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Plant Methods

Abelardo Montesinos-López, Osval A Montesinos-López, Gustavo de Los Campos, José Crossa, Juan Burgueño, Francisco Javier Luna-Vazquez
[This corrects the article DOI: 10.1186/s13007-018-0314-7.].
2018: Plant Methods
Hann Ling Wong, Akira Akamatsu, Qiong Wang, Masayuki Higuchi, Tomonori Matsuda, Jun Okuda, Ken-Ichi Kosami, Noriko Inada, Tsutomu Kawasaki, Takako Kaneko-Kawano, Shingo Nagawa, Li Tan, Yoji Kawano, Ko Shimamoto
Background: Small GTPases act as molecular switches that regulate various plant responses such as disease resistance, pollen tube growth, root hair development, cell wall patterning and hormone responses. Thus, to monitor their activation status within plant cells is believed to be the key step in understanding their roles. Results: We have established a plant version of a Förster resonance energy transfer (FRET) probe called Ras and interacting protein chimeric unit (Raichu) that can successfully monitor activation of the rice small GTPase OsRac1 during various defence responses in cells...
2018: Plant Methods
Xu Wang, Daljit Singh, Sandeep Marla, Geoffrey Morris, Jesse Poland
Background: Plant height is an important morphological and developmental phenotype that directly indicates overall plant growth and is widely predictive of final grain yield and biomass. Currently, manually measuring plant height is laborious and has become a bottleneck for genetics and breeding programs. The goal of this research was to evaluate the performance of five different sensing technologies for field-based high throughput plant phenotyping (HTPP) of sorghum [ Sorghum bicolor (L...
2018: Plant Methods
Batirtze Prats-Mateu, Martin Felhofer, Anna de Juan, Notburga Gierlinger
Background: Plant cell walls are nanocomposites based on cellulose microfibrils embedded in a matrix of polysaccharides and aromatic polymers. They are optimized for different functions (e.g. mechanical stability) by changing cell form, cell wall thickness and composition. To reveal the composition of plant tissues in a non-destructive way on the microscale, Raman imaging has become an important tool. Thousands of Raman spectra are acquired, each one being a spatially resolved molecular fingerprint of the plant cell wall...
2018: Plant Methods
Abelardo Montesinos-López, Osval A Montesinos-López, Gustavo de Los Campos, José Crossa, Juan Burgueño, Francisco Javier Luna-Vazquez
Background: Modern agriculture uses hyperspectral cameras with hundreds of reflectance data at discrete narrow bands measured in several environments. Recently, Montesinos-López et al. (Plant Methods 13(4):1-23, 2017a. 10.1186/s13007-016-0154-2; Plant Methods 13(62):1-29, 2017b. 10.1186/s13007-017-0212-4) proposed using functional regression analysis (as functional data analyses) to help reduce the dimensionality of the bands and thus decrease the computational cost. The purpose of this paper is to discuss the advantages and disadvantages that functional regression analysis offers when analyzing hyperspectral image data...
2018: Plant Methods
Leandro do Prado Ribeiro, Adriana Lídia Santana Klock, João Américo Wordell Filho, Marco Aurélio Tramontin, Marília Almeida Trapp, Axel Mithöfer, Christian Nansen
Background: In studies of plant stress signaling, a major challenge is the lack of non-invasive methods to detect physiological plant responses and to characterize plant-plant communication over time and space. Results: We acquired time series of phytocompound and hyperspectral imaging data from maize plants from the following treatments: (1) individual non-infested plants, (2) individual plants experimentally subjected to herbivory by green belly stink bug (no visible symptoms of insect herbivory), (3) one plant subjected to insect herbivory and one control plant in a separate pot but inside the same cage, and (4) one plant subjected to insect herbivory and one control plant together in the same pot...
2018: Plant Methods
Pooja Rani Aggarwal, Papri Nag, Pooja Choudhary, Niranjan Chakraborty, Subhra Chakraborty
Background: Chickpea ( Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efficient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhizogenes -mediated root transformation of chickpea. Results: Transformation positive roots were obtained on selection medium after two weeks of A...
