685 results match your criteria Plant Methods [Journal]


Accuracy assessment of plant height using an unmanned aerial vehicle for quantitative genomic analysis in bread wheat.

Plant Methods 2019 15;15:37. Epub 2019 Apr 15.

1Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 China.

Background: Plant height is an important selection target since it is associated with yield potential, stability and particularly with lodging resistance in various environments. Rapid and cost-effective estimation of plant height from airborne devices using a digital surface model can be integrated with academic research and practical wheat breeding programs. A bi-parental wheat population consisting of 198 doubled haploid lines was used for time-series assessments of progress in reaching final plant height and its accuracy was assessed by quantitative genomic analysis. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-019-0419-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463666PMC
April 2019
1 Read

In vitro propagation method for production of morphologically and genetically stable plants of different strawberry cultivars.

Plant Methods 2019 13;15:36. Epub 2019 Apr 13.

1Department of Horticultural Science, Kyungpook National University, Daegu, 4165122 South Korea.

Background: As strawberries are susceptible to somaclonal variation when propagated by tissue culture techniques, it is challenging to obtain the true-to-type plants necessary for continuous production of fruits of stable quality. Therefore, we aimed to develop an in vitro propagation method for the production of true-to-type plants of five different strawberry cultivars from meristems cultured in media containing different concentrations of kinetin (Kn).

Results: For all the cultivars, shoot induction was successful only in the meristems cultured in the medium without Kn and the medium containing 0. Read More

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http://dx.doi.org/10.1186/s13007-019-0421-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461810PMC

Selection and validation of reference genes for quantitative expression analysis of miRNAs and mRNAs in Poplar.

Plant Methods 2019 6;15:35. Epub 2019 Apr 6.

1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China.

Background: Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) is a rapid and sensitive approach to identify miRNA and protein-coding gene expression in plants. However, because of the specially designated reverse transcription and shorter PCR products, very few reference genes have been identified for the quantitative analysis of miRNA expression in plants, and different internal reference genes are needed to normalize the expression of miRNAs and mRNA genes respectively. Therefore, it is particularly important to select the suitable common reference genes for normalization of quantitative PCR of miRNA and mRNA. Read More

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http://dx.doi.org/10.1186/s13007-019-0420-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451301PMC

Alternative methods of estimating the water potential at turgor loss point in genotypes.

Plant Methods 2019 4;15:34. Epub 2019 Apr 4.

University Centre Myerscough, Bilsborrow, Preston, Lancashire PR3 0RY UK.

Background: Selecting for drought tolerance in urban tree species can have a significant influence on survival rates, aftercare requirements and performance. The water potential at turgor loss point (π) is gaining popularity as a trait to help determine drought tolerance to aid tree selection. Therefore, it is important to understand if differing methods used to measure or calculate π deliver consistent results. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-019-0410-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448274PMC
April 2019
1 Read

3DCellAtlas Meristem: a tool for the global cellular annotation of shoot apical meristems.

Plant Methods 2019 4;15:33. Epub 2019 Apr 4.

3School of Biosciences, College of Life and Environmental and Life Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK.

Modern imaging approaches enable the acquisition of 3D and 4D datasets capturing plant organ development at cellular resolution. Computational analyses of these data enable the digitization and analysis of individual cells. In order to fully harness the information encoded within these datasets, annotation of the cell types within organs may be performed. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-019-0413-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448224PMC
April 2019
1 Read

Week-long imaging of cell divisions in the Arabidopsis root meristem.

Plant Methods 2019 25;15:30. Epub 2019 Mar 25.

Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003 USA.

Background: Characterizing the behaviors of dynamic systems requires capturing them with high temporal and spatial resolution. Owing to its transparency and genetic tractability, the root lends itself well to live imaging when combined with cell and tissue-specific fluorescent reporters. We developed a novel 4D imaging method that utilizes simple confocal microscopy and readily available components to track cell divisions in the root stem cell niche and surrounding region for up to 1 week. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-019-0417-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6446972PMC
March 2019
2 Reads

Dynamic monitoring of biomass of rice under different nitrogen treatments using a lightweight UAV with dual image-frame snapshot cameras.

Plant Methods 2019 27;15:32. Epub 2019 Mar 27.

1College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 People's Republic of China.

