662 results match your criteria Plant Methods [Journal]


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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-019-0397-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364415PMC
February 2019

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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-019-0395-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6359797PMC
February 2019

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-019-0386-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329080PMC
January 2019
5 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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
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

View Article

Download full-text PDF

Source
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

View Article

Download full-text PDF

Source
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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
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

View Article

Download full-text PDF

Source
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

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0382-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297969PMC
December 2018
7 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

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0379-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297944PMC
December 2018
13 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

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0378-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297985PMC
December 2018
16 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

View Article

Download full-text PDF

Source
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

View Article

Download full-text PDF

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

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0371-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260876PMC
November 2018
2 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

View Article

Download full-text PDF

Source
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

Measuring ethylene in postharvest biology research using the laser-based ETD-300 ethylene detector.

Plant Methods 2018 28;14:105. Epub 2018 Nov 28.

Massey AgriTech Partnership, Massey University, Private Bag 11222, Palmerston North, 4412 New Zealand.

Background: Ability to measure ethylene is an important aspect of postharvest management, as knowledge of endogenous ethylene production is used in assessing physiological status, while response of crops to exogenous ethylene informs efforts needed to control unwanted ripening. An ethylene monitoring device with a laser-based photoacoustic detector, ETD-300, was recently developed by Sensor Sense B.V. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0372-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260721PMC
November 2018
1 Read

Histology-guided high-resolution AP-SMALDI mass spectrometry imaging of wheat- interaction at the root-shoot junction.

Plant Methods 2018 17;14:103. Epub 2018 Nov 17.

1Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.

Background: Fungal pathogens like can cause severe yield losses and mycotoxin contamination of food and feed worldwide. We recently showed its ability to systemically colonize wheat via root infection. However, the molecular response of wheat to Fusarium root rot (FRR) infection and systemic spread is still unknown. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0368-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240423PMC
November 2018
4 Reads

Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility.

Plant Methods 2018 17;14:102. Epub 2018 Nov 17.

1Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan.

Background: To investigate plant hybrid sterility, we studied interspecific hybrids of two cultivated rice species, Asian rice () and African rice (). Male gametes of these hybrids display complete sterility owing to a dozen of hybrid sterility loci, termed loci, but this complicated genetic system remains poorly understood.

Results: Microspores from these interspecific hybrids form sterile pollen but are viable at the immature stage. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0370-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240274PMC
November 2018
12 Reads

A method to calculate the number of wheat seedlings in the 1st to the 3rd leaf growth stages.

Plant Methods 2018 16;14:101. Epub 2018 Nov 16.

1Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009 China.

Background: The number of cultivated wheat seedlings per unit area allows calculation of plant density. Wheat seedling density provides emergence data and this is useful for improving crop management. The number of wheat seedlings is typically determined by visual counts but this is time-consuming and laborious. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0369-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6238276PMC
November 2018
2 Reads
3.102 Impact Factor

Detection and analysis of wheat spikes using Convolutional Neural Networks.

Plant Methods 2018 15;14:100. Epub 2018 Nov 15.

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

Background: Field phenotyping by remote sensing has received increased interest in recent years with the possibility of achieving high-throughput analysis of crop fields. Along with the various technological developments, the application of machine learning methods for image analysis has enhanced the potential for quantitative assessment of a multitude of crop traits. For wheat breeding purposes, assessing the production of wheat spikes, as the grain-bearing organ, is a useful proxy measure of grain production. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0366-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6236889PMC
November 2018
11 Reads

Investigating the microstructure of plant leaves in 3D with lab-based X-ray computed tomography.

Plant Methods 2018 12;14:99. Epub 2018 Nov 12.

1Division of Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK.

Background: Leaf cellular architecture plays an important role in setting limits for carbon assimilation and, thus, photosynthetic performance. However, the low density, fine structure, and sensitivity to desiccation of plant tissue has presented challenges to its quantification. Classical methods of tissue fixation and embedding prior to 2D microscopy of sections is both laborious and susceptible to artefacts that can skew the values obtained. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0367-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231253PMC
November 2018
9 Reads

Transient co-expression with three -glycosylation enzymes allows production of GalNAc--glycosylated Granulocyte-Colony Stimulating Factor in .

