Articles

TasselNetv2: in-field counting of wheat spikes with context-augmented local regression networks

Authors: Haipeng Xiong, Zhiguo Cao, Hao Lu, Simon Madec, Liang Liu and Chunhua Shen

Study on measurement method for apple root morphological parameters based on Labview

Traditional measurements of apple seedling roots often rely on manual measurements and existing root scanners on the market. Manual measurement requires a lot of labor and time, and subjective reasons may caus...

Authors: Yu Liu, Ji Qian, Xin Yang, Bao Di and Juan Zhou

Testing deep placement of an ¹⁵N tracer as a method for in situ deep root phenotyping of wheat, barley and ryegrass

Deep rooting is one of the most promising plant traits for improving crop yield under water-limited conditions. Most root phenotyping methods are designed for laboratory-grown plants, typically measuring very ...

Authors: Si Chen, Simon Fiil Svane and Kristian Thorup-Kristensen

Non-invasive diagnosis of viability in seeds and lichens by infrared thermography under controlled environmental conditions

Non-invasive procedures for the diagnosis of viability of plant or fungal tissues would be valuable for scientific, industrial and biomonitoring purposes. Previous studies showed that infrared thermography (IR...

Authors: Beatriz Fernández-Marín, Othmar Buchner, Gerald Kastberger, Federica Piombino, José Ignacio García-Plazaola and Ilse Kranner

Deep learning for image-based large-flowered chrysanthemum cultivar recognition

Cultivar recognition is a basic work in flower production, research, and commercial application. Chinese large-flowered chrysanthemum (Chrysanthemum × morifolium Ramat.) is miraculous because of its high ornament...

Authors: Zhilan Liu, Jue Wang, Ye Tian and Silan Dai

A quick and efficient hydroponic potato infection method for evaluating potato resistance and Ralstonia solanacearum virulence

Potato, the third most important crop worldwide, plays a critical role in human food security. Brown rot, one of the most destructive potato diseases caused by Ralstonia solanacearum, results in huge economic los...

Authors: Huijuan Wang, Jinxue Hu, Yao Lu, Mancang Zhang, Ning Qin, Ruize Zhang, Yizhe He, Dongdong Wang, Yue Chen, Cuizhu Zhao, Núria S. Coll, Marc Valls, Qin Chen and Haibin Lu

An efficient system composed of maize protoplast transfection and HPLC–MS for studying the biosynthesis and regulation of maize benzoxazinoids

Insect herbivory poses a major threat to maize. Benzoxazinoids are important anti-insect secondary metabolites in maize, whose biosynthetic pathway has been extensively studied. However, yet little is known ab...

Authors: Lei Gao, Guojing Shen, Lingdan Zhang, Jinfeng Qi, Cuiping Zhang, Canrong Ma, Jing Li, Lei Wang, Saif Ul Malook and Jianqiang Wu

Blocking and re-arrangement of pots in greenhouse experiments: which approach is more effective?

Observations measured in field and greenhouse experiments always contain errors. These errors can arise from measurement error, local or positional conditions of the experimental units, or from the randomizati...

Authors: Jens Hartung, Juliane Wagener, Reiner Ruser and Hans-Peter Piepho

High-throughput long paired-end sequencing of a Fosmid library by PacBio

Large insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection...

Authors: Zhaozhao Dai, Tong Li, Jiadong Li, Zhifei Han, Yonglong Pan, Sha Tang, Xianmin Diao and Meizhong Luo

DeepSeedling: deep convolutional network and Kalman filter for plant seedling detection and counting in the field

Plant population density is an important factor for agricultural production systems due to its substantial influence on crop yield and quality. Traditionally, plant population density is estimated by using eit...

Authors: Yu Jiang, Changying Li, Andrew H. Paterson and Jon S. Robertson

Nourseothricin N-acetyl transferase (NAT), a new selectable marker for nuclear gene expression in Chlamydomonas

Chlamydomonas reinhardtii is a unicellular green alga, which is a most commonly used model organism for basic research and biotechnological applications. Generation of transgenic strains, which usually requires s...