Background: Unmanned aerial vehicle (UAV)-based remote sensing provides a flexible, low-cost, and efficient approach to monitor crop growth status at fine spatial and temporal resolutions, and has a high potential to accelerate breeding process and improve precision field management.

Method: In this study, we discussed the use of lightweight UAV with dual image-frame snapshot cameras to estimate aboveground biomass (AGB) and panicle biomass (PB) of rice at different growth stages with different nitrogen (N) treatments. The spatial-temporal variations in the typical vegetation indices (VIs) and AGB were first investigated, and the accuracy of crop surface model (CSM) extracted from the Red Green Blue (RGB) images at two different stages were also evaluated. Read More

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http://dx.doi.org/10.1186/s13007-019-0418-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6436235PMC

Evaluation of reference genes for normalizing RT-qPCR in leaves and suspension cells of under various stimuli.

Plant Methods 2019 26;15:31. Epub 2019 Mar 26.

1Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture/Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571737 Hainan People's Republic of China.

Background: Reverse transcription quantitative real-time PCR (RT-qPCR) is a widely used approach for investigating gene expression levels in plants because of its high reproducibility, sensitivity, accuracy and rapidness. Evaluation of reference genes for normalizing RT-qPCR data is a necessary step, especially in new plant varieties. is a precious medicinal plant belonging to the family of Cephalotaxaceae and no RT-qPCR studies have been reported on it. Read More

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http://dx.doi.org/10.1186/s13007-019-0415-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434779PMC

Adaptive minirhizotron for pepper roots observation and its installation based on root system architecture traits.

Plant Methods 2019 23;15:29. Epub 2019 Mar 23.

1Department of Engineering College, Nanjing Agricultural University, Nanjing, 210031 China.

Background: Root is the principal part of plants to absorb water and nutrient, anchor the plant and affect yield and quality. Non-destructive detection of root traits is difficult to perform due to the hidden nature of the root. Therefore, improved methods to measure roots are necessary to support plant breeding, and optimization of cultivation and management. Read More

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http://dx.doi.org/10.1186/s13007-019-0414-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431063PMC

Evaluation of grain yield based on digital images of rice canopy.

Plant Methods 2019 22;15:28. Epub 2019 Mar 22.

1Jiangxi Institute of Red Soil, National Engineering and Technology Research, Center for Red Soil Improvement; Scientific Observational and Experimental Station of Arable Land Conservation in Jiangxi, Ministry of Agriculture, Nanchang, 331717 People's Republic of China.

Background: Rice canopy changes are associated with changes in the red light (R), green light (G), and blue light (B) value parameters of digital images. To rapidly diagnose the responses of rice to nitrogen (N) fertilizer application and planting density, a simple model based on digital images was developed for predicting and evaluating rice yield.

Results: N application rate and planting density had significant effects on rice yield. Read More

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http://dx.doi.org/10.1186/s13007-019-0416-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429754PMC

Correction to: Detection and analysis of wheat spikes using Convolutional Neural Networks.

Plant Methods 2019 20;15:27. Epub 2019 Mar 20.

1Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, Adelaide, 5095 Australia.

[This corrects the article DOI: 10.1186/s13007-018-0366-8.]. Read More

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http://dx.doi.org/10.1186/s13007-019-0405-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425585PMC

Construction of a large-scale semi-field facility to study genotypic differences in deep root growth and resources acquisition.

Plant Methods 2019 20;15:26. Epub 2019 Mar 20.

1Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark.

Background: Roots are vital organs for plants, and the effective use of resources from the soil is important for yield stability. However, phenotypic variation in root traits among crop genotypes is mostly unknown and field screening of root development is costly and labour demanding. As a consequence, new methods are needed to investigate root traits of fully grown crops under field conditions, particularly roots in the deeper soil horizons. Read More

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http://dx.doi.org/10.1186/s13007-019-0409-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425565PMC

Discrimination between regional biotypes of using a simple MALDI-TOF MS-based method for use with seeds.

Plant Methods 2019 14;15:25. Epub 2019 Mar 14.

CABI, Bakeham Lane, Egham, Surrey TW20 9TY UK.

