Articles

Fast photosynthesis measurements for phenotyping photosynthetic capacity of rice

Over the past decades, the structural and functional genomics of rice have been deeply studied, and high density of molecular genetic markers have been developed. However, the genetic variation in leaf photosy...

Authors: Tingting Du, Ping Meng, Jianliang Huang, Shaobing Peng and Dongliang Xiong

Computer vision and machine learning enabled soybean root phenotyping pipeline

Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vis...

Authors: Kevin G. Falk, Talukder Z. Jubery, Seyed V. Mirnezami, Kyle A. Parmley, Soumik Sarkar, Arti Singh, Baskar Ganapathysubramanian and Asheesh K. Singh

A high-throughput screening method to identify proteins involved in unfolded protein response of the endoplasmic reticulum in plants

The unfolded protein response (UPR) is a highly conserved process in eukaryotic organisms that plays a crucial role in adaptation and development. While the most ubiquitous components of this pathway have been...

Authors: André Alcântara, Denise Seitner, Fernando Navarrete and Armin Djamei

A method for functional testing constitutive and ligand-induced interactions of lysin motif receptor proteins

Plant receptors with lysin motifs (LsyM) recognize microbial signals such as fungal chitin and lipo-chitooligosaccharidic Nod factors of nitrogen-fixing rhizobia. It is generally assumed that ligand-induced di...

Authors: Chun-Lian Li, De-Xing Xue, Yi-Han Wang, Zhi-Ping Xie and Christian Staehelin

Phenotyping analysis of maize stem using micro-computed tomography at the elongation and tasseling stages

Micro-computed tomography (μCT) bring a new opportunity to accurately quantify micro phenotypic traits of maize stem