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AraDQ: an automated digital phenotyping software for quantifying disease symptoms of flood-inoculated Arabidopsis seedlings Plant Methods (IF 5.1) Pub Date : 2024-03-16 Jae Hoon Lee, Unseok Lee, Ji Hye Yoo, Taek Sung Lee, Je Hyeong Jung, Hyoung Seok Kim
Plant scientists have largely relied on pathogen growth assays and/or transcript analysis of stress-responsive genes for quantification of disease severity and susceptibility. These methods are destructive to plants, labor-intensive, and time-consuming, thereby limiting their application in real-time, large-scale studies. Image-based plant phenotyping is an alternative approach that enables automated
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Optimization of the selection of suitable harvesting periods for medicinal plants: taking Dendrobium officinale as an example Plant Methods (IF 5.1) Pub Date : 2024-03-16 Peiyuan Li, Tao shen, Li Li, Yuanzhong Wang
Dendrobium officinale is a medicinal plant with high commercial value. The Dendrobium officinale market in Yunnan is affected by the standardization of medicinal material quality control and the increase in market demand, mainly due to the inappropriate harvest time, which puts it under increasing resource pressure. In this study, considering the high polysaccharide content of Dendrobium leaves and
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Maximizing efficiency in sunflower breeding through historical data optimization Plant Methods (IF 5.1) Pub Date : 2024-03-16 Javier Fernández-González, Bertrand Haquin, Eliette Combes, Karine Bernard, Alix Allard, Julio Isidro y Sánchez
Genomic selection (GS) has become an increasingly popular tool in plant breeding programs, propelled by declining genotyping costs, an increase in computational power, and rediscovery of the best linear unbiased prediction methodology over the past two decades. This development has led to an accumulation of extensive historical datasets with genotypic and phenotypic information, triggering the question
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Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in Arabidopsis using liquid chromatography-tandem mass spectrometry Plant Methods (IF 5.1) Pub Date : 2024-03-16 Michal Karady, Pavel Hladík, Kateřina Cermanová, Petra Jiroutová, Ioanna Antoniadi, Rubén Casanova-Sáez, Karin Ljung, Ondřej Novák
Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major
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Characterizing reference genes for high-fidelity gene expression analysis under different abiotic stresses and elicitor treatments in fenugreek leaves Plant Methods (IF 5.1) Pub Date : 2024-03-16 Amin Ebrahimi, Shahrokh Gharanjik, Elham Azadvari, Sajad Rashidi-Monfared
Quantifying gene expression is a critical aspect of applied genomics research across all organisms, and real-time PCR has emerged as a powerful tool for this purpose. However, selecting appropriate internal control genes for data normalization presents specific challenges. This study aimed to identify suitable reference genes for gene expression analysis under various conditions, encompassing salinity
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LysipheN: a gravimetric IoT device for near real-time high-frequency crop phenotyping: a case study on common beans Plant Methods (IF 5.1) Pub Date : 2024-03-14 Duvan Pineda-Castro, Harold Diaz, Jonatan Soto, Milan Oldřich Urban
Climate instability directly affects agro-environments. Water scarcity, high air temperature, and changes in soil biota are some factors caused by environmental changes. Verified and precise phenotypic traits are required for assessing the impact of various stress factors on crop performance while keeping phenotyping costs at a reasonable level. Experiments which use a lysimeter method to measure transpiration
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An efficient protocol for extracting thylakoid membranes and total leaf proteins from Posidonia oceanica and other polyphenol-rich plants Plant Methods (IF 5.1) Pub Date : 2024-03-11 Quentin Charras, Pascal Rey, Dorian Guillemain, Fabian Dourguin, Hugo Laganier, Sacha Peschoux, Roland Molinié, Marwa Ismaël, Stefano Caffarri, Catherine Rayon, Colette Jungas
The extraction of thylakoids is an essential step in studying the structure of photosynthetic complexes and several other aspects of the photosynthetic process in plants. Conventional protocols have been developed for selected land plants grown in controlled conditions. Plants accumulate defensive chemical compounds such as polyphenols to cope with environmental stresses. When the polyphenol levels
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Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR Plant Methods (IF 5.1) Pub Date : 2024-03-05 Mohammad Ali, Dávid Polgári, Adél Sepsi, Levente Kontra, Ágnes Dalmadi, Zoltán Havelda, László Sági, András Kis
Interspecific hybridisation is a powerful tool for increasing genetic diversity in plant breeding programmes. Hexaploid wheat (Triticum aestivum, 2n = 42) × barley (Hordeum vulgare, 2n = 14) intergeneric hybrids can contribute to the transfer of agronomically useful traits by creating chromosome addition or translocation lines as well as full hybrids. Information on the karyotype of hybrid progenies