Background: We have recently developed a simple, rapid, and relatively-cheap method for matrix-assisted laser-desorption and ionisation time-of-flight mass spectroscopy (MALDI-TOF MS) sample preparation that is applicable to plant material (in addition to microbial and insect material), and have used this to discriminate between closely-related species and between regional biotypes of the invasive weed (commonly known as Himalayan balsam) using leaf samples. In the current paper, we have developed a complementary MALDI-TOF MS-based method for use with seeds. We have employed a combination of principal-component analysis and blind-tested comparison between reference-sample MALDI-TOF MS spectra and test-sample spectra to discriminate, on the basis of the acid-soluble seed-protein spectra generated by our method, between four regional biotypes of from within the UK that differ in their susceptibility to the biological control agent Himalayan balsam rust ( var. Read More

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http://dx.doi.org/10.1186/s13007-019-0412-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416845PMC

Utilization of computer vision and multispectral imaging techniques for classification of cowpea () seeds.

Plant Methods 2019 12;15:24. Epub 2019 Mar 12.

3Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d'Angers, Angers, France.

Background: The traditional methods for evaluating seeds are usually performed through destructive sampling followed by physical, physiological, biochemical and molecular determinations. Whilst proven to be effective, these approaches can be criticized as being destructive, time consuming, labor intensive and requiring experienced seed analysts. Thus, the objective of this study was to investigate the potential of computer vision and multispectral imaging systems supported with multivariate analysis for high-throughput classification of cowpea () seeds. Read More

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http://dx.doi.org/10.1186/s13007-019-0411-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417027PMC
March 2019
1 Read

Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids.

Plant Methods 2019 9;15:23. Epub 2019 Mar 9.

1Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy.

Background: Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-019-0408-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408755PMC
March 2019
3 Reads

Multicolour three dimensional structured illumination microscopy of immunolabeled plant microtubules and associated proteins.

Plant Methods 2019 9;15:22. Epub 2019 Mar 9.

Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.

Background: In the present work, we provide an account of structured illumination microscopy (SIM) imaging of fixed and immunolabeled plant probes. We take advantage of SIM, to superresolve intracellular structures at a considerable z-range and circumvent its low temporal resolution capacity during the study of living samples. Further, we validate the protocol for the imaging of fixed transgenic material expressing fluorescent protein-based markers of different subcellular structures. Read More

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http://dx.doi.org/10.1186/s13007-019-0406-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408805PMC

Rapid validation of transcriptional enhancers using agrobacterium-mediated transient assay.

Plant Methods 2019 6;15:21. Epub 2019 Mar 6.

1Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA.

Background: Enhancers are one of the most important classes of -regulatory elements (CREs) and play key roles in regulation of transcription in higher eukaryotes. Enhancers are difficult to identify because they lack positional constraints relative to their cognate genes. Excitingly, several recent studies showed that plant enhancers can be predicted based on their distinct features associated with open chromatin. Read More

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http://dx.doi.org/10.1186/s13007-019-0407-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402126PMC

Comparison of efficiency and time to regeneration of -mediated transformation methods in .

Plant Methods 2019 28;15:20. Epub 2019 Feb 28.

1Department of Genetics and Biochemistry, Clemson University, Clemson, USA.

Background: Tissue culture transformation of plants has an element of art to it, with protocols passed on between labs but often not directly compared. As has become popular as a model system for legumes, rapid transformation is critical, and many protocols exist, with varying results.

Results: The ecotypes, R108 and A17, were utilized to compare the effect of a modification to a previously used protocol based on shoot explants on the percentage of transformed plants produced from calli. Read More

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http://dx.doi.org/10.1186/s13007-019-0404-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6394069PMC
February 2019

SpotCard: an optical mark recognition tool to improve field data collection speed and accuracy.

Plant Methods 2019 22;15:19. Epub 2019 Feb 22.

Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA UK.

Background: When taking photographs of plants in the field, it is often necessary to record additional information such as sample number, biological replicate number and subspecies. Manual methods of recording such information are slow, often involve laborious transcription from hand-written notes or the need to have a laptop or tablet on site, and present a risk by separating written data capture from image capture. Existing tools for field data capture focus on recording information rather than capturing pictures of plants. Read More

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http://dx.doi.org/10.1186/s13007-019-0403-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385457PMC
February 2019
1 Read

Spatial referencing of chlorophyll fluorescence images for quantitative assessment of infection propagation in leaves demonstrated on the ice plant: pathosystem.

Plant Methods 2019 20;15:18. Epub 2019 Feb 20.

