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Plant Methods

Filipe Couto Alves, Ítalo Stefanine Correa Granato, Giovanni Galli, Danilo Hottis Lyra, Roberto Fritsche-Neto, Gustavo de Los Campos
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. Bayesian models offer a very flexible framework for hybrid prediction. The Bayesian methodology can be used with parametric and semi-parametric assumptions for additive and non-additive effects. Furthermore, samples from the posterior distribution of Bayesian models can be used to estimate the variance due to general and specific combining abilities even in cases where additive and non-additive effects are not mutually orthogonal...
2019: Plant Methods
Raghav Khanna, Lukas Schmid, Achim Walter, Juan Nieto, Roland Siegwart, Frank Liebisch
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...
2019: Plant Methods
Haiyang Wang, Lana Shabala, Meixue Zhou, Sergey Shabala
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)...
2019: Plant Methods
Yanjun Su, Fangfang Wu, Zurui Ao, Shichao Jin, Feng Qin, Boxin Liu, Shuxin Pang, Lingli Liu, Qinghua Guo
Background: Maize ( Zea mays 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. Although light detection and ranging (lidar) technology showed great potential in acquiring three-dimensional (3D) vegetation information, it has been rarely used in monitoring maize phenotype dynamics at an individual plant level...
2019: Plant Methods
Liang Han, Guijun Yang, Huayang Dai, Bo Xu, Hao Yang, Haikuan Feng, Zhenhai Li, Xiaodong Yang
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...
2019: Plant Methods
Geun Cheol Song, Myoungjoo Riu, Choong-Min Ryu
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. We therefore attempted to optimise BVC emissions from bacteria grown on solid medium and synthetic BVC treatment in order to maximise plant growth and induced resistance in a miniature greenhouse system...
2019: Plant Methods
Lei Zhang, Li-Na Qin, Zi-Rui Zeng, Chang-Zheng Wu, Yuan-Yong Gong, Lai-Hua Liu, Feng-Qiu Cao
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 Arabidopsis 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...
2019: Plant Methods
Wenbing Su, Yuan Yuan, Ling Zhang, Yuanyuan Jiang, Xiaoqing Gan, Yunlu Bai, Jiangrong Peng, Jincheng Wu, Yuexue Liu, Shunquan Lin
Background: Loquat ( Eriobotrya japonica ) 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...
2019: Plant Methods
Max R Lien, Richard J Barker, Zhiwei Ye, Matthew H Westphall, Ruohan Gao, Aditya Singh, Simon Gilroy, Philip A Townsend
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., using tram, drone, or airplane mounted instruments. The field setting introduces a wide range of uncontrolled environmental variables that make validation and interpretation of spectral responses challenging, and as such lab- and greenhouse-deployed systems for plant studies and phenotyping are of increasing interest...
2019: Plant Methods
Liejian Huang, Hong Wang, Muhammad Qasim Shahid, Bingshan Zeng
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 Acacia auriculiformis . Results: We carried out the bud induction trials under open conditions to screen out an effective antibacterial agent for open tissue culture of A...
2019: Plant Methods
Charles Veys, Fokion Chatziavgerinos, Ali AlSuwaidi, James Hibbert, Mark Hansen, Gytis Bernotas, Melvyn Smith, Hujun Yin, Stephen Rolfe, Bruce Grieve
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 Pyrenopeziza brassicae in Brassica napus ...
2019: Plant Methods
Christophe Moni, Hanna Silvennoinen, Bruce A Kimball, Erling Fjelldal, Marius Brenden, Ingunn Burud, Andreas Flø, Daniel P Rasse
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...
2019: Plant Methods
Mark Müller-Linow, Jens Wilhelm, Christoph Briese, Tobias Wojciechowski, Ulrich Schurr, Fabio Fiorani
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...
2019: Plant Methods
Astrid Elisabeth Mork-Jansson, Lutz Andreas Eichacker
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. We have shown that membrane integral light-harvesting-like protein, LIL3, binds chlorophyll a with a Kd of 146 nM in vitro by thermophoresis...
2019: Plant Methods
Rupam Kumar Bhunia, Lucas J Showman, Adarsh Jose, Basil J Nikolau
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...
2018: Plant Methods
Lukas Roth, Andreas Hund, Helge Aasen
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. Additionally, if mapping areas with UASs, one has to consider concepts related to ground control points (GCPs), viewing geometry and way-point flights...
2018: Plant Methods
Nathan D Miller, Scott C Stelpflug, Shawn M Kaeppler, Edgar P Spalding
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. Results: An electronic force transducer measured imbibition of single maize kernels with very high resolution but low throughput...
2018: Plant Methods
Akitomo Kawasaki, Shoko Okada, Chunyan Zhang, Emmanuel Delhaize, Ulrike Mathesius, Alan E Richardson, Michelle Watt, Matthew Gilliham, Peter R Ryan
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...
2018: Plant Methods
Miriam Tannenbaum, Avital Sarusi-Portuguez, Ronen Krispil, Michal Schwartz, Olga Loza, Jennifer I C Benichou, Assaf Mosquna, Ofir Hakim
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. However, these sequences are hindered by the packaging of DNA to chromatin...
2018: Plant Methods
Fabien Miart, Jean-Xavier Fontaine, Christophe Pineau, Hervé Demailly, Brigitte Thomasset, Olivier Van Wuytswinkel, Karine Pageau, François Mesnard
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. Current strategies to phenotype soluble mucilage are restricted to visual evaluations or are highly time-consuming...
2018: Plant Methods
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