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Non-destructive real-time monitoring of underground root development with distributed fiber optic sensing Plant Methods (IF 5.1) Pub Date : 2024-02-29 Mika Tei, Fumiyuki Soma, Ettore Barbieri, Yusaku Uga, Yosuke Kawahito
Crop genetic engineering for better root systems can offer practical solutions for food security and carbon sequestration; however, soil layers prevent the direct visualization of plant roots, thus posing a challenge to effective phenotyping. Here, we demonstrate an original device with a distributed fiber-optic sensor for fully automated, real-time monitoring of underground root development. We show
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An open-source controller to build a dynamic light intensity setup Plant Methods (IF 5.1) Pub Date : 2024-02-28 Ludovico Caracciolo, John Philippi, Tom P. J. M. Theeuwen, Herbert van Amerongen, Jeremy Harbinson
The development and physiology of plants are influenced by light intensity and its changes. Despite the significance of this phenomenon, there is a lack of understanding regarding the processes light regulates. This lack of understanding is partly due to the complexity of plant’s responses, but also due to the limited availability of light setups capable of producing specific light patterns. While
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Crop insect pest detection based on dilated multi-scale attention U-Net Plant Methods (IF 5.1) Pub Date : 2024-02-26 Xuqi Wang, Shanwen Zhang, Ting Zhang
Crop pests seriously affect the yield and quality of crops. Accurately and rapidly detecting and segmenting insect pests in crop leaves is a premise for effectively controlling insect pests. Aiming at the detection problem of irregular multi-scale insect pests in the field, a dilated multi-scale attention U-Net (DMSAU-Net) model is constructed for crop insect pest detection. In its encoder, dilated
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Predicting abiotic stress-responsive miRNA in plants based on multi-source features fusion and graph neural network Plant Methods (IF 5.1) Pub Date : 2024-02-24 Liming Chang, Xiu Jin, Yuan Rao, Xiaodan Zhang
More and more studies show that miRNA plays a crucial role in plants' response to different abiotic stresses. However, traditional experimental methods are often expensive and inefficient, so it is important to develop efficient and economical computational methods. Although researchers have developed machine learning-based method, the information of miRNAs and abiotic stresses has not been fully exploited
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Correction: Wheat physiology predictor: predicting physiological traits in wheat from hyperspectral reflectance measurements using deep learning Plant Methods (IF 5.1) Pub Date : 2024-02-24 Robert T. Furbank, Viridiana Silva-Perez, John R. Evans, Anthony G. Condon, Gonzalo M. Estavillo, Wennan He, Saul Newman, Richard Poiré, Ashley Hall, Zhen He
Correction to: Plant Methods (2021) 17:108 https://doi.org/10.1186/s13007-021-00806-6 In the original publication of the article [1], the previous link https://plantpredict.shinyapps.io/PredictionShiny/ should have been changed to the new link https://wheatpredictor.appf.org.au/. The original article has been corrected. Furbank, R.T., Silva-Perez, V., Evans, J.R. et al. Wheat physiology predictor:
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Towards portable MRI in the plant sciences Plant Methods (IF 5.1) Pub Date : 2024-02-18 Shannan Blystone, Magali Nuixe, Amidou Sissou Traoré, Hervé Cochard, Catherine Picon-Cochard, Guilhem Pagés
Plant physiology and structure are constantly changing according to internal and external factors. The study of plant water dynamics can give information on these changes, as they are linked to numerous plant functions. Currently, most of the methods used to study plant water dynamics are either invasive, destructive, or not easily accessible. Portable magnetic resonance imaging (MRI) is a field undergoing
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Exploring the impact of light intensity under speed breeding conditions on the development and growth of lentil and chickpea Plant Methods (IF 5.1) Pub Date : 2024-02-18 Mohammed Mitache, Aziz Baidani, Bouchaib Bencharki, Omar Idrissi
The use of high-performant varieties could help to improve the production of food legumes and thus meet the demand of the growing world population. However, long periods needed to develop new varieties through traditional breeding are a major obstacle. Thus, new techniques allowing faster genetic advance are needed. Speed breeding using longer periods of light exposure on plants, appears to be a good
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Injection-based hairy root induction and plant regeneration techniques in Brassicaceae Plant Methods (IF 5.1) Pub Date : 2024-02-17 Veronika Jedličková, Marie Štefková, Terezie Mandáková, Juan Francisco Sánchez López, Marek Sedláček, Martin A. Lysak, Hélène S. Robert