4Department of Plant Physiology and Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland.

Background: Chlorophyll fluorescence analysis is one of the non-invasive techniques widely used to detect and quantify the stress-induced changes in the photosynthetic apparatus. Quantitative information is obtained as a series of images and the specific fluorescence parameters are evaluated inside the regions of interest outlined separately on each leaf image. As the performance of photosynthesis is highly heterogeneous over a leaf surface, the areas of interest selected for generating numeric data are crucial for a reliable analysis. Read More

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http://dx.doi.org/10.1186/s13007-019-0401-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381734PMC
February 2019
6 Reads

Improved estimation of aboveground biomass in wheat from RGB imagery and point cloud data acquired with a low-cost unmanned aerial vehicle system.

Plant Methods 2019 20;15:17. Epub 2019 Feb 20.

National Engineering and Technology Center for Information Agriculture (NETCIA), Key Laboratory for Crop System Analysis and Decision Making, Ministry of Agriculture and Rural Affairs, Jiangsu Key Laboratory for Information Agriculture, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, One Weigang, Nanjing, 210095 Jiangsu China.

Background: Aboveground biomass (AGB) is a widely used agronomic parameter for characterizing crop growth status and predicting grain yield. The rapid and accurate estimation of AGB in a non-destructive way is useful for making informed decisions on precision crop management. Previous studies have investigated vegetation indices (VIs) and canopy height metrics derived from Unmanned Aerial Vehicle (UAV) data to estimate the AGB of various crops. Read More

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http://dx.doi.org/10.1186/s13007-019-0402-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381699PMC
February 2019
2 Reads

Protocol: an improved method to quantify activation of systemic acquired resistance (SAR).

Plant Methods 2019 14;15:16. Epub 2019 Feb 14.

Dpto. Biología Celular, Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Campus de Teatinos, 29071 Málaga, Spain.

Background: Plant responses triggered upon detection of an invading pathogen include the generation of a number of mobile signals that travel to distant tissues and determine an increased resistance in distal, uninfected tissues, a defense response known as systemic acquired resistance (SAR). The more direct means of measuring activation of SAR by a primary local infection is the quantification of pathogen multiplication in distal, systemic sites of secondary infection. However, while such assay provides a biologically relevant quantification of SAR, it is hampered by experimental variation, requiring many repetitions for reliable results. Read More

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http://dx.doi.org/10.1186/s13007-019-0400-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6374889PMC
February 2019

The estimation of crop emergence in potatoes by UAV RGB imagery.

Plant Methods 2019 12;15:15. Epub 2019 Feb 12.

1Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences (CAAS)/Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crops, Ministry of Agriculture, Beijing, China.

Background: Crop emergence and canopy cover are important physiological traits for potato ( L.) cultivar evaluation and nutrients management. They play important roles in variety screening, field management and yield prediction. Read More

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http://dx.doi.org/10.1186/s13007-019-0399-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6371461PMC
February 2019
1 Read

Bayesian analysis and prediction of hybrid performance.

Plant Methods 2019 7;15:14. Epub 2019 Feb 7.

1Departments of Epidemiology and Biostatistics, Statistics and Probability and Institute of Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Dr. Office 1311, East Lansing, USA.

Background: The selection of hybrids is an essential step in maize breeding. However, evaluating a large number of hybrids in field trials can be extremely costly. However, genomic models can be used to predict the expected performance of un-tested genotypes. Read More

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http://dx.doi.org/10.1186/s13007-019-0388-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366084PMC
February 2019
1 Read

A spatio temporal spectral framework for plant stress phenotyping.

Plant Methods 2019 6;15:13. Epub 2019 Feb 6.

2Crop Science Group, Department of Environmental Systems Science, ETH Zürich, Zurich, Switzerland.

Background: Recent advances in high throughput phenotyping have made it possible to collect large datasets following plant growth and development over time, and those in machine learning have made inferring phenotypic plant traits from such datasets possible. However, there remains a dirth of datasets following plant growth under stress conditions along with methods for inferring them using only remotely sensed data, especially under a combination of multiple stress factors such as drought, weeds and nutrient deficiency. Such stress factors and their combinations are commonly encountered during crop production and being able to accurately detect and treat such stress conditions in an automated and timely manner can provide a major boost to farm yields with minimal resource input. Read More

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http://dx.doi.org/10.1186/s13007-019-0398-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364450PMC
February 2019
2 Reads

Developing a high-throughput phenotyping method for oxidative stress tolerance in barley roots.