Authors: Xinjia Yang, Jialin Peng and Junmin Pan

Improving the efficiency of soybean breeding with high-throughput canopy phenotyping

In the early stages of plant breeding programs high-quality phenotypes are still a constraint to improve genetic gain. New field-based high-throughput phenotyping (HTP) platforms have the capacity to rapidly a...

Authors: Fabiana Freitas Moreira, Anthony Ahau Hearst, Keith Aric Cherkauer and Katy Martin Rainey

Machine learning driven non-invasive approach of water content estimation in living plant leaves using terahertz waves

The demand for effective use of water resources has increased because of ongoing global climate transformations in the agriculture science sector. Cost-effective and timely distributions of the appropriate amo...

Authors: Adnan Zahid, Hasan T. Abbas, Aifeng Ren, Ahmed Zoha, Hadi Heidari, Syed A. Shah, Muhammad A. Imran, Akram Alomainy and Qammer H. Abbasi

Root phenotypic detection of different vigorous maize seeds based on Progressive Corrosion Joining algorithm of image

The root phenotypes of different vigorous maize seeds vary a lot. Imaging roots of growing maize is a non-invasive, affordable and high throughput approach. However, it’s difficult to get integral root images ...

Authors: Wei Lu, Ye Li and Yiming Deng

Combining gene expression programming and genetic algorithm as a powerful hybrid modeling approach for pear rootstocks tissue culture media formulation

Predicting impact of plant tissue culture media components on explant proliferation is important especially in commercial scale for optimizing efficient culture media. Previous studies have focused on predicti...

Authors: Saeid Jamshidi, Abbas Yadollahi, Mohammad Mehdi Arab, Mohammad Soltani, Maliheh Eftekhari, Hamed Sabzalipoor, Abdollatif Sheikhi and Jalal Shiri

Proteomics: a powerful tool to study plant responses to biotic stress

In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed fr...

Authors: Yahui Liu, Song Lu, Kefu Liu, Sheng Wang, Luqi Huang and Lanping Guo

An improved method of constructing degradome library suitable for sequencing using Illumina platform

Post-transcriptional gene regulation is one of the critical layers of overall gene expression programs and microRNAs (miRNAs) play an indispensable role in this process by guiding cleavage on the messenger RNA...

Authors: Yong-Fang Li, Miao Zhao, Menglei Wang, Junqiang Guo, Li Wang, Jie Ji, Zongbo Qiu, Yun Zheng and Ramanjulu Sunkar

Sensory assessment of Cercospora beticola sporulation for phenotyping the partial disease resistance of sugar beet genotypes

Due to its high damaging potential, Cercospora leaf spot (CLS) caused by Cercospora beticola is a continuous threat to sugar beet production worldwide. Breeding for disease resistance is hampered by the quantitat...

Authors: Erich-Christian Oerke, Marlene Leucker and Ulrike Steiner

Correction to: Contour analysis for interpretable leaf shape category discovery

Unfortunately, the original version of the article [1] contained an error in figure 7. The names of species Umus minor and Acer campestre were interchanged. The corrected figure 7 is given below:

Authors: Jorge Victorino and Francisco Gómez

A low-cost aeroponic phenotyping system for storage root development: unravelling the below-ground secrets of cassava (Manihot esculenta)

Root and tuber crops are becoming more important for their high source of carbohydrates, next to cereals. Despite their commercial impact, there are significant knowledge gaps about the environmental and inher...

Authors: Michael Gomez Selvaraj, Maria Elker Montoya-P, John Atanbori, Andrew P. French and Tony Pridmore

A simple and rapid protocol for the genetic transformation of Ensete ventricosum

Enset (Ensete ventricosum), also known as Ethiopian banana, is a food security crop for more than 20 million people in Ethiopia. As conventional breeding of enset is very challenging, genetic engineering is an al...