Hairy roots constitute a valuable tissue culture system for species that are difficult to propagate through conventional seed-based methods. Moreover, the generation of transgenic plants derived from hairy roots can be facilitated by employing carefully designed hormone-containing media. We initiated hairy root formation in the rare crucifer species Asperuginoides axillaris via an injection-based protocol
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PlantNh-Kcr: a deep learning model for predicting non-histone crotonylation sites in plants Plant Methods (IF 5.1) Pub Date : 2024-02-15 Yanming Jiang, Renxiang Yan, Xiaofeng Wang
Lysine crotonylation (Kcr) is a crucial protein post-translational modification found in histone and non-histone proteins. It plays a pivotal role in regulating diverse biological processes in both animals and plants, including gene transcription and replication, cell metabolism and differentiation, as well as photosynthesis. Despite the significance of Kcr, detection of Kcr sites through biological
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Optimizing speed breeding and seed/pod chip based genotyping techniques in pigeonpea: A way forward for high throughput line development Plant Methods (IF 5.1) Pub Date : 2024-02-14 Prakash I. Gangashetty, Shruthi H. Belliappa, Naresh Bomma, Vinutha Kanuganahalli, Sobhan Babu Sajja, Sunita Choudhary, Ramanagouda Gaviyappanavar, Deekshitha Bomireddy, V. Anil Kumar, Jwala Pranati, Mamta Sharma, Manish K. Pandey
The challenge of pigeonpea breeding lies in its photosensitivity and seasonal specificity. This poses a problem to the breeder, as it restricts to single generation advancement in a year. Currently, the cross to cultivar gap is twelve to thirteen years resulting in a limited number of varietal releases over the past six decades. Shortening the breeding cycle was need of the hour, unlikely achieved
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A Cotyledon-based Virus-Induced Gene Silencing (Cotyledon-VIGS) approach to study specialized metabolism in medicinal plants Plant Methods (IF 5.1) Pub Date : 2024-02-12 Yongliang Liu, Ruiqing Lyu, Joshua J. Singleton, Barunava Patra, Sitakanta Pattanaik, Ling Yuan
Virus-induced gene silencing (VIGS) is widely used in plant functional genomics. However, the efficiency of VIGS in young plantlets varies across plant species. Additionally, VIGS is not optimized for many plant species, especially medicinal plants that produce valuable specialized metabolites. We evaluated the efficacy of five-day-old, etiolated seedlings of Catharanthus roseus (periwinkle) for VIGS
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Small- and medium-sized rice fields identification in hilly areas using all available sentinel-1/2 images Plant Methods (IF 5.1) Pub Date : 2024-02-04 Lihua Wang, Hao Ma, Yanghua Gao, Shengbo Chen, Songling Yang, Peng Lu, Li Fan, Yumiao Wang
Mastering the spatial distribution and planting area of paddy can provide a scientific basis for monitoring rice production, and planning grain production layout. Previous remote sensing studies on paddy concentrated in the plain areas with large-sized fields, ignored the fact that rice is also widely planted in vast hilly regions. In addition, the land cover types here are diverse, rice fields are
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Correction: A deep learning model for predicting risks of crop pests and diseases from sequential environmental data Plant Methods (IF 5.1) Pub Date : 2024-02-04 Sangyeon Lee, Choa Mun Yun
Correction to: Plant Methods (2023) 19:145 https://doi.org/10.1186/s13007-023-01122-x In this article [1], the e-mail address of the corresponding author, Choa Mun Yun was incorrectly given as sangyeonlee230@gmail.com but should have been cmunyun@sherpaspace.com. Lee S, Yun CM. A deep learning model for predicting risks of crop pests and diseases from sequential environmental data. Plant Methods 2023;19:145
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Prediction of fruit characteristics of grafted plants of Camellia oleifera by deep neural networks Plant Methods (IF 5.1) Pub Date : 2024-02-04 Fan Yang, Yuhuan Zhou, Jiayi Du, Kailiang Wang, Leyan Lv, Wei Long
Camellia oleifera, an essential woody oil tree in China, propagates through grafting. However, in production, it has been found that the interaction between rootstocks and scions may affect fruit characteristics. Therefore, it is necessary to predict fruit characteristics after grafting to identify suitable rootstock types. This study used Deep Neural Network (DNN) methods to analyze the impact of
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A hyperspectral deep learning attention model for predicting lettuce chlorophyll content Plant Methods (IF 5.1) Pub Date : 2024-02-03 Ziran Ye, Xiangfeng Tan, Mengdi Dai, Xuting Chen, Yuanxiang Zhong, Yi Zhang, Yunjie Ruan, Dedong Kong
The phenotypic traits of leaves are the direct reflection of the agronomic traits in the growth process of leafy vegetables, which plays a vital role in the selection of high-quality leafy vegetable varieties. The current image-based phenotypic traits extraction research mainly focuses on the morphological and structural traits of plants or leaves, and there are few studies on the phenotypes of physiological