Plant Methods 2019 6;15:12. Epub 2019 Feb 6.

Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001 Australia.

Background: More than 20% of the world's agricultural land is affected by salinity, resulting in multibillion-dollar penalties and jeopardising food security. While the recent progress in molecular technologies has significantly advanced plant breeding for salinity stress tolerance, accurate plant phenotyping remains a bottleneck of many breeding programs. We have recently shown the existence of a strong causal link between salinity and oxidative stress tolerance in cereals (wheat and barley). Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-019-0397-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364415PMC
February 2019
5 Reads

Evaluating maize phenotype dynamics under drought stress using terrestrial lidar.

Plant Methods 2019 4;15:11. Epub 2019 Feb 4.

1State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.

Background: Maize ( L.) is the third most consumed grain in the world and improving maize yield is of great importance of the world food security, especially under global climate change and more frequent severe droughts. Due to the limitation of phenotyping methods, most current studies only focused on the responses of phenotypes on certain key growth stages. Read More

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http://dx.doi.org/10.1186/s13007-019-0396-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360786PMC
February 2019
2 Reads

Modeling maize above-ground biomass based on machine learning approaches using UAV remote-sensing data.

Plant Methods 2019 4;15:10. Epub 2019 Feb 4.

Key Laboratory of Quantitative Remote Sensing in Agriculture of Ministry of Agriculture, Beijing Research Center for Information Technology in Agriculture, Beijing, 100097 China.

Background: Above-ground biomass (AGB) is a basic agronomic parameter for field investigation and is frequently used to indicate crop growth status, the effects of agricultural management practices, and the ability to sequester carbon above and below ground. The conventional way to obtain AGB is to use destructive sampling methods that require manual harvesting of crops, weighing, and recording, which makes large-area, long-term measurements challenging and time consuming. However, with the diversity of platforms and sensors and the improvements in spatial and spectral resolution, remote sensing is now regarded as the best technical means for monitoring and estimating AGB over large areas. Read More

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http://dx.doi.org/10.1186/s13007-019-0394-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360736PMC
February 2019
1 Read

Beyond the two compartments Petri-dish: optimising growth promotion and induced resistance in cucumber exposed to gaseous bacterial volatiles in a miniature greenhouse system.

Plant Methods 2019 2;15. Epub 2019 Feb 2.

1Molecular Phytobacteriology Laboratory, KRIBB, Daejeon, 34141 South Korea.

Background: Bacterial volatiles promote plant growth and elicit immunity responses in plants grown in two-compartment Petri dishes. Due to the limitations of bacterial volatile compound (BVC) treatments such as their high evaporation rates, it is convenient to apply BVCs in closed systems such as greenhouses. However, the concentrations of BVCs must be optimised. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-019-0395-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359797PMC
February 2019
1 Read
3.102 Impact Factor

Molecular identification of a root apical cell-specific and stress-responsive enhancer from an enhancer trap line.

Plant Methods 2019 31;15. Epub 2019 Jan 31.

4Shanghai Centre for Plant Stress Biology of Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602 China.

Background: Plant root apex is the major part to direct the root growth and development by responding to various signals/cues from internal and soil environments. To study and understand root system biology particularly at a molecular and cellular level, an T-DNA insertional enhancer trap line J3411 expressing reporters (GFP) only in the root tip was adopted in this study to isolate a DNA fragment.

Results: Using nested PCR, DNA sequencing and sequence homology search, the T-DNA insertion site(s) and its flanking genes were characterised in J3411 line. Read More

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http://dx.doi.org/10.1186/s13007-019-0393-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354418PMC
January 2019
1 Read
3.102 Impact Factor

Selection of the optimal reference genes for expression analyses in different materials of .

Plant Methods 2019 28;15. Epub 2019 Jan 28.

1Key Laboratory of Innovation and Utilization of Horticultural Crop Resources in South China (Ministry of Agriculture), College of Horticulture, South China Agricultural University, Guangzhou, 510642 China.

