) in the U.S., causing millions of dollars in damage each year. Using resistant genotypes has proven a successful strategy to limit the disease, but resistance selection still relies on visual inspection for symptoms, which can lead to misclassification due to human error and the presence of ‘escaped susceptibles’ (i.e., susceptible individuals with no visible symptoms due to either an extended asymptomatic phase of the disease or the lack of adequate disease pressure to become infected). Here, we propose the use of near-infrared (NIR) spectroscopy and chemometrics to improve the accuracy of how phenotypes are rated. We collected and analyzed phloem and needle spectra from 34 non-related families replicated across eight stands in three states in the southeastern region of the U.S. using a portable, handheld NIR spectrometer. We also used a benchtop Fourier-transformed mid-infrared (FT-IR) spectrometer to analyze phloem phenolic extracts of the same samples, as this phenotyping approach has proved successful in other pathosystems. Our results show a moderate association between the phloem spectra and resistance, and models built with NIR spectra were able to classify extremes (i.e., very resistant or very susceptible) with up to 69 ​% testing accuracy. This study provides a framework for using NIR spectroscopy for phenotyping loblolly pine resistance against pathogens and advocates for using alternative technologies in forestry.

PMID:41416181 | PMC:PMC12710050 | DOI:10.1016/j.plaphe.2025.100066

Biodes Res. 2025 Feb 27;7(1):100001. doi: 10.1016/j.bidere.2025.100001. eCollection 2025 Mar.

ABSTRACT

Agrobacterium mediated plant transformation largely depends on two distinct strain lineages – C58 and Ach5. To better serve the plant transformation community, we have created a suite of auxotrophic and auxotrophic recombinant deficient mutants of C58 derivatives EHA105, GV3101::pMP90, and Ach5 derivative LBA4404. While these derivatives are useful, having additional strain backgrounds available would help expand the repertoire for plant transformation even further. Toward that end, two underutilized hypervirulent strains are K599 (NCPPB 2659), and Chry5-but disarmed variants are not easily accessible. To improve availability, we produced disarmed versions of A. rhizogenes strain K599 and A. tumefaciens strain Chry5 and introduced the same desirable mutations as with the other lineages. Each thymidine auxotrophy and recombination deficiency were introduced to existing and newly disarmed Agrobacterium strains via loss of function mutations conferred to thyA and recA, respectively, through CRISPR-mediated base-editing of codons amenable to nonsense mutation. To streamline the editing process, we created a series of visually marked single component base-editor vectors and a corresponding guide-filtering Geneious Prime wrapper plugin for expedited guide filtering. These new strains, the simplified CRISPR-mediated base-editor plasmids, and streamlined workflow will improve the ease with which future Agrobacterium strain derivatives are created while also supporting plant transformation at large.

PMID:41415724 | PMC:PMC12709902 | DOI:10.1016/j.bidere.2025.100001

Science. 2025 Dec 18;390(6779):1232-1233. doi: 10.1126/science.aed2724. Epub 2025 Dec 18.

ABSTRACT

Plant pathogens use secreted effectors to trick plant cells into providing sugary treats.

PMID:41411454 | DOI:10.1126/science.aed2724