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Completing the picture of field-grown cereal crops: a new method for detailed leaf surface models in wheat Plant Methods (IF 5.1) Pub Date : 2024-02-03 Marie Theiß, Angelina Steier, Uwe Rascher, Mark Müller-Linow
The leaf angle distribution (LAD) is an important structural parameter of agricultural crops that influences light interception, radiation fluxes and consequently plant performance. Therefore, LAD and its parametrized form, the Beta distribution, is used in many photosynthesis models. However, in field cultivations, these parameters are difficult to assess and cereal crops in particular pose challenges
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Editing of the ethylene biosynthesis gene in carnation using CRISPR-Cas9 ribonucleoprotein complex Plant Methods (IF 5.1) Pub Date : 2024-02-02 Oluwaseun Suleimon Adedeji, Aung Htay Naing, Hyunhee Kang, Junping Xu, Mi Young Chung, Chang Kil Kim
The study aimed to edit ethylene (ET) biosynthesis genes [1-aminocyclopropane-1-carboxylic acid (ACC) synthetase 1 (ACS1) and ACC oxidase 1 (ACO1)] in carnation using the CRISPR/Cas9 ribonucleoprotein (RNP) complex system. Initially, the conserved regions of the target genes (ACS1 and ACO1) were validated for the generation of different single guide RNAs (sgRNAs), followed by the use of an in vitro
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Using near-infrared spectroscopy to predict nitrogen and phosphorus concentrations of herbarium specimens under different storage conditions Plant Methods (IF 5.1) Pub Date : 2024-02-01 Paul Kühn, Tobias Proß, Christine Römermann, Karsten Wesche, Helge Bruelheide
Herbaria are becoming increasingly important as archives of biodiversity, and play a central role in taxonomic and biogeographic studies. There is also an ongoing interest in functional traits and the way they mediate interactions between a plant species and its environment. Herbarium specimens allow tracking trait values over time, and thus, capturing consequences of anthropogenic activities such
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SeptoSympto: a precise image analysis of Septoria tritici blotch disease symptoms using deep learning methods on scanned images Plant Methods (IF 5.1) Pub Date : 2024-02-01 Laura Mathieu, Maxime Reder, Ali Siah, Aurélie Ducasse, Camilla Langlands-Perry, Thierry C. Marcel, Jean-Benoît Morel, Cyrille Saintenac, Elsa Ballini
Investigations on plant-pathogen interactions require quantitative, accurate, and rapid phenotyping of crop diseases. However, visual assessment of disease symptoms is preferred over available numerical tools due to transferability challenges. These assessments are laborious, time-consuming, require expertise, and are rater dependent. More recently, deep learning has produced interesting results for
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Efficient transformation of the isolated microspores of Chinese cabbage (Brassica rapa L. ssp. pekinensis) by particle bombardment Plant Methods (IF 5.1) Pub Date : 2024-01-30 Yujia Liu, Shujiang Zhang, Shifan Zhang, Hui Zhang, Guoliang Li, Rifei Sun, Fei Li
The low efficiency of genetic transformation in Chinese cabbage (Brassica rapa L. ssp. pekinensis) is the key problem affecting functional verification. Particle bombardment is a widely used method along with the Agrobacterium-mediated method. As a physical means, it has almost no restrictions on the type of host and a wide range of receptor types, which largely avoids the restriction of explants.
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A method to determine antifungal activity in seed exudates by nephelometry Plant Methods (IF 5.1) Pub Date : 2024-01-29 Benjamin Hubert, Muriel Marchi, Joseph Ly Vu, Camille Tranchant, Łukasz P. Tarkowski, Olivier Leprince, Julia Buitink
One of the levers towards alternative solutions to pesticides is to improve seed defenses against pathogens, but a better understanding is needed on the type and regulation of existing pathways during germination. Dormant seeds are able to defend themselves against microorganisms during cycles of rehydration and dehydration in the soil. During imbibition, seeds leak copious amounts of exudates. Here
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A method for small-sized wheat seedlings detection: from annotation mode to model construction Plant Methods (IF 5.1) Pub Date : 2024-01-29 Suwan Wang, Jianqing Zhao, Yucheng Cai, Yan Li, Xuerui Qi, Xiaolei Qiu, Xia Yao, Yongchao Tian, Yan Zhu, Weixing Cao, Xiaohu Zhang
The number of seedlings is an important indicator that reflects the size of the wheat population during the seedling stage. Researchers increasingly use deep learning to detect and count wheat seedlings from unmanned aerial vehicle (UAV) images. However, due to the small size and diverse postures of wheat seedlings, it can be challenging to estimate their numbers accurately during the seedling stage
