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Plant Methods

Zohaib Khan, Vahid Rahimi-Eichi, Stephan Haefele, Trevor Garnett, Stanley J Miklavcic
Background: Unmanned aerial vehicles offer the opportunity for precision agriculture to efficiently monitor agricultural land. A vegetation index (VI) derived from an aerially observed multispectral image (MSI) can quantify crop health, moisture and nutrient content. However, due to the high cost of multispectral sensors, alternate, low-cost solutions have lately received great interest. We present a novel method for model-based estimation of a VI using RGB color images. The non-linear spatio-spectral relationship between the RGB image of vegetation and the index computed by its corresponding MSI is learned through deep neural networks...
2018: Plant Methods
C R Gedling, E M Ali, A Gunadi, J J Finer, K Xie, Y Liu, N Yoshikawa, F Qu, A E Dorrance
Background: Virus induced gene silencing (VIGS) is a powerful genomics tool for interrogating the function of plant genes. Unfortunately, VIGS vectors often produce disease symptoms that interfere with the silencing phenotypes of target genes, or are frequently ineffective in certain plant genotypes or tissue types. This is especially true in crop plants like soybean [ Glycine max (L.) Merr]. To address these shortcomings, we modified the inoculation procedure of a VIGS vector based on Apple latent spherical virus (ALSV)...
2018: Plant Methods
Karthikeyan Alagarsamy, Lubobi Ferdinand Shamala, Shu Wei
Background: Camellia sinensis var. sinensis is widely grown for tea beverages that possess significant health promoting effects. Studies on tea plant genetics and breeding are hindered due to its recalcitrance to Agrobacterium -mediated genetic transformation. Among the possible reasons, oxidation of phenolics released from explant tissues and bactericidal effects of tea polyphenols during the process of transformation play a role in the plant recalcitrance. The aim of the present study was to alleviate the harmful effects of phenolic compounds using in - planta transformation...
2018: Plant Methods
Lingxiao Zhao, Ting Pan, Dongwei Guo, Cunxu Wei
Background: Storage starch in starchy seed influences the seed weight and texture, and determines its applications in food and nonfood industries. Starch granules from different plant sources have significantly different shapes and sizes, and even more the difference exists in the different regions of the same tissue. Therefore, it is very important to in situ investigate the morphology and distribution of starch in the whole seed. However, a simple and rapid method is deficient to prepare the whole section of starchy seed for investigating the morphology and distribution of starch in the whole seeds for a large number of samples...
2018: Plant Methods
Shan Lu, Fan Lu, Wenqiang You, Zheyi Wang, Yu Liu, Kenji Omasa
Background: Leaf chlorophyll content (LCC) provides valuable information about plant physiology. Most of the published chlorophyll vegetation indices at the leaf level have been based on the spectral characteristics of the adaxial leaf surface, thus, they are not appropriate for estimating LCC when both the adaxial and abaxial leaf surfaces influence the spectral reflectance. We attempted to address this challenge by measuring the spectral reflectance of the adaxial and abaxial leaf surfaces of several plant species at different growth stages using a portable field spectroradiometer...
2018: Plant Methods
Sunitha Shiva, Regina Enninful, Mary R Roth, Pamela Tamura, Krishna Jagadish, Ruth Welti
Background: Lipidomics plays an important role in understanding plant adaptation to different stresses and improving our knowledge of the genes underlying lipid metabolism. Lipidomics involves lipid extraction, sample preparation, mass spectrometry analysis, and data interpretation. One of the practical challenges for large-scale lipidomics studies on plant leaves is the requirement of an efficient and rapid extraction method. Results: A single-extraction method with a polar solvent mixture gives results comparable to a widely used, multi-extraction method when tested on both Arabidopsis thaliana and Sorghum bicolor leaf tissue...
2018: Plant Methods
Hao Liu, Ying Gao, Xiaobo Song, Qingguo Ma, Junpei Zhang, Dong Pei
Background: Juglans is a difficult-to-root tree. In the present study, we successfully rejuvenated stock plants by grafting and then burying them horizontally. Results: Rooting rates of rejuvenated shoots were 98.1% 20 days after cutting. We recorded spatial and temporal variation in endogenous indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellin A 3 (GA 3 ) and zeatin-riboside (ZR) under root induction. The four types of endohormones were mainly confined to the phloem sieve and companion cells (S&Cs) at the base of either rejuvenated or mature soft shoots...
2018: Plant Methods
M Valerio Giuffrida, Feng Chen, Hanno Scharr, Sotirios A Tsaftaris
Background: Image-based plant phenotyping has become a powerful tool in unravelling genotype-environment interactions. The utilization of image analysis and machine learning have become paramount in extracting data stemming from phenotyping experiments. Yet we rely on observer (a human expert) input to perform the phenotyping process. We assume such input to be a 'gold-standard' and use it to evaluate software and algorithms and to train learning-based algorithms. However, we should consider whether any variability among experienced and non-experienced (including plain citizens) observers exists...
2018: Plant Methods
Loay Al-Zube, Wenhuan Sun, Daniel Robertson, Douglas Cook
Background: Stalk lodging is a serious challenge in the production of maize and sorghum. A comprehensive understanding of lodging will likely require accurate characterizations of the mechanical properties of such plants. One of the most important mechanical properties for structural analysis of bending is the modulus of elasticity. The purpose of this study was to measure the modulus of elasticity of dry, mature maize rind tissues using three different loading modes ( bending , compression and tensile ), and to determine the accuracy and reliability of each test method...
