Author: slquinlan

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

Ecol Lett. 2025 Dec;28(12):e70283. doi: 10.1111/ele.70283.

ABSTRACT

Predicting the effects of climate change on plant and animal populations is an urgent challenge for understanding the fate of biodiversity under global change. At the surface, quantifying how climate drives the vital rates that underlie population dynamics appears simple, yet many decisions are required to connect climate to demographic data. Competing approaches have emerged in the literature with little consensus around best practices. Here we provide a practical guide for how to best link vital rates to climate for the purposes of inference and projection of population dynamics. We first describe the sources of demographic and climate data underlying population models. We then focus on best practices to model the relationships between vital rates and climate, highlighting what we can learn from mechanistic and phenomenological models. Finally, we discuss the challenges of prediction and forecasting in the face of uncertainty about climate-demographic relationships as well as future climate. We conclude by suggesting ways forward to build this field of research into one that makes robust forecasts of population persistence, with opportunities for synthesis across species.

PMID:41400311 | DOI:10.1111/ele.70283

New Phytol. 2025 Dec 15. doi: 10.1111/nph.70824. Online ahead of print.

ABSTRACT

Pollen grains exhibit remarkable morphological diversity, shaped by selective pressures from environmental factors and mechanical constraints. Here, we investigate macroevolutionary patterns of pollen morphology in Apiales, an order of angiosperms with significant ecological and geographical diversity, to disentangle the roles of climate and functional constraints. We analyzed pollen morphology in 158 species of Apiales using morphometric and multivariate evolutionary approaches to evaluate the influence of climate and biomechanical constraints on traits such as pollen wall thickness, aperture structure, and overall grain shape, and to test for evidence of harmomegathy-related adaptation. Our results reveal three key findings. First, climate showed no significant effect on pollen size, challenging long-standing assumptions. Second, climate strongly influences pollen architecture, with drier, more seasonal climates being consistently associated with reduced apertures and thicker pollen walls. Finally, we detected an evolutionary lag, with changes in pollen wall thickness preceding aperture modifications, indicating that biomechanical constraints have shaped evolutionary trajectories. These results demonstrate that climate-driven adaptations in pollen architecture are mediated by functional constraints, consistent with a dynamic interaction between environmental selection and biomechanical properties of the pollen wall.

PMID:41398687 | DOI:10.1111/nph.70824

Front Fungal Biol. 2025 Nov 27;6:1714008. doi: 10.3389/ffunb.2025.1714008. eCollection 2025.

ABSTRACT

Beauveria bassiana (Balsamo) Vuillemin is a well-known entomopathogenic fungus that occupies diverse ecological niches, including soilborne, epiphytic, and endophytic habitats. Its capacity to function as an endophyte has received growing interest in potential applications for sustainable pest management, particularly in woody perennial systems where delivery and persistence of biological control agents are challenging. This study investigated endophytic colonization of peach (Prunus persica Batsch) seedlings by B. bassiana and quantified production of the insecticidal secondary metabolite beauvericin (BEA) in and on plant tissues. Seedlings were inoculated via foliar spray or soil drench. Fungal recovery was assessed from leaf, stem, and root tissues. Colonization patterns indicated systemic movement, however foliar spray increased recovery from leaf tissues and soil drench increased recovery from roots over time. BEA concentrations varied significantly by tissue type, inoculation method, and surface sterilization status. The highest levels were detected in non-surface-sterilized leaves of foliar-sprayed plants, measured two weeks post-inoculation. Surface sterilization prior to extraction significantly reduced detected concentrations, suggesting that BEA is primarily produced by epiphytic fungal growth. Larval bioassays with Tenebrio molitor L. revealed increased mortality associated with foliar-sprayed tissues, aligning with observed BEA levels and suggesting localized insecticidal activity. These findings demonstrate that the spatial dynamics of fungal colonization and metabolite localization are critical considerations for the effective deployment of B. bassiana in biocontrol strategies. Further research is needed to determine how environmental factors, host physiology, fungal strain, and time influence secondary metabolite production in and on plants treated with B. bassiana.

PMID:41393922 | PMC:PMC12695560 | DOI:10.3389/ffunb.2025.1714008

PLoS Biol. 2025 Dec 12;23(12):e3003560. doi: 10.1371/journal.pbio.3003560. Online ahead of print.

ABSTRACT

Variants in the protein kinase CDKL5 cause CDKL5 Deficiency Disorder (CDD), a severe neurodevelopmental condition characterized by seizures, developmental delay, and intellectual disability. The Chlamydomonas homolog of CDKL5, LF5, is a flagellar protein whose loss leads to elongated flagella. Here, we combine live-cell imaging, immunofluorescence, and biochemical approaches including mass spectrometry to define how CDKL5 activity is regulated and how its loss alters ciliary function. We find that Chlamydomonas CDKL5 is activated by LF2, a cyclin-dependent kinase, through phosphorylation of its activation loop. This activation controls CDKL5 localization in steady-state cilia, down-regulates its IFT-mediated transport as flagella reach steady-state, controls ciliary abundance of IFT proteins, and controls phosphorylation of the tubulin-binding domain of IFT74, thereby influencing flagellar length. Mouse Cdkl5 shows similar properties: it localizes within cilia, its loss leads to ciliary elongation, and its localization depends on both its kinase activity and Cdk20, the mammalian ortholog of LF2. These results extend our understanding of ciliary length control, challenge the prevailing model that CDKL5 is activated by autophosphorylation, and suggest that CDD pathogenesis arises, at least in part, from disruption of this conserved ciliary regulatory pathway.

PMID:41385589 | DOI:10.1371/journal.pbio.3003560