Authors: Jonathan Matheka, Jaindra Nath Tripathi, Ibsa Merga, Endale Gebre and Leena Tripathi

A novel strategy to enhance terpenoids production using cambial meristematic cells of Tripterygium wilfordii Hook. f.

Tripterygium wilfordii Hook. f. (T. wilfordii) is an important medicinal plant with anti-inflammatory, immunosuppressive and anti-tumor activities. The main bioactive ingredients are diterpenoids and triterpenoid...

Authors: Yadi Song, Shang Chen, Xiujuan Wang, Rui Zhang, Lichan Tu, Tianyuan Hu, Xihong Liu, Yifeng Zhang, Luqi Huang and Wei Gao

Instantaneous and non-destructive relative water content estimation from deep learning applied to resonant ultrasonic spectra of plant leaves

Non-contact resonant ultrasound spectroscopy (NC-RUS) has been proven as a reliable technique for the dynamic determination of leaf water status. It has been already tested in more than 50 plant species. In pa...

Authors: María Dolores Fariñas, Daniel Jimenez-Carretero, Domingo Sancho-Knapik, José Javier Peguero-Pina, Eustaquio Gil-Pelegrín and Tomás Gómez Álvarez-Arenas

Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry

Sugar phosphates are important intermediates of central carbon metabolism in biological systems, with roles in glycolysis, the pentose–phosphate pathway, tricarboxylic acid (TCA) cycle, and many other biosynth...

Authors: Umut Rende, Totte Niittylä and Thomas Moritz

A bacterial assay for rapid screening of IAA catabolic enzymes

Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of...

Authors: Federica Brunoni, Silvio Collani, Jan Šimura, Markus Schmid, Catherine Bellini and Karin Ljung

Development, progress and future prospects in cryobiotechnology of Lilium spp.

Lilium is one of the most popular flower crops worldwide, and some species are also used as vegetables and medicines. The availability of and easy access to diverse Lilium genetic resources are essential for plan...

Authors: Jing-Wei Li, Xiao-Chen Zhang, Min-Rui Wang, Wen-Lu Bi, M. Faisal, Jaime A. Teixeira da Silva, Gayle M. Volk and Qiao-Chun Wang

Remote estimation of rice LAI based on Fourier spectrum texture from UAV image

The accurate estimation of rice LAI is particularly important to monitor rice growth status. Remote sensing, as a non-destructive measurement technology, has been proved to be useful for estimating vegetation ...

Authors: Bo Duan, Yating Liu, Yan Gong, Yi Peng, Xianting Wu, Renshan Zhu and Shenghui Fang

Principal variable selection to explain grain yield variation in winter wheat from features extracted from UAV imagery

Automated phenotyping technologies are continually advancing the breeding process. However, collecting various secondary traits throughout the growing season and processing massive amounts of data still take g...

Authors: Jiating Li, Arun-Narenthiran Veeranampalayam-Sivakumar, Madhav Bhatta, Nicholas D. Garst, Hannah Stoll, P. Stephen Baenziger, Vikas Belamkar, Reka Howard, Yufeng Ge and Yeyin Shi

Image analysis-based recognition and quantification of grain number per panicle in rice

The number grain per panicle of rice is an important phenotypic trait and a significant index for variety screening and cultivation management. The methods that are currently used to count the number of grains...

Authors: Wei Wu, Tao Liu, Ping Zhou, Tianle Yang, Chunyan Li, Xiaochun Zhong, Chengming Sun, Shengping Liu and Wenshan Guo

An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

Despite wheat being a worldwide staple, it is still considered the most difficult to transform out of the main cereal crops. Therefore, for the wheat research community, a freely available and effective wheat ...