Plant Methods 2018 6;14:98. Epub 2018 Nov 6.

1School of Engineering and Sciences, Tecnologico de Monterrey, Campus Monterrey, Av. Eugenio Garza Sada 2501 Sur, C.P. 64849 Monterrey, NL Mexico.

Background: Expression of economically relevant proteins in alternative expression platforms, especially plant expression platforms, has gained significant interest in recent years. A special interest in working with plants as bioreactors for the production of pharmaceutical proteins is related to low production costs, product safety and quality. Among the different properties that plants can also offer for the production of recombinant proteins, protein glycosylation is crucial since it may have an impact on pharmaceutical functionality and/or stability. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0363-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219069PMC
November 2018
4 Reads
3.102 Impact Factor

Whole plant chamber to examine sensitivity of cereal gas exchange to changes in evaporative demand.

Plant Methods 2018 1;14:97. Epub 2018 Nov 1.

1Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ UK.

Background: Improving plant water use efficiency (WUE) is a major target for improving crop yield resilience to adverse climate change. Identifying genetic variation in WUE usually relies on instantaneous measurements of photosynthesis (An) and transpiration (Tr), or integrative measurements of carbon isotope discrimination, at the leaf level. However, leaf gas exchange measurements alone do not adequately represent whole plant responses, especially if evaporative demand around the plant changes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0357-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211548PMC
November 2018
1 Read

A protocol combining multiphoton microscopy and propidium iodide for deep 3D root meristem imaging in rice: application for the screening and identification of tissue-specific enhancer trap lines.

Plant Methods 2018 29;14:96. Epub 2018 Oct 29.

1CIRAD, UMR-AGAP, Université de Montpellier, Avenue Agropolis, 34398 Montpellier Cedex 5, France.

Background: The clear visualization of 3D organization at the cellular level in plant tissues is needed to fully understand plant development processes. Imaging tools allow the visualization of the main fluorophores and in vivo growth monitoring. Confocal microscopy coupled with the use of propidium iodide (PI) counter-staining is one of the most popular tools used to characterize the structure of root meristems in . Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0364-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206838PMC
October 2018
7 Reads

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

Plant Methods 2018 29;14:95. Epub 2018 Oct 29.

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.

Background: An efficient transformation protocol is a primary requisite to study and utilize the genetic potential of any plant species. A quick transformation system is also crucial for the functional analysis of genes along with the study of proteins and their interactions in vivo. Presently, however, quick and effective transformation systems are still lacking for many plant species including pineapple. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0365-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205801PMC
October 2018
2 Reads
3.102 Impact Factor

Time-to-event analysis to evaluate dormancy status of single-bud cuttings: an example for grapevines.

Plant Methods 2018 27;14:94. Epub 2018 Oct 27.

1AgWeatherNet Program, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350 USA.

Background: The reduced growth of plants during the winter causes a lack in the perceptibility of the phenological events making challenging the study of dormancy. For deciduous crops, dormancy is generally determined by evaluating budbreak of single-node cuttings that are exposed to conditions suitable for growth. However, the absence of a statistical basis for analyzing and interpreting the budbreak behavior evaluated as the percent budbreak, the average time to budbreak and the time to reach 50% budbreak, has caused inconsistent and contradictory criteria to identify the dormancy status of different deciduous crops. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0361-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203998PMC
October 2018
5 Reads

-mediated transformation systems of .

Plant Methods 2018 26;14:93. Epub 2018 Oct 26.

1School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH UK.

Background: Genetic transformation is a valuable tool and an important procedure in plant functional genomics contributing to gene discovery, allowing powerful insights into gene function and genetically controlled characteristics. species provide one of the best-known examples of heteromorphic flower development, a breeding system which has attracted considerable attention, including that of Charles Darwin. Molecular approaches, including plant transformation give the best opportunity to define and understand the role of genes involved in floral heteromorphy in the common primrose, , along with other species. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0360-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204026PMC
October 2018
7 Reads

Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH).