Background: Loquat () is a subtropical tree bearing fruit that ripens during late spring and early summer, which is the off-season for fruit production. The specific flowering habit of loquat, which starts in fall and ends in winter, has attracted an increasing number of researchers who believe that it may represent an ideal model for studying flowering shift adaptations to climate change in Rosaceae. These studies require an understanding of gene expression patterns within the fruit and other tissues of this plant. Read More

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http://dx.doi.org/10.1186/s13007-019-0391-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348664PMC
January 2019
2 Reads
3.102 Impact Factor

A low-cost and open-source platform for automated imaging.

Plant Methods 2019 28;15. Epub 2019 Jan 28.

1Russell Labs, University of Wisconsin-Madison, 1630 Linden Drive, Madison, WI 53706 USA.

Background: Remote monitoring of plants using hyperspectral imaging has become an important tool for the study of plant growth, development, and physiology. Many applications are oriented towards use in field environments to enable non-destructive analysis of crop responses due to factors such as drought, nutrient deficiency, and disease, e.g. Read More

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http://dx.doi.org/10.1186/s13007-019-0392-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6348682PMC
January 2019
2 Reads

Chlorothalonil: an effective bacteriostatic agent for bud induction of under open condition (non-axenic).

Plant Methods 2019 25;15. Epub 2019 Jan 25.

1Research Institute of Tropical Forestry, CAF, 682# Guangshan 1 Road, Guangzhou, 510520 Guangdong China.

Background: Open tissue culture technique could be simplified by using different bacteriostatic agents. There is a great difference in the bacteriostatic effects of different antimicrobial agents on various explants. However, there is no report about the effective bacteriostatic agent for open tissue culture of . Read More

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http://dx.doi.org/10.1186/s13007-019-0390-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346562PMC
January 2019
9 Reads

Multispectral imaging for presymptomatic analysis of light leaf spot in oilseed rape.

Plant Methods 2019 24;15. Epub 2019 Jan 24.

1e-Agri Sensors Centre, School of Electrical and Electronic Engineering, University of Manchester, Sackville Street, Manchester, M1 3BU UK.

Background: The use of spectral imaging within the plant phenotyping and breeding community has been increasing due its utility as a non-invasive diagnostic tool. However, there is a lack of imaging systems targeted specifically at plant science duties, resulting in low precision for canopy-scale measurements. This study trials a prototype multispectral system designed specifically for plant studies and looks at its use as an early detection system for visually asymptomatic disease phases, in this case in . Read More

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http://dx.doi.org/10.1186/s13007-019-0389-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345015PMC
January 2019

Controlled infrared heating of an artic meadow: challenge in the vegetation establishment stage.

Plant Methods 2019 19;15. Epub 2019 Jan 19.

1Norwegian Institute for Bioeconomy Research - NIBIO, Høgskoleveien 7, 1430 Ås, Norway.

Background: Global warming is going to affect both agricultural production and carbon storage in soil worldwide. Given the complexity of the soil-plant-atmosphere continuum, in situ experiments of climate warming are necessary to predict responses of plants and emissions of greenhouse gases (GHG) from soils. Arrays of infrared (IR) heaters have been successfully applied in temperate and tropical agro-ecosystems to produce uniform and large increases in canopy surface temperature across research plots. Read More

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http://dx.doi.org/10.1186/s13007-019-0387-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339320PMC
January 2019
2 Reads

Plant Screen Mobile: an open-source mobile device app for plant trait analysis.

Plant Methods 2019 11;15. Epub 2019 Jan 11.

1IBG-2: Plant Sciences, Institute for Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany.

Background: The development of leaf area is one of the fundamental variables to quantify plant growth and physiological function and is therefore widely used to characterize genotypes and their interaction with the environment. To date, analysis of leaf area often requires elaborate and destructive measurements or imaging-based methods accompanied by automation that may result in costly solutions. Consequently in recent years there is an increasing trend towards simple and affordable sensor solutions and methodologies. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-019-0386-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329080PMC
January 2019
10 Reads

A strategy to characterize chlorophyll protein interaction in LIL3.

Plant Methods 2019 5;15. Epub 2019 Jan 5.

Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, 4021 Stavanger, Norway.