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Improvement of germination rate and hybridization to facilitate breeding of an industrial oil crop, Euphorbia lagascae Spreng Plant Methods (IF 5.1) Pub Date : 2024-01-24 Maram Istaitieh, Jim F. Todd, Rene C. Van Acker, Mohsen Yoosefzadeh-Najafabadi, Istvan Rajcan
The potential of plant-based sources of vernolic acid to provide agricultural producers with a market diversification opportunity and industrial manufacturers with a renewable, environmentally friendly chemical feedstock is immense. The herbaceous wild spurge or caper spurge (Euphorbia lagascae Spreng) is the most promising source of vernolic acid, containing an average oil content of 50%, of which
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An efficient grafting method for phytoplasma transmission in Catharanthus roseus Plant Methods (IF 5.1) Pub Date : 2024-01-20 Ho-Chun Chang, Jen-Chih Chen
Phytoplasmas are parasitic plant pathogens that reside intracellularly within the sieve tube cells. Phytoplasmas induce various symptoms, including floral virescence, phyllody, leaf yellowing, and witches’-broom. Currently, it is challenging to culture phytoplasma in vitro. In the laboratory, phytoplasmas are generally maintained in alternative host plants, such as Catharanthus roseus. Grafting is
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Automatic 3D cell segmentation of fruit parenchyma tissue from X-ray micro CT images using deep learning Plant Methods (IF 5.1) Pub Date : 2024-01-19 Leen Van Doorselaer, Pieter Verboven, Bart Nicolai
High quality 3D information of the microscopic plant tissue morphology—the spatial organization of cells and intercellular spaces in tissues—helps in understanding physiological processes in a wide variety of plants and tissues. X-ray micro-CT is a valuable tool that is becoming increasingly available in plant research to obtain 3D microstructural information of the intercellular pore space and individual
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LeTra: a leaf tracking workflow based on convolutional neural networks and intersection over union Plant Methods (IF 5.1) Pub Date : 2024-01-17 Federico Jurado-Ruiz, Thu-Phuong Nguyen, Joseph Peller, María José Aranzana, Gerrit Polder, Mark G. M. Aarts
The study of plant photosynthesis is essential for productivity and yield. Thanks to the development of high-throughput phenotyping (HTP) facilities, based on chlorophyll fluorescence imaging, photosynthetic traits can be measured in a reliable, reproducible and efficient manner. In most state-of-the-art HTP platforms, these traits are automatedly analyzed at individual plant level, but information
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Cryopreservation of Abies alba × A. numidica and Pinus nigra embryogenic tissues by stepwise dehydration method Plant Methods (IF 5.1) Pub Date : 2024-01-17 Teresa Hazubska-Przybył, Mikołaj Krzysztof Wawrzyniak, Agata Obarska, Terezia Salaj
Cryopreservation makes it possible to preserve plant biodiversity for thousands of years in ex situ storage. The stepwise dehydration method is a simple and versatile cryopreservation technique based on the vitrification phenomenon. However, the commonly used dimethyl sulfoxide (DMSO) in this cryopreservation technique is considered harmful for plant material, thus alternative methods are needed to
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Exploring genetic variability under extended photoperiod in lentil (Lens Culinaris Medik): vegetative and phenological differentiation according to genetic material’s origins Plant Methods (IF 5.1) Pub Date : 2024-01-13 Mohammed Mitache, Aziz Baidani, Bouchaib Bencharki, Omar Idrissi
Lentil is an important pulse that contributes to global food security and the sustainability of farming systems. Hence, it is important to increase the production of this crop, especially in the context of climate changes through plant breeding aiming at the development of high-yielding and climate-smart cultivars. However, conventional plant breeding approaches are time and resources consuming. Thus
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Genomic prediction for root and yield traits of barley under a water availability gradient: a case study comparing different spatial adjustments Plant Methods (IF 5.1) Pub Date : 2024-01-12 Biructawit B. Tessema, Miguel A. Raffo, Xiangyu Guo, Simon F. Svane, Lene Krusell, Jens Due Jensen, Anja Karine Ruud, Marta Malinowska, Kristian Thorup-Kristensen, Just Jensen
In drought periods, water use efficiency depends on the capacity of roots to extract water from deep soil. A semi-field phenotyping facility (RadiMax) was used to investigate above-ground and root traits in spring barley when grown under a water availability gradient. Above-ground traits included grain yield, grain protein concentration, grain nitrogen removal, and thousand kernel weight. Root traits
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Assessing data analysis techniques in a high-throughput meiosis-like induction detection system Plant Methods (IF 5.1) Pub Date : 2024-01-12 Tanner M. Cook, Eva Biswas, Somak Dutta, Siddique I. Aboobucker, Sara Hazinia, Thomas Lübberstedt