Authors: Sadiye Hayta, Mark A. Smedley, Selcen U. Demir, Robert Blundell, Alison Hinchliffe, Nicola Atkinson and Wendy A. Harwood

Protocol for rapid clearing and staining of fixed Arabidopsis ovules for improved imaging by confocal laser scanning microscopy

A salient topic in developmental biology relates to the molecular and genetic mechanisms that underlie tissue morphogenesis. Modern quantitative approaches to this central question frequently involve digital c...

Authors: Rachele Tofanelli, Athul Vijayan, Sebastian Scholz and Kay Schneitz

An optimised CRISPR/Cas9 protocol to create targeted mutations in homoeologous genes and an efficient genotyping protocol to identify edited events in wheat

Targeted genome editing using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system has been applied in a large number of plant species. Using a gene-specific single guide RNA (sgR...

Authors: Xiucheng Cui, Margaret Balcerzak, Johann Schernthaner, Vivijan Babic, Raju Datla, Elizabeth K. Brauer, Natalie Labbé, Rajagopal Subramaniam and Thérèse Ouellet

A cell death assay in barley and wheat protoplasts for identification and validation of matching pathogen AVR effector and plant NLR immune receptors

Plant disease resistance to host-adapted pathogens is often mediated by host nucleotide-binding and leucine-rich repeat (NLR) receptors that detect matching pathogen avirulence effectors (AVR) inside plant cel...

Authors: Isabel M. L. Saur, Saskia Bauer, Xunli Lu and Paul Schulze-Lefert

Assessing plant performance in the Enviratron

Assessing the impact of the environment on plant performance requires growing plants under controlled environmental conditions. Plant phenotypes are a product of genotype × environment (G × E), and the Envirat...

Authors: Yin Bao, Scott Zarecor, Dylan Shah, Taylor Tuel, Darwin A. Campbell, Antony V. E. Chapman, David Imberti, Daniel Kiekhaefer, Henry Imberti, Thomas Lübberstedt, Yanhai Yin, Dan Nettleton, Carolyn J. Lawrence-Dill, Steven A. Whitham, Lie Tang and Stephen H. Howell

Phenotyping viral infection in sweetpotato using a high-throughput chlorophyll fluorescence and thermal imaging platform

Virus diseases caused by co-infection with Sweet potato feathery mottle virus (SPFMV) and Sweetpotato chlorotic stunt virus (SPCSV) are a severe problem in the production of sweetpotato (Ipomoea batatas L.). Trad...

Authors: Linping Wang, Sylvain Poque and Jari P. T. Valkonen

Establishment and optimization of mRNA in situ hybridization system in turnip (Brassica rapa var. rapa)

In situ hybridization (ISH) is a general molecular biological technique used to determine the spatiotemporal expression of genes in many species. In the past few years, numerous ISH protocols have been establi...

Authors: Cheng Li, Simin Hu, Qidong Lei, Chongde Wang, Yunqiang Yang, Yongping Yang and Xudong Sun

Spatially resolved transcriptomics reveals plant host responses to pathogens

Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large s...

Authors: Michael Giolai, Walter Verweij, Ashleigh Lister, Darren Heavens, Iain Macaulay and Matthew D. Clark

Correction to: Soybean iron deficiency chlorosis high throughput phenotyping using an unmanned aircraft system

In the original article [1], under the subheading “Image data processing”, last paragraph, last sentence that reads as “The least …… data collection” was incorrectly published. The correct sentence should read...

Authors: Austin A. Dobbels and Aaron J. Lorenz

Contour analysis for interpretable leaf shape category discovery

The categorical description of leaf shapes is of paramount importance in ecology, taxonomy and paleobotanical studies. Classification systems proposed by domain experts support these descriptions. Despite the ...

Authors: Jorge Victorino and Francisco Gómez

Isolating phyllotactic patterns embedded in the secondary growth of sweet cherry (Prunus avium L.) using magnetic resonance imaging

Epicormic branches arise from dormant buds patterned during the growth of previous years. Dormant epicormic buds remain just below the surface of trees, pushed outward from the pith during secondary growth, bu...