2018: Plant Methods
Peng Wang, Longyun Guo, Rohit Jaini, Antje Klempien, Rachel M McCoy, John A Morgan, Natalia Dudareva, Clint Chapple
Background: Metabolic fluxes represent the functional phenotypes of biochemical pathways and are essential to reveal the distribution of precursors among metabolic networks. Although analysis of metabolic fluxes, facilitated by stable isotope labeling and mass spectrometry detection, has been applied in the studies of plant metabolism, we lack experimental measurements for carbon flux towards lignin, one of the most abundant polymers in nature. Results: We developed a feeding strategy of excised Arabidopsis stems with 13 C labeled phenylalanine (Phe) for the analysis of lignin biosynthetic flux...
2018: Plant Methods
Haipeng Li, Kun Li, Yutao Guo, Jinggong Guo, Kaiting Miao, Jose R Botella, Chun-Peng Song, Yuchen Miao
Background: Genetically modified cotton accounts for 64% of the world's cotton growing area (22.3 million hectares). The genome sequencing of the diploid cotton progenitors Gossypium raimondii and Gossypium arboreum as well as the cultivated Gossypium hirsutum has provided a wealth of genetic information that could be exploited for crop improvement. Unfortunately, gene functional characterization in cotton is lagging behind other economically important crops due to the low efficiency, lengthiness and technical complexity of the available stable transformation methods...
2018: Plant Methods
R Makanza, M Zaman-Allah, J E Cairns, J Eyre, J Burgueño, Ángela Pacheco, C Diepenbrock, C Magorokosho, A Tarekegne, M Olsen, B M Prasanna
Background: Grain yield, ear and kernel attributes can assist to understand the performance of maize plant under different environmental conditions and can be used in the variety development process to address farmer's preferences. These parameters are however still laborious and expensive to measure. Results: A low-cost ear digital imaging method was developed that provides estimates of ear and kernel attributes i.e., ear number and size, kernel number and size as well as kernel weight from photos of ears harvested from field trial plots...
2018: Plant Methods
Miriam Gil-Monreal, Manuel Fernandez-Escalada, Mercedes Royuela, Ana Zabalza
Background: Hydroponic systems are a convenient platform for plant cultivation when treatments are applied to the roots because they provide precise control of the composition of the growth medium, ensuring the availability of different compounds. A problem arises when axenic conditions are needed but the treatment of choice (exogenous organic acids or sugars) promote the growth of unwanted microorganisms. Moreover, axenic conditions are usually applied in liquid and semi-liquid growing systems, where oxygen availability can be compromised, if no aeration is provided...
2018: Plant Methods
Min-Rui Wang, Wen Yang, Lei Zhao, Jing-Wei Li, Ke Liu, Jing-Wei Yu, Yun-Feng Wu, Qiao-Chun Wang
Background: Preservation of plant virus is a fundamental requirement in all types of virus-related research and applied applications. Development of efficient, reliable strategies for long-term preservation of plant virus would largely assist these studies. Results: The present study reported a novel biotechnology allowing cryopreservation of Apple stem grooving virus (ASGV) in living shoot tips. Following cryopreservation by droplet-vitrification or encapsulation-dehydration, about 62-67% of shoot regrowth and 100% of ASGV cryopreservation were obtained...
2018: Plant Methods
Stefan Thomas, Jan Behmann, Angelina Steier, Thorsten Kraska, Onno Muller, Uwe Rascher, Anne-Katrin Mahlein
Background: Phenotyping is a bottleneck for the development of new plant cultivars. This study introduces a new hyperspectral phenotyping system, which combines the high throughput of canopy scale measurements with the advantages of high spatial resolution and a controlled measurement environment. Furthermore, the measured barley canopies were grown in large containers (called Mini-Plots), which allow plants to develop field-like phenotypes in greenhouse experiments, without being hindered by pot size...
