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Plant Methods

Tomohiro Yanagi, Kenta Shirasawa, Mayuko Terachi, Sachiko Isobe
Background: Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry...
2017: Plant Methods
David Legland, Fadi El-Hage, Valérie Méchin, Matthieu Reymond
Background: Crop species are of increasing interest both for cattle feeding and for bioethanol production. The degradability of the plant material largely depends on the lignification of the tissues, but it also depends on histological features such as the cellular morphology or the relative amount of each tissue fraction. There is therefore a need for high-throughput phenotyping systems that quantify the histology of plant sections. Results: We developed custom image processing and an analysis procedure for quantifying the histology of maize stem sections coloured with FASGA staining and digitalised with whole microscopy slide scanners...
2017: Plant Methods
Hao Lu, Zhiguo Cao, Yang Xiao, Bohan Zhuang, Chunhua Shen
Background: Accurately counting maize tassels is important for monitoring the growth status of maize plants. This tedious task, however, is still mainly done by manual efforts. In the context of modern plant phenotyping, automating this task is required to meet the need of large-scale analysis of genotype and phenotype. In recent years, computer vision technologies have experienced a significant breakthrough due to the emergence of large-scale datasets and increased computational resources...
2017: Plant Methods
Nathan Hughes, Karen Askew, Callum P Scotson, Kevin Williams, Colin Sauze, Fiona Corke, John H Doonan, Candida Nibau
Background: Wheat is one of the most widely grown crop in temperate climates for food and animal feed. In order to meet the demands of the predicted population increase in an ever-changing climate, wheat production needs to dramatically increase. Spike and grain traits are critical determinants of final yield and grain uniformity a commercially desired trait, but their analysis is laborious and often requires destructive harvest. One of the current challenges is to develop an accurate, non-destructive method for spike and grain trait analysis capable of handling large populations...
2017: Plant Methods
Dominic Williams, Avril Britten, Susan McCallum, Hamlyn Jones, Matt Aitkenhead, Alison Karley, Ken Loades, Ankush Prashar, Julie Graham
Hyperspectral imaging is a technology that can be used to monitor plant responses to stress. Hyperspectral images have a full spectrum for each pixel in the image, 400-2500 nm in this case, giving detailed information about the spectral reflectance of the plant. Although this technology has been used in laboratory-based controlled lighting conditions for early detection of plant disease, the transfer of such technology to imaging plants in field conditions presents a number of challenges. These include problems caused by varying light levels and difficulties of separating the target plant from its background...
2017: Plant Methods
Heng Zhang, Zhenyi Chen, Taihao Li, Na Chen, Wenjie Xu, Shupeng Liu
Background: Flos Chrysanthemi, as a part of Chinese culture for a long history, is valuable for not only environmental decoration but also the medicine and food additive. Due to their voluminously various breeds and extensive distributions worldwide, it is burdensome to make recognition and classification among numerous cultivars with conventional methods which still rest on the level of morphologic observation and description. As a fingerprint spectrum for parsing molecular information, surface-enhanced Raman scattering (SERS) could be a suitable candidate technique to characterize and distinguish the inter-cultivar differences at molecular level...
2017: Plant Methods
Jorge Gago, Alisdair R Fernie, Zoran Nikoloski, Takayuki Tohge, Sebastiá Martorell, José Mariano Escalona, Miquel Ribas-Carbó, Jaume Flexas, Hipólito Medrano
Background: There is currently a high requirement for field phenotyping methodologies/technologies to determine quantitative traits related to crop yield and plant stress responses under field conditions. Methods: We employed an unmanned aerial vehicle equipped with a thermal camera as a high-throughput phenotyping platform to obtain canopy level data of the vines under three irrigation treatments. High-resolution imagery (< 2.5 cm/pixel) was employed to estimate the canopy conductance (gc ) via the leaf energy balance model...