Strategies to understand meiotic processes have relied on cytogenetic and mutant analysis. However, thus far in vitro meiosis induction is a bottleneck to laboratory-based plant breeding as factor(s) that switch cells in crops species from mitotic to meiotic divisions are unknown. A high-throughput system that allows researchers to screen multiple candidates for their meiotic induction role using low-cost
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Cucumber mosaic virus-induced gene and microRNA silencing in water dropwort (Oenanthe javanica (Blume) DC) Plant Methods (IF 5.1) Pub Date : 2024-01-11 Zhen He, Shuangyu Sheng, Lingqi Wang, Tingting Dong, Kun Zhang, Liangjun Li
Water dropwort (Oenanthe javanica (Blume) DC), an aquatic perennial plant from the Apiaceae family, rich in dietary fibert, vitamins, and minerals. It usually grows in wet soils and water. Despite accumulating the transcriptomic data, gene function research on water dropwort is still far behind than that of the other crops. The cucumber mosaic virus (CMV) induced gene silencing was established to study
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Monitoring of plant water uptake by measuring root dielectric properties on a fine timescale: diurnal changes and response to leaf excision Plant Methods (IF 5.1) Pub Date : 2024-01-09 Imre Cseresnyés, Anna Füzy, Sándor Kabos, Bettina Kelemen, Kálmán Rajkai, Tünde Takács
The measurement of root dielectric response is a useful non-destructive method to evaluate root growth and function. Previous studies tracked root development throughout the plant growing cycle by single-time electrical measurements taken repeatedly. However, it is known that root conductivity and uptake activity can change rapidly, coupled with the day/night cycles of photosynthetic and transpiration
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Mitochondrial DNA editing in potato through mitoTALEN and mitoTALECD: molecular characterization and stability of editing events Plant Methods (IF 5.1) Pub Date : 2024-01-05 Alessandro Nicolia, Nunzia Scotti, Nunzio D’Agostino, Giovanna Festa, Lorenza Sannino, Gaetano Aufiero, Shin-ichi Arimura, Teodoro Cardi
The aim of this study was to evaluate and characterize the mutations induced by two TALE-based approaches, double-strand break (DSB) induction by the FokI nuclease (mitoTALEN) and targeted base editing by the DddA cytidine deaminase (mitoTALECD), to edit, for the first time, the mitochondrial genome of potato, a vegetatively propagated crop. The two methods were used to knock out the same mitochondrial
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Optimization of preparation and transformation of protoplasts from Populus simonii × P. nigra leaves and subcellular localization of the major latex protein 328 (MLP328) Plant Methods (IF 5.1) Pub Date : 2024-01-04 Ping Yang, Yao Sun, Xin Sun, Yao Li, Lei Wang
Populus simonii × P. nigra is an ideal material for studying the molecular mechanisms of woody plants. In recent years, research on Populus simonii × P. nigra has increasingly focused on the application of transgenic technology to improve salt tolerance. However, the rapid characterization of gene functions has been hampered by the long growth cycle and exceedingly poor transformation efficiency. Protoplasts
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A novel in-situ-process technique constructs whole circular cpDNA library Plant Methods (IF 5.1) Pub Date : 2024-01-03 Qiang Zhou, Xianlong Ding, Hongjie Wang, Zunaira Farooq, Liang Wang, Shouping Yang
The chloroplast genome (cp genome) is directly related to the study and analysis of molecular phylogeny and evolution of plants in the phylogenomics era. The cp genome, whereas, is highly plastic and exists as a heterogeneous mixture of sizes and physical conformations. It is advantageous to purify/enrich the circular chloroplast DNA (cpDNA) to reduce sequence complexity in cp genome research. Large-insert
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RPIOSL: construction of the radiation transfer model for rice leaves Plant Methods (IF 5.1) Pub Date : 2024-01-03 Shuang Xiang, Zhongyu Jin, Jinpeng Li, Fenghua Yu, Tongyu Xu
The radiative transfer model of vegetation leaves simulates the transmission mechanism of light inside the vegetation and simulates the reflectivity of blades according to the change law of different components in the process of plant growth. Based on the PIOSL model, this paper combines PIOSL with the structure of rice leaves to construct a radiation transfer model for rice leaves. The parameters
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Gray mold and anthracnose disease detection on strawberry leaves using hyperspectral imaging Plant Methods (IF 5.1) Pub Date : 2023-12-19 Baohua Zhang, Yunmeng Ou, Shuwan Yu, Yuchen Liu, Ying Liu, Wei Qiu
Gray mold and anthracnose are the main factors affecting strawberry quality and yield. Accurate and rapid early disease identification is of great significance to achieve precise targeted spraying to avoid large-scale spread of diseases and improve strawberry yield and quality. However, the characteristics between early disease infected and healthy leaves are very similar, making the early identification