Background: The function of proteins is at large determined by cofactors selectively bound to protein structure. Without chlorophyll specifically bound to protein, light harvesting and photosynthesis would not be possible. The binding of chlorophyll to light harvesting proteins has been extensively studied in reconstitution assays using proteins expressed in vitro; however, the mechanism of the reconstitution reaction remained unclear. Read More

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http://dx.doi.org/10.1186/s13007-018-0385-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6320596PMC
January 2019
2 Reads

Combined use of cutinase and high-resolution mass-spectrometry to query the molecular architecture of cutin.

Plant Methods 2018 26;14:117. Epub 2018 Dec 26.

1Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, 3254 Molecular Biology Building, 2437 Pammel Drive, Ames, IA 50011 USA.

Background: Cutin is a complex, highly cross-linked polyester consisting of hydroxylated and epoxidated acyl lipid monomers. Because of the complexity of the polymer it has been difficult to define the chemical architecture of the polymer, which has further limited the ability to identify the catalytic components that assemble the polymer. Analogous to methods that define the structure of oligosaccharides, we demonstrate a strategy that utilizes cutinase to generate cutin subfragments consisting of up to four monomeric units, whose structure and spatial distribution in the polymer is revealed by high-resolution mass spectrometry. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-018-0384-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306009PMC
December 2018
2 Reads

PhenoFly Planning Tool: flight planning for high-resolution optical remote sensing with unmanned areal systems.

Plant Methods 2018 21;14:116. Epub 2018 Dec 21.

Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, 8092 Zurich, Switzerland.

Background: Driven by a huge improvement in automation, unmanned areal systems (UAS) are increasingly used for field observations and high-throughput phenotyping. Today, the bottleneck does not lie in the ability to fly a drone anymore, but rather in the appropriate flight planning to capture images with sufficient quality. Proper flight preparation for photography with digital frame cameras should include relevant concepts such as view, sharpness and exposure calculations. Read More

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http://dx.doi.org/10.1186/s13007-018-0376-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302310PMC
December 2018
2 Reads

A machine vision platform for measuring imbibition of maize kernels: quantification of genetic effects and correlations with germination.

Plant Methods 2018 21;14:115. Epub 2018 Dec 21.

1Department of Botany, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706 USA.

Background: Imbibition (uptake of water by a dry seed) initiates the germination process. An automated method for quantifying imbibition would enable research on the genetic elements that influence the underlying hydraulic and biochemical processes. In the case of crop research, a high throughput imbibition assay could be used to investigate seed quality topics or to improve yield by selecting varieties with superior germination characteristics. Read More

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http://dx.doi.org/10.1186/s13007-018-0383-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302439PMC
December 2018
1 Read

A sterile hydroponic system for characterising root exudates from specific root types and whole-root systems of large crop plants.

Plant Methods 2018 20;14:114. Epub 2018 Dec 20.

1CSIRO Agriculture and Food, Canberra, ACT Australia.

Background: Plant roots release a variety of organic compounds into the soil which alter the physical, chemical and biological properties of the rhizosphere. Root exudates are technically challenging to measure in soil because roots are difficult to access and exudates can be bound by minerals or consumed by microorganisms. Exudates are easier to measure with hydroponically-grown plants but, even here, simple compounds such as sugars and organic acids can be rapidly assimilated by microorganisms. Read More

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http://dx.doi.org/10.1186/s13007-018-0380-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300921PMC
December 2018
2 Reads

Regulatory chromatin landscape in roots uncovered by coupling INTACT and ATAC-seq.

Plant Methods 2018 20;14:113. Epub 2018 Dec 20.

1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.

Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. Read More

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http://dx.doi.org/10.1186/s13007-018-0381-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300899PMC
December 2018
1 Read

MuSeeQ, a novel supervised image analysis tool for the simultaneous phenotyping of the soluble mucilage and seed morphometric parameters.

Plant Methods 2018 18;14:112. Epub 2018 Dec 18.

1Laboratoire de Biologie des Plantes et Innovation, EA-3900, UPJV, UFR des Sciences, 33 rue St Leu, 80039 Amiens, France.

Background: The mucilage is a model to study the polysaccharide biosynthesis since it is produced in large amounts and composed of complex polymers. In addition, it is of great economic interest for its technical and nutritional value. A fast method for phenotyping the released mucilage and the seed morphometric parameters will be useful for fundamental, food, pharmaceutical and breeding researches. Read More

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http://dx.doi.org/10.1186/s13007-018-0377-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297999PMC
December 2018
1 Read

A simple and efficient CRISPR/Cas9 platform for induction of single and multiple, heritable mutations in barley ( L.).