2018: Plant Methods
Jie Wu, Qian Wu, Loïc Pagès, Yeqing Yuan, Xiaolei Zhang, Mingwei Du, Xiaoli Tian, Zhaohu Li
Background: In order to efficiently determine genotypic differences in rooting patterns of crops, novel hardware and software are needed simultaneously to characterize dynamics of root development. Results: We describe a prototype robotic monitoring platform-the RhizoChamber-Monitor for analyzing growth patterns of plant roots automatically. The RhizoChamber-Monitor comprises an automatic imaging system for acquiring sequential images of roots which grow on a cloth substrate in custom rhizoboxes, an automatic irrigation system and a flexible shading arrangement...
2018: Plant Methods
Chun-Xia Zeng, Peter M Hollingsworth, Jing Yang, Zheng-Shan He, Zhi-Rong Zhang, De-Zhu Li, Jun-Bo Yang
Background: The world's herbaria contain millions of specimens, collected and named by thousands of researchers, over hundreds of years. However, this treasure has remained largely inaccessible to genetic studies, because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates...
2018: Plant Methods
Wenxian Liang, Xiaoxing Zou, Rebeca Carballar-Lejarazú, Lingjiao Wu, Weihong Sun, Xueyuan Yuan, Songqing Wu, Pengfei Li, Hui Ding, Lin Ni, Wei Huang, Shuangquan Zou
Background: Quantitative real-time reverse transcription-polymerase chain reaction has been widely used in gene expression analysis, however, to have reliable and accurate results, reference genes are necessary to normalize gene expression under different experimental conditions. Several reliable reference genes have been reported in plants of Traditional Chinese Medicine, but none have been identified for Euscaphis konishii Hayata. Results: In this study, 12 candidate reference genes, including 3 common housekeeping genes and 9 novel genes based on E...
2018: Plant Methods
Michael Penzkofer, Andrea Baron, Annette Naumann, Andrea Krähmer, Hartwig Schulz, Heidi Heuberger
Background: The essential oil is an important compound of the root and rhizome of medicinally used valerian ( Valeriana officinalis L. s.l.), with a stated minimum content in the European pharmacopoeia. The essential oil is located in droplets, of which the position and distribution in the total root cross-section of different valerian varieties, root thicknesses and root horizons are determined in this study using an adapted fluorescence-microscopy and automatic imaging analysis method...
2018: Plant Methods
Jinggong Guo, Kun Li, Lifeng Jin, Rui Xu, Kaiting Miao, Fengbo Yang, Chaoya Qi, Lin Zhang, Jose R Botella, Ran Wang, Yuchen Miao
Background: The CRISPR/Cas9 system is being used for genome editing purposes by many research groups in multiple plant species. Traditional sequencing methods to identify homozygous mutants are time-consuming, laborious and expensive. Results: We have developed a method to screen CRISPR/Cas9-induced mutants through Mutation Sites Based Specific Primers Polymerase Chain Reaction (MSBSP-PCR). The MSBSP-PCR method was successfully used to identify homozygous/biallelic mutants in Nicotiana tabacum and Arabidopsis thaliana , and we speculate that it can be used for the identification of CRISPR/Cas9-induced mutants in other plant species...
2018: Plant Methods
Joshua Chopin, Pankaj Kumar, Stanley J Miklavcic
Background: One of the main challenges associated with image-based field phenotyping is the variability of illumination. During a single day's imaging session, or between different sessions on different days, the sun moves in and out of cloud cover and has varying intensity. How is one to know from consecutive images alone if a plant has become darker over time, or if the weather conditions have simply changed from clear to overcast? This is a significant problem to address as colour is an important phenotypic trait that can be measured automatically from images...
2018: Plant Methods
Vladimíra Nožková, Petr Šmíd, Pavel Horváth, Miroslav Hrabovský, Petr Ilík
Background: When a plant is wounded, a rapid hydraulic surge, acting probably as a systemic signal, spreads from the site of injury throughout the plant and leads to small transient deformation of tissues. So far, the propagation of hydraulic surge has been monitored by contact and thus potentially invasive methods. Results: Here we present a non-invasive optical method, which allows simultaneous monitoring of micrometric shift of two opposite stem margins. The usefulness of this method was demonstrated by the measurement of the hydraulic surge propagation in a tobacco ( Nicotiana tabacum (L...
2018: Plant Methods
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