2017: Plant Methods
Jinyuan Tao, Huwei Sun, Pengyuan Gu, Zhihao Liang, Xinni Chen, Jiajing Lou, Guohua Xu, Yali Zhang
BACKGROUND: Cytokinins play many essential roles in plant growth and development, mainly through signal transduction pathways. Although the cytokinin signaling pathway in rice has been clarified, no synthetic reporter for cytokinin signaling output has been reported for rice. The sensitive synthetic reporter two-component signaling sensor (TCSn) is used in the model plant Arabidopsis; however, whether the reporter reflects the cytokinin signaling output pattern in rice remains unclear...
2017: Plant Methods
Charikleia Schoina, Klaas Bouwmeester, Francine Govers
BACKGROUND: The oomycete Phytophthora infestans causes late blight on potato and tomato. Despite extensive research, the P. infestans-host interaction is still poorly understood. To find new ways to further unravel this interaction we established a new infection system using MsK8 tomato cells. These cells grow in suspension and can be maintained as a stable cell line that is representative for tomato. RESULTS: MsK8 cells can host several Phytophthora species pathogenic on tomato...
2017: Plant Methods
Frederik Dethloff, Isabel Orf, Joachim Kopka
BACKGROUND: Conventional metabolomics approaches face the problem of hidden metabolic phenotypes where only fluxes are altered but pool sizes stay constant. Metabolic flux experiments are used to detect such hidden flux phenotypes. These experiments are, however, time consuming, may be cost intensive, and involve specialists for modeling. We fill the gap between conventional metabolomics and flux modeling. We present rapid stable isotope tracing assays and analysis strategies of (13)C labeling data...
2017: Plant Methods
Aftab A Khan, Ashraf El-Sayed, Asma Akbar, Arianna Mangravita-Novo, Shaheen Bibi, Zunaira Afzal, David J Norman, Gul Shad Ali
BACKGROUND: Most current methods for constructing guide RNAs (gRNA) for the CRISPR/Cas9 genome editing system, depend on traditional cloning using specific type IIS restriction enzymes and DNA ligation. These methods consist of multiple steps of cloning, and are time consuming, resource intensive and not flexible. These issues are particularly exacerbated when multiple guide RNAs need to be assembled in one plasmid such as for multiplexing or for the paired nickases approach. Furthermore, identification of functional gRNA clones usually requires expensive in vitro screening...
2017: Plant Methods
Xun Tang, Ning Zhang, Huaijun Si, Alejandro Calderón-Urrea
BACKGROUND: Real-time quantitative PCR (RT-qPCR) is the most commonly used method for accurately detecting gene expression patterns. As part of RT-qPCR analysis, normalization of the data requires internal control gene(s) that display uniform expression under different biological conditions. However, no invariable internal control gene exists, and therefore more than one reference gene is needed to normalize RT-qPCR results. Identification of stable reference genes in potato will improve assay accuracy for selecting stress-tolerance genes and identifying molecular mechanisms conferring stress tolerance in this species...
2017: Plant Methods
Mariana Zavala-López, Silverio García-Lara
BACKGROUND: Phenolic acids are a major group of secondary metabolites widely distributed in plants. In the case of maize, the major proportion of these metabolites occurs in the edible grain and their antioxidant activities are associated with improvements in human health. However, conventional extraction of secondary metabolites is very time consuming and generates a substantial amount of solvent waste. One approach to resolve these limitations is the use of microscale approaches, which minimize the quantity of solvents required, as well as the sample amounts and processing times...
2017: Plant Methods
Amy Lowe, Nicola Harrison, Andrew P French
This review explores how imaging techniques are being developed with a focus on deployment for crop monitoring methods. Imaging applications are discussed in relation to both field and glasshouse-based plants, and techniques are sectioned into 'healthy and diseased plant classification' with an emphasis on classification accuracy, early detection of stress, and disease severity. A central focus of the review is the use of hyperspectral imaging and how this is being utilised to find additional information about plant health, and the ability to predict onset of disease...