Plant Methods 2018 24;14:92. Epub 2018 Oct 24.

1Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA.

Background: is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of that causes high crop loss. Currently, there are no available methods for the microscopic detection of from leaves of impatiens, which may be contributing to the spread of the disease. Fluorescence in situ hybridization (FISH) is a sensitive and robust method that uses sequence-specific, fluorescence-labeled oligonucleotide probes to detect target organisms from the environment. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0362-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199785PMC
October 2018
1 Read

A simple and inexpensive method for practical storage of field-sample proteins for subsequent MALDI-TOF MS analysis.

Plant Methods 2018 15;14:90. Epub 2018 Oct 15.

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

Background: Protein-containing samples can readily be characterised and/or identified using matrix-assisted laser-desorption and ionisation time-of-flight mass spectrometry (MALDI-TOF MS). This technique however requires relatively-fresh biological material that contains proteins that have not yet undergone significant degradation. For field-work collection of samples, problems are often encountered due to delays between collection and sample processing, sample storage (possibly at elevated temperature and/or humidity in some climates), quarantine/regulatory restrictions on the transfer of living biological materials across national borders, and the potential to transfer unwanted microorganisms via non-living biological materials. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0358-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192001PMC
October 2018
8 Reads

Pyrite cloning: a single tube and programmed reaction cloning with restriction enzymes.

Plant Methods 2018 17;14:91. Epub 2018 Oct 17.

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA.

Background: Insertion of engineered DNA fragments into bacterial vectors is the foundation of recombinant DNA technology, yet existing methods are still laborious, require many steps, depend on specific vector configuration, or require expensive reagents.

Results: We have developed a method, called "Pyrite" cloning that combines the traditional restriction enzyme digestion and ligation reaction in a single tube and uses a programmed thermocycler reaction, allowing rapid and flexible cloning in a single tube. After the Pyrite reaction and transformation, approximately 50% colonies contain the expected insert, which can be easily and quickly determined by colony PCR or blue-white colony screening. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0359-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192209PMC
October 2018
1 Read

Cryo-laser scanning confocal microscopy of diffusible plant compounds.

Plant Methods 2018 13;14:89. Epub 2018 Oct 13.

1UR 1268 Biopolymères Interactions Assemblages, INRA, 44300 Nantes, France.

Background: The in vivo observation of diffusible components, such as ions and small phenolic compounds, remains a challenge in turgid plant organs. The analytical techniques used to localize such components in water-rich tissue with a large field of view are lacking. It remains an issue to limit compound diffusion during sample preparation and observation processes. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0356-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186079PMC
October 2018
2 Reads
3.102 Impact Factor

Cowpea and abiotic stresses: identification of reference genes for transcriptional profiling by qPCR.

Plant Methods 2018 12;14:88. Epub 2018 Oct 12.

2Genetics Department, Universidade Federal de Pernambuco, Recife, Pernambuco Brazil.

Background: Due to cowpea ability to fix nitrogen in poor soils and relative tolerance to drought and salt stresses, efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Real-time quantitative PCR (qPCR) has been widely used as the most reliable method to measure gene expression, due to its high accuracy and specificity. In the present study, nine candidate reference genes were rigorously tested for their application in normalization of qPCR data onto roots of four distinct cowpea accessions under two abiotic stresses: root dehydration and salt (NaCl, 100 mM). Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0354-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182843PMC
October 2018
12 Reads

In vitro thermotherapy-based methods for plant virus eradication.

Plant Methods 2018 6;14:87. Epub 2018 Oct 6.

1State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China.