Authors: Mitchell Eithun, James Larson, Gregory Lang, Daniel H. Chitwood and Elizabeth Munch

Silencing of the phytoene desaturase (PDS) gene affects the expression of fruit-ripening genes in tomatoes

Past research has shown that virus-induced phytoene desaturase (PDS) gene silencing via agroinjection in the attached and detached fruit of tomato plants results in a pale-yellow fruit phenotype. Although the PDS

Authors: Aung Htay Naing, Swum Yi Kyu, Phyo Phyo Win Pe, Kyeung Il Park, Je Min Lee, Ki Byung Lim and Chang Kil Kim

High throughput procedure utilising chlorophyll fluorescence imaging to phenotype dynamic photosynthesis and photoprotection in leaves under controlled gaseous conditions

As yields of major crops such as wheat (T. aestivum) have begun to plateau in recent years, there is growing pressure to efficiently phenotype large populations for traits associated with genetic advancement in y...

Authors: Lorna McAusland, Jonathan A. Atkinson, Tracy Lawson and Erik H. Murchie

Improving plant transient expression through the rational design of synthetic 5′ and 3′ untranslated regions

The growing field of plant molecular farming relies on expression vectors that allow high yields of recombinant proteins to be produced through transient gene expression. While numerous expression vectors curr...

Authors: Hadrien Peyret, James K. M. Brown and George P. Lomonossoff

Utilizing trait networks and structural equation models as tools to interpret multi-trait genome-wide association studies

Plant breeders seek to develop cultivars with maximal agronomic value, which is often assessed using numerous, often genetically correlated traits. As intervention on one trait will affect the value of another...

Authors: Mehdi Momen, Malachy T. Campbell, Harkamal Walia and Gota Morota

Terahertz spectral imaging based quantitative determination of spatial distribution of plant leaf constituents

Plant leaves have heterogeneous structures composed of spatially variable distribution of liquid, solid, and gaseous matter. Such contents and distribution characteristics correlate with the leaf vigor and phy...

Authors: Ziyi Zang, Jie Wang, Hong-Liang Cui and Shihan Yan

Understanding glycaemic control and current approaches for screening antidiabetic natural products from evidence-based medicinal plants

Type 2 Diabetes Mellitus has reached epidemic proportions as a result of over-nutrition and increasingly sedentary lifestyles. Current therapies, although effective, are not without limitations. These limitati...

Authors: Chintha Lankatillake, Tien Huynh and Daniel A. Dias

Root Hair Sizer: an algorithm for high throughput recovery of different root hair and root developmental parameters

The root is an important organ for water and nutrient uptake, and soil anchorage. It is equipped with root hairs (RHs) which are elongated structures increasing the exchange surface with the soil. RHs are also...

Authors: Marjorie Guichard, Jean-Marc Allain, Michele Wolfe Bianchi and Jean-Marie Frachisse

Measuring crops in 3D: using geometry for plant phenotyping

Using 3D sensing for plant phenotyping has risen within the last years. This review provides an overview on 3D traits for the demands of plant phenotyping considering different measuring techniques, derived tr...

Authors: Stefan Paulus

DARLING: a device for assessing resistance to lodging in grain crops

Stalk lodging (breakage of plant stems prior to harvest) is a major problem for both farmers and plant breeders. A limiting factor in addressing this problem is the lack of a reliable method for phenotyping st...

Authors: Douglas D. Cook, Witold de la Chapelle, Ting-Che Lin, Shien Yang Lee, Wenhuan Sun and Daniel J. Robertson

EnRoot: a narrow-diameter, inexpensive and partially 3D-printable minirhizotron for imaging fine root production

Fine root production is one of the least well understood components of the carbon cycle in terrestrial ecosystems. Minirhizotrons allow accurate and non-destructive sampling of fine root production. Small and ...

Authors: Marie Arnaud, Andy J. Baird, Paul J. Morris, Angela Harris and Jonny J. Huck