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A highly efficient protocol for isolation of protoplast from China, Assam and Cambod types of tea plants [Camellia sinensis (L.) O. Kuntze] Plant Methods (IF 5.1) Pub Date : 2023-12-15 Abhishek Kumar, Nikhil Rawat, Shweta Thakur, Rohit Joshi, Shiv Shanker Pandey
Tea is the most popular beverage worldwide second only to water. Its demand is tremendously rising due to increased awareness of its medicinal importance. The quality and uses of tea depend on the tea-types which are mainly three types including China, Assam and Cambod type having distinct compositions of secondary metabolites. Huge variation in secondary metabolites in different tea-types and cultivars
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Ripening dynamics revisited: an automated method to track the development of asynchronous berries on time-lapse images Plant Methods (IF 5.1) Pub Date : 2023-12-14 Benoit Daviet, Christian Fournier, Llorenç Cabrera-Bosquet, Thierry Simonneau, Maxence Cafier, Charles Romieu
Grapevine berries undergo asynchronous growth and ripening dynamics within the same bunch. Due to the lack of efficient methods to perform sequential non-destructive measurements on a representative number of individual berries, the genetic and environmental origins of this heterogeneity, remain nearly unknown. To address these limitations, we propose a method to track the growth and coloration kinetics
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A deep learning model for predicting risks of crop pests and diseases from sequential environmental data Plant Methods (IF 5.1) Pub Date : 2023-12-14 Sangyeon Lee, Choa Mun Yun
Crop pests reduce productivity, so managing them through early detection and prevention is essential. Data from various modalities are being used to predict crop diseases by applying machine learning methodology. In particular, because growth environment data is relatively easy to obtain, many attempts are made to predict pests and diseases using it. In this paper, we propose a model that predicts
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A protocol for a turbidimetric assay using a Saccharomyces cerevisiae thiamin biosynthesis mutant to estimate total vitamin B1 content in plant tissue samples Plant Methods (IF 5.1) Pub Date : 2023-12-13 Simon Strobbe, Jana Verstraete, Teresa B. Fitzpatrick, Christophe Stove, Dominique Van Der Straeten
Understanding thiamin (thiamine; vitamin B1) metabolism in plants is crucial, as it impacts plant nutritional value as well as stress tolerance. Studies aimed at elucidating novel aspects of thiamin in plants rely on adequate assessment of thiamin content. Mass spectrometry-based methods provide reliable quantification of thiamin as well as closely related biomolecules. However, these techniques require
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Seed protein biotyping in Amaranthus species: a tool for rapid identification of weedy amaranths of concern Plant Methods (IF 5.1) Pub Date : 2023-12-11 Maxime Murphy, Julia Hubert, Ruojing Wang, Leonardo Galindo-González
The Amaranthus genus contains at least 20 weedy and invasive species, including Amaranthus palmeri (palmer’s amaranth) and Amaranthus tuberculatus (tall waterhemp), two species of regulatory concern in North America, impacting production and yield in crops like corn, soybean and cotton. Amaranthus tuberculatus is regulated in Canada with limited establishment, while current climate models predict a
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Novel in silico screening system for plant defense activators using deep learning-based prediction of reactive oxygen species accumulation Plant Methods (IF 5.1) Pub Date : 2023-12-08 Masayuki Kogoshi, Daiki Nishio, Nobutaka Kitahata, Hayato Ohwada, Kazuyuki Kuchitsu, Hideyuki Mizuno, Takamitsu Kurusu
Plant defense activators offer advantages over pesticides by avoiding the emergence of drug-resistant pathogens. However, only a limited number of compounds have been reported. Reactive oxygen species (ROS) act as not only antimicrobial agents but also signaling molecules that trigger immune responses. They also affect various cellular processes, highlighting the potential ROS modulators as plant defense
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Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein–protein interactions Plant Methods (IF 5.1) Pub Date : 2023-12-07 Kewei Zhou, Chenping Lei, Jingyan Zheng, Yan Huang, Ziding Zhang
Protein–protein interactions (PPIs) are heavily involved in many biological processes. Consequently, the identification of PPIs in the model plant Arabidopsis is of great significance to deeply understand plant growth and development, and then to promote the basic research of crop improvement. Although many experimental Arabidopsis PPIs have been determined currently, the known interactomic data of
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Two Arabidopsis promoters drive seed-coat specific gene expression in pennycress and camelina Plant Methods (IF 5.1) Pub Date : 2023-12-06 Xin Li, Victoria Yell, Xu Li