Production of virus-free plants is necessary to control viral diseases, import novel cultivars from other countries, exchange breeding materials between countries or regions and preserve plant germplasm. In vitro techniques represent the most successful approaches for virus eradication. In vitro thermotherapy-based methods, including combining thermotherapy with shoot tip culture, chemotherapy, micrografting or shoot tip cryotherapy, have been successfully established for efficient eradication of various viruses from almost all of the most economically important crops. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0355-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6173849PMC
October 2018
11 Reads

Hyperspectral band selection using genetic algorithm and support vector machines for early identification of charcoal rot disease in soybean stems.

Plant Methods 2018 3;14:86. Epub 2018 Oct 3.

1Department of Electrical and Computer Engineering, Iowa State University, Ames, IA USA.

Background: Charcoal rot is a fungal disease that thrives in warm dry conditions and affects the yield of soybeans and other important agronomic crops worldwide. There is a need for robust, automatic and consistent early detection and quantification of disease symptoms which are important in breeding programs for the development of improved cultivars and in crop production for the implementation of disease control measures for yield protection. Current methods of plant disease phenotyping are predominantly visual and hence are slow and prone to human error and variation. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0349-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169113PMC
October 2018
1 Read

Optimization of CRISPR/Cas9 genome editing in cotton by improved sgRNA expression.

Plant Methods 2018 3;14:85. Epub 2018 Oct 3.

1State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, 475004 Henan People's Republic of China.

Background: When developing CRISPR/Cas9 systems for crops, it is crucial to invest time characterizing the genome editing efficiency of the CRISPR/Cas9 cassettes, especially if the transformation system is difficult or time-consuming. Cotton is an important crop for the production of fiber, oil, and biofuel. However, the cotton stable transformation is usually performed using taking between 8 and 12 months to generate T plants. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13007-018-0353-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169012PMC
October 2018
13 Reads

Hyperspectral imaging: a novel approach for plant root phenotyping.

Plant Methods 2018 3;14:84. Epub 2018 Oct 3.

4Computational Science Center, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria.

Background: Root phenotyping aims to characterize root system architecture because of its functional role in resource acquisition. RGB imaging and analysis procedures measure root system traits via colour contrasts between roots and growth media or artificial backgrounds. In the case of plants grown in soil-filled rhizoboxes, where the colour contrast can be poor, it is hypothesized that root imaging based on spectral signatures improves segmentation and provides additional knowledge on physico-chemical root properties. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0352-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169016PMC
October 2018
3 Reads

Functional intron-derived miRNAs and host-gene expression in plants.

Plant Methods 2018 24;14:83. Epub 2018 Sep 24.

1Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PD Wageningen, The Netherlands.

Background: Recently, putative pre-miRNAs locations have been identified in the introns of plant genes, raising the question whether such genes can show a dual functionality by having both correct maturation of the host gene pre-mRNA and maturation of the miRNAs from the intron. Here, we demonstrated that such dual functionality is indeed possible, using as host gene the firefly luciferase gene with intron (ffgLUC), and different artificial intronic miRNAs (aimiRNA) placed within the intron of ffgLUC.

Results: The miRNAs were based on the structure of the natural miR319a. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0351-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151947PMC
September 2018
15 Reads
3.102 Impact Factor

A method for real-time classification of insect vectors of mosaic and brown streak disease in cassava plants for future implementation within a low-cost, handheld, in-field multispectral imaging sensor.

Plant Methods 2018 20;14:82. Epub 2018 Sep 20.

1School of Electrical and Electronic Engineering, University of Manchester, Oxford Road, Manchester, M13 9PL UK.

Background: The paper introduces a multispectral imaging system and data-processing approach for the identification and discrimination of morphologically indistinguishable cryptic species of the destructive crop pest, the whitefly . This investigation and the corresponding system design, was undertaken in two phases under controlled laboratory conditions. The first exploited a prototype benchtop variant of the proposed sensor system to analyse four cryptic species of whitefly reared under similar conditions. Read More

View Article

Download full-text PDF

Source
https://plantmethods.biomedcentral.com/articles/10.1186/s130
Publisher Site
http://dx.doi.org/10.1186/s13007-018-0350-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148801PMC
September 2018
7 Reads