2018: Plant Methods
Kaori Sakai, Ludivine Taconnat, Nero Borrega, Jennifer Yansouni, Véronique Brunaud, Christine Paysant-Le Roux, Etienne Delannoy, Marie-Laure Martin Magniette, Loïc Lepiniec, Jean Denis Faure, Sandrine Balzergue, Bertrand Dubreucq
Background: Genome-wide characterization of tissue- or cell-specific gene expression is a recurrent bottleneck in biology. We have developed a sensitive approach based on ultra-low RNA sequencing coupled to laser assisted microdissection for analyzing different tissues of the small Arabidopsis embryo. Methods and results: We first characterized the number of genes detected according to the quantity of tissue yield and total RNA extracted. Our results revealed that as low as 0...
2018: Plant Methods
F E Marmisolle, M L García, C A Reyes
Background: Due to the nature of viral RNA genomes, RNA viruses depend on many RNA-binding proteins (RBP) of viral and host origin for replication, dissemination and evasion of host RNA degradation pathways. Some viruses interfere with the microRNA (miRNA) pathway to generate better fitness. The development of an adjusted, reliable and sensitive ribonucleoprotein immunoprecipitation (RIP) assay is needed to study the interaction between RBP of different origin (including viral origin) and miRNA precursors...
2018: Plant Methods
Rasmus Dahl-Lassen, Jan van Hecke, Henning Jørgensen, Christian Bukh, Birgit Andersen, Jan K Schjoerring
Background: The amino acid profile of plants is an important parameter in assessments of their growth potential, resource-use efficiency and/or quality as food and feed. Screening studies may involve large number of samples but the classical amino acid analysis is limited by the fact that it is very time consuming with typical chromatographic run times of 70 min or more. Results: We have here developed a high-throughput method for analysis of amino acid profiles in plant materials...
2018: Plant Methods
Julio V Schneider, Renate Rabenstein, Jens Wesenberg, Karsten Wesche, Georg Zizka, Jörg Habersetzer
Background: Leaf venation traits are important for many research fields such as systematics and evolutionary biology, plant physiology, climate change, and paleoecology. In spite of an increasing demand for vein trait data, studies are often still data-limited because the development of methods that allow rapid generation of large sets of vein data has lagged behind. Recently, non-destructive X-ray technology has proven useful as an alternative to traditional slow and destructive chemical-based methods...
2018: Plant Methods
Jordan Ubbens, Mikolaj Cieslak, Przemyslaw Prusinkiewicz, Ian Stavness
Deep learning presents many opportunities for image-based plant phenotyping. Here we consider the capability of deep convolutional neural networks to perform the leaf counting task. Deep learning techniques typically require large and diverse datasets to learn generalizable models without providing a priori an engineered algorithm for performing the task. This requirement is challenging, however, for applications in the plant phenotyping field, where available datasets are often small and the costs associated with generating new data are high...
2018: Plant Methods
Danny Awty-Carroll, John Clifton-Brown, Paul Robson
Background: Miscanthus is a leading second generation bio-energy crop. It is mostly rhizome propagated; however, the increasing use of seed is resulting in a greater need to investigate germination. Miscanthus seed are small, germination is often poor and carried out without sterilisation; therefore, automated methods applied to germination detection must be able to cope with, for example, thresholding of small objects, low germination frequency and the presence or absence of mould. Results: Machine learning using k-NN improved the scoring of different phenotypes encountered in Miscanthus seed...
2018: Plant Methods
Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Background: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data...
2018: Plant Methods
Javier Tello, María Ignacia Montemayor, Astrid Forneck, Javier Ibáñez
Background: Low pollen viability may limit grapevine yield under certain conditions, causing relevant economic losses to grape-growers. It is usually evaluated by the quantification of the number of viable and non-viable pollen grains that are present in a sample after an adequate pollen grain staining procedure. Although the manual counting of both types of grains is the simplest and most sensitive approach, it is a laborious and time-demanding process. In this regard, novel image-based approaches can assist in the objective, accurate and cost-effective phenotyping of this trait...
2018: Plant Methods
Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael Goodin, Vladimir Orbovic
Background: Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work efficiently with many gene constructs, and there is a need for a more robust transient expression system in citrus leaves. Biolistic particle delivery is an alternative to Agrobacterium transformation, and in some plants, such as Arabidopsis, gives higher transformation rates in leaf tissues than Agrobacterium...
2018: Plant Methods
Mohammed Albaqami, Anireddy S N Reddy
Background: Pre-mRNA splicing is an essential post-transcriptional process in all eukaryotes. In vitro splicing systems using nuclear or cytoplasmic extracts from mammalian cells, yeast, and Drosophila have provided a wealth of mechanistic insights into assembly and composition of the spliceosome, splicing regulatory proteins and mechanisms of pre-mRNA splicing in non-plant systems. The lack of an in vitro splicing system prepared from plant cells has been a major limitation in splicing research in plants...
2018: Plant Methods
Ji Zhou, Christopher Applegate, Albor Dobon Alonso, Daniel Reynolds, Simon Orford, Michal Mackiewicz, Simon Griffiths, Steven Penfield, Nick Pullen
Background: Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cross-referencing results between experiments, making automated phenotypic analysis problematic...
2017: Plant Methods
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