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Plant Methods
Scopus
ISSN 1746-4811 · BMC · 1,629 articles in the index
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Journal Article
The Tonoplast Topology Index—a new metric for describing vacuole organization
Abstract Background The plant vacuole arises by orchestrated interplay of membrane trafficking, cytoskeletal rearrangements and a variety of signaling pathways. In the root, the characteristic large central vacuole develops by endomembrane reorganization occurring mainly in the transition zone. The…
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Journal Article
MoEGP: an efficient crop genomic prediction approach based on the mixture of experts network
Abstract Background Genomic prediction plays a pivotal role in assessing crop germplasm resources, accelerating crop breeding, and enhancing genetic improvement. The mixture of experts network (MoE), has been successfully applied in the fields of natural language processing and image recognition…
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Journal Article
Establishment of fluorescent protein-tagged lines for investigating dynamic localization of organelle and other cell structures in rice pollen tube
Abstract Eukaryotic cells consist of various organelles, each responsible for specific biological processes, making the understanding of protein subcellular localization essential for determining their potential functions. However, the rapid polar growth of pollen tubes requires careful…
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Journal Article
Protoplast isolation and transient gene expression in Suaeda aralocaspica, a halophyte with single-cell C4 anatomy
Abstract Background Suaeda aralocaspica, an annual halophyte belonging to the Amaranthaceae family, is widely distributed in saline-alkali and arid habitats, exhibiting remarkable stress tolerance. This species has evolved a unique single-cell C4 (SCC4) photosynthetic pathway, where both C4 and C3…
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Journal Article
Assisting species differentiation and taxonomic classification by hyperspectral imaging: an example from the parasitic plant realm
Abstract Background Cuscuta, a genus of parasitic plants, poses a threat to global agriculture by infesting a wide variety of economically important crops and facilitating the transmission of plant viruses. Accurate species identification is crucial for management but is traditionally based on…
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Journal Article
Integrated experimental and computational workflows for single-cell transcriptomics in plants
Abstract Background Single-cell transcriptomics is a powerful approach to resolve cellular heterogeneity, yet its application in plants is constrained by challenges in tissue preparation, nuclei isolation, and transcriptome quality. Optimized experimental and computational workflows are essential…
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Journal Article
Crop phenotype prediction using SNP context and whole-genome feature embedding based on DNABERT-2
Abstract Background Modern agriculture demands precise genomic prediction to accelerate elite crop breeding, yet traditional genomic prediction approaches, such as genomic best linear unbiased prediction (GBLUP) and Bayesian methods, focus primarily on the cumulative effect of individual SNPs, thus…
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Journal Article
Profiling DNA-protein interactions in Meloidogyne incognita using dCas9-based affinity purification
Abstract Background The root-knot nematode Meloidogyne incognita, is a highly destructive parasite that manipulates host plant processes through effector proteins, affecting agriculture globally. Despite advances in genomic and transcriptomic studies, the regulatory mechanisms controlling effector…
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Journal Article
Introduction of the Ribo-BiFC method to plants using a split mVenus approach
Abstract Background Translation is a fundamental process for every living organism. In plants, the rate of translation is tightly modulated during development and in responses to environmental cues. However, it is challenging to measure the actual translation state of the tissues in vivo. Results…
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Journal Article
Evaluation of one-image 3D reconstruction for plant model generation
Abstract Generating accurate and visually realistic 3D models of plants from single-view images is crucial yet remains challenging due to plants’ intricate geometry and frequent occlusions. This capability matters because it supplements current plant datasets and enables non-destructive…
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Journal Article
Cross-species optimization of nuclei isolation in ten plant species
Abstract Single-cell technologies are transforming plant biology, yet broadly transferable nuclei isolation remains a key bottleneck for snRNA-seq. We developed a reproducible, cost-efficient Percoll-based workflow that is applicable to multiple maize tissues and nine additional plant species. In…
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Journal Article
MicroDeblurNet: high-fidelity restoration of spatially variant defocus in microscopic images for cucumber downy mildew
Abstract Microscopic imaging provides essential visual evidence for pathogen monitoring, but its shallow depth of field and the three-dimensional height variation of spores lead to pronounced defocus blur and structural degradation. Restoring such images is therefore crucial for reliable spore…
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Journal Article
High-density field-based 3D reconstruction of rice architecture across diverse cultivars for genome-wide association studies
Abstract Background Rice plant architecture underpins yield and grain quality, yet two obstacles impede accurate field characterization in dense paddies. First, single-plant reconstruction is constrained by severe inter-plant occlusion, cluttered backgrounds, and limited viewpoints. These factors…
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Journal Article
Organ-level 3D phenotyping of saffron using a low-cost dual-camera workflow
Abstract Background Precise, non-destructive phenotyping of saffron during vegetative growth is critical for optimizing corm yield and accelerating breeding programs, yet systematic 3D measurements have remained elusive due to extreme morphological challenges: ultra-narrow leaves, severe mutual…
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Journal Article
OpenEar: an ultra-affordable, high-throughput, and accurate maize ear phenotyping system
Abstract Crop phenotyping of important agronomic traits in field conditions at single-plant resolution has long been a major bottleneck in both genetic analysis (e.g. large-scale association/linkage analysis) and breeding applications (e.g. genomic prediction/selection). Despite growing interest…
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Journal Article
Paft-wpest: wolfberry pests fine-grained classification method based on generative self-supervised learning
Abstract Fine-grained pest recognition is a key component of intelligent pest monitoring and precise control, and it is important for ensuring agricultural production safety. This paper proposes a generative self-supervised learning-based pest recognition model, termed PAFT-WPest, to address…
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Journal Article
Deep aerenchyma: a transformer-based pipeline for scalable phenotyping of rice root aerenchyma lacunae across environments
Abstract Background Quantification of rice root anatomical traits such as cortical aerenchyma lacunae is key to understanding rice adaptation to diverse water regimes and to support climate-smart breeding. Aerenchyma lacunae contributes to rice internal gas transport and influences methane…
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Journal Article
PlasmiDB: an open-source and customizable database for plasmid lifecycle management in multi-user, multi-project plant molecular biology laboratories
Abstract Background Functional genomics in plant biology relies on the generation, reuse, and long-term management of large numbers of plasmids produced through diverse cloning strategies. As collections expand across users and projects, laboratories face increasing challenges in organization…
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