Plant Methods 2018 18;14:111. Epub 2018 Dec 18.

1Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, 05-870 Radzików, Błonie, Poland.

Background: Genome editing of monocot plants can be accomplished by using the components of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR associated Cas9) technology specifically optimized for these types of plants. Here, we present the development of RNA-guided Cas9 system for simplex and multiplex genome editing in barley.

Results: We developed a set of customizable RNA-guided Cas9 binary vectors and sgRNA modules for simplex and multiplex editing in barley. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-018-0382-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297969PMC
December 2018
18 Reads

Reference genes identification for normalization of qPCR under multiple stresses in .

Plant Methods 2018 18;14:110. Epub 2018 Dec 18.

1Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.

Background: Real-time quantitative PCR has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. Wild barley ( (Trin.) Link) is a wild relative species in Triticeae that has strong tolerance to abiotic stresses and extremely wide adaptation. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-018-0379-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297944PMC
December 2018
28 Reads
3.102 Impact Factor

Volatilomics: a non-invasive technique for screening plant phenotypic traits.

Plant Methods 2018 18;14:109. Epub 2018 Dec 18.

1Research Unit Environmental Simulation (EUS), Institute for Biochemical Plant Pathology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.

Background: Climate change represents a grand challenge for agricultural productivity. Understanding complex plant traits such as stress tolerance, disease resistance or crop yield is thus essential for breeding and the development of sustainable agriculture strategies. When screening for the most robust plant phenotypes, fast, high-throughput phenotyping represents the means of choice. Read More

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https://plantmethods.biomedcentral.com/articles/10.1186/s130
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http://dx.doi.org/10.1186/s13007-018-0378-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297985PMC
December 2018
24 Reads

Methodological approach for predicting and mapping the phenological adaptation of tropical maize ( L.) using multi-environment trials.

Plant Methods 2018 7;14:108. Epub 2018 Dec 7.

International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations, Avenue, Gigiri, P. O. Box 1041-00621, Nairobi, Kenya.

Background: The phenological development of the maize crop from emergence through flowering to maturity, usually expressed as a rate (i.e. 1/duration), is largely controlled by temperature in the tropics. Read More

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http://dx.doi.org/10.1186/s13007-018-0375-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6284281PMC
December 2018
1 Read

User-friendly extraction and multistage tandem mass spectrometry based analysis of lipid-linked oligosaccharides in microalgae.

Plant Methods 2018 5;14:107. Epub 2018 Dec 5.

1UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Univ, 76000 Rouen, France.

Background: Protein -glycosylation is initiated within the endoplasmic reticulum through the synthesis of a lipid-linked oligosaccharides (LLO) precursor. This precursor is then transferred on neo-synthesized proteins through the action of the oligosaccharyltransferase giving birth to glycoproteins. The -linked glycans bore by the glycoproteins are then processed into oligomannosides prior to the exit of the glycoproteins from the endoplasmic reticulum and its entrance into the Golgi apparatus. Read More

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http://dx.doi.org/10.1186/s13007-018-0374-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280548PMC
December 2018
2 Reads

Sensitive and high throughput quantification of abscisic acid based on quantitative real time immuno-PCR.

Plant Methods 2018 24;14:104. Epub 2018 Nov 24.

1Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China.

Background: Abscisic acid (ABA) functions as a stress phytohormone in many growth and developmental processes in plants. The ultra-sensitive determination of ABA would help to better understand its vital roles and action mechanisms.

Results: We report a new sensitive and high throughput quantitative real time immuno-PCR (qIPCR) method based on biotin-avidin linkage system for ABA determination in plants. Read More

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http://dx.doi.org/10.1186/s13007-018-0371-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260876PMC
November 2018
3 Reads
3.102 Impact Factor

Correction to: Simple protoplast isolation system for gene expression and protein interaction studies in pineapple ( L.).

Plant Methods 2018 1;14:106. Epub 2018 Dec 1.

1State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Lab of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Crop Sciences, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian Province China.

[This corrects the article DOI: 10.1186/s13007-018-0365-9.]. Read More

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http://dx.doi.org/10.1186/s13007-018-0373-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6271580PMC
December 2018
1 Read
3.102 Impact Factor