Pennycress and camelina are two important novel biofuel oilseed crop species. Their seeds contain high content of oil that can be easily converted into biodiesel or jet fuel, while the left-over materials are usually made into press cake meals for feeding livestock. Therefore, the ability to manipulate the seed coat encapsulating the oil- and protein-rich embryos is critical for improving seed oil
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Whole mount multiplexed visualization of DNA, mRNA, and protein in plant-parasitic nematodes Plant Methods (IF 5.1) Pub Date : 2023-12-04 Alexis L. Sperling, Sebastian Eves-van den Akker
Plant-parasitic nematodes compromise the agriculture of a wide variety of the most common crops worldwide. Obtaining information on the fundamental biology of these organisms and how they infect the plant has been restricted by the ability to visualize intact nematodes using small molecule stains, antibodies, or in situ hybridization. Consequently, there is limited information available about the internal
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An efficient screening system of disease-resistant genes from wild apple, Malus sieversii in response to Valsa mali pathogenic fungus Plant Methods (IF 5.1) Pub Date : 2023-12-02 Xuejing Wen, Jiangxue Yuan, Tohir A. Bozorov, Abdul Waheed, Gulnaz Kahar, Yakupjan Haxim, Xiaojie Liu, Lili Huang, Daoyuan Zhang
For molecular breeding of future apples, wild apple (Malus sieversii), the primary progenitor of domesticated apples, provides abundant genetic diversity and disease-resistance traits. Valsa canker (caused by the fungal pathogen Valsa mali) poses a major threat to wild apple population as well as to cultivated apple production in China. In the present study, we developed an efficient system for screening
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A novel visual marker to distinguish haploids from doubled haploids in rice (Oryza sativa, L) at early growth stages Plant Methods (IF 5.1) Pub Date : 2023-12-01 Chaitanya Ghalagi, Malavalli Rajashekar Namratha, Kavita Kotyal, Shiva Prakash, Basavaiah Mohan Raju
Doubled haploid technology, which enables the generation of homozygous lines in a single step, is one of the modern tools being employed for accelerating breeding processes in different crops. In rice, a globally important staple food crop, doubled haploid production through androgenesis is increasingly being employed in breeding programs. Amongst the androgenic rice lines, doubled haploids are formed
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Regulating bulb dormancy release and flowering in lily through chemical modulation of intercellular communication Plant Methods (IF 5.1) Pub Date : 2023-11-28 Yajie Zhao, Wenqiang Pan, Yin Xin, Jingxiang Wu, Rong Li, Jinxin Shi, Shuo Long, Lianwei Qu, Yingdong Yang, Mingfang Yi, Jian Wu
Lily is a bulbous plant with an endogenous dormancy trait. Fine-tuning bulb dormancy release is still a challenge in the development of bulb storage technology. In this study, we identified three regulators of symplastic transport, 2,3-Butanedione oxime (BDM), N-Ethyl maleimide (NEM), and 2-Deoxy-D-glucose (DDG), that also regulate bulb dormancy release. We demonstrated that BDM and DDG inhibited callose
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A highlightedly improved method for isolating and characterizing calcium oxalate crystals from tubercles of Mammillaria schumannii Plant Methods (IF 5.1) Pub Date : 2023-11-27 Changying Li, Chunli Chen, Lihong Qin, Dengyue Zheng, Qian Du, Qiandong Hou, Xiaopeng Wen
Calcium oxalate (CaOx) is the most prevalent and widespread biomineral in plants and is involved in protective and/or defensive functions against abiotic stress factors. It is, however, expected that this function has an extremely significant contribution to growth processes in plants bearing large amounts of CaOx, such as cacti growing in desert environment. In our research, small-sized CaOx crystals
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Comparison of two novel methods for counting wheat ears in the field with terrestrial LiDAR Plant Methods (IF 5.1) Pub Date : 2023-11-26 Yangyang Gu, Hongxu Ai, Tai Guo, Peng Liu, Yongqing Wang, Hengbiao Zheng, Tao Cheng, Yan Zhu, Weixing Cao, Xia Yao
The metrics for assessing the yield of crops in the field include the number of ears per unit area, the grain number per ear, and the thousand-grain weight. Typically, the ear number per unit area contributes the most to the yield. However, calculation of the ear number tends to rely on traditional manual counting, which is inefficient, labour intensive, inaccurate, and lacking in objectivity. In this
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Correction: Low-cost and automated phenotyping system “Phenomenon” for multi-sensor in situ monitoring in plant in vitro culture Plant Methods (IF 5.1) Pub Date : 2023-11-25 Hans Bethge, Traud Winkelmann, Patrick Lüdeke, Thomas Rath
Correction: Plant Methods (2023) 19:42 https://doi.org/10.1186/s13007-023-01018-w In the original version of the article, the affiliation ‘Institute of Horticultural Production Systems, Section of Woody Plant and Propagation Physiology, Leibniz Universitätt Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany’ for first author, Hans Bethge was missing. The original article [1] has been corrected