2017: Plant Methods
Li Qiongyan, Jinhai Cai, Bettina Berger, Mamoru Okamoto, Stanley J Miklavcic
BACKGROUND: The spike of a cereal plant is the grain-bearing organ whose physical characteristics are proxy measures of grain yield. The ability to detect and characterise spikes from 2D images of cereal plants, such as wheat, therefore provides vital information on tiller number and yield potential. RESULTS: We have developed a novel spike detection method for wheat plants involving, firstly, an improved colour index method for plant segmentation and, secondly, a neural network-based method using Laws texture energy for spike detection...
2017: Plant Methods
César Ramiro Martínez-González, Rosario Ramírez-Mendoza, Jaime Jiménez-Ramírez, Clemente Gallegos-Vázquez, Isolda Luna-Vega
BACKGROUND: Genomic DNA extracted from species of Cactaceae is often contaminated with significant amounts of mucilage and pectin. Pectin is one of the main components of cellular walls, whereas mucilage is a complex polysaccharide with a ramified structure. Thus, pectin- and mucilage-free extraction of DNA is a key step for further downstream PCR-based analyses. RESULTS: We tested our DNA extraction method on cladode tissue (juvenile, adult, and herbaria exemplars) of 17 species of Opuntia Mill...
2017: Plant Methods
Martijn Fiers, Jorin Hoogenboom, Alice Brunazzi, Tom Wennekes, Gerco C Angenent, Richard G H Immink
BACKGROUND: Floral timing is a carefully regulated process, in which the plant determines the optimal moment to switch from the vegetative to reproductive phase. While there are numerous genes known that control flowering time, little information is available on chemical compounds that are able to influence this process. We aimed to discover novel compounds that are able to induce flowering in the model plant Arabidopsis. For this purpose we developed a plant-based screening platform that can be used in a chemical genomics study...
2017: Plant Methods
Tomasz Jagielski, Jan Gawor, Zofia Bakuła, Karolina Zuchniewicz, Iwona Żak, Robert Gromadka
BACKGROUND: The complex cell wall structure of algae often precludes efficient extraction of their genetic material. The purpose of this study was to design a next-generation sequencing-suitable DNA isolation method for unicellular, achlorophyllous, yeast-like microalgae of the genus Prototheca, the only known plant pathogens of both humans and animals. The effectiveness of the newly proposed scheme was compared with five other, previously described methods, commonly used for DNA isolation from plants and/or yeasts, available either as laboratory-developed, in-house assays, based on liquid nitrogen grinding or different enzymatic digestion, or as commercially manufactured kits...
2017: Plant Methods
Verena Pfahler, Federica Tamburini, Stefano M Bernasconi, Emmanuel Frossard
BACKGROUND: Changing the phosphorus (P) nutrition leads to changes in plant metabolism. The aim of this study was to investigate how these changes are reflected in the distribution of (33)P and the isotopic composition of oxygen associated to P (δ(18)OP) in different plant parts of soybean (Glycine max cv. Toliman). Two P pools were extracted sequentially with 0.3 M trichloroacetic acid (TCA P) and 10 M nitric acid (HNO3; residual P). RESULTS: The δ(18)OP of TCA P in the old leaves of the - P plants (23...
2017: Plant Methods
Samuel Joalland, Claudio Screpanti, Frank Liebisch, Hubert Vincent Varella, Alain Gaume, Achim Walter
BACKGROUND: Phenotyping technologies are expected to provide predictive power for a range of applications in plant and crop sciences. Here, we use the disease pressure of Beet Cyst Nematodes (BCN) on sugar beet as an illustrative example to test the specific capabilities of different methods. Strong links between the above and belowground parts of sugar beet plants have made BCN suitable targets for use of non-destructive phenotyping methods. We compared the ability of visible light imaging, thermography and spectrometry to evaluate the effect of BCN on the growth of sugar beet plants...
2017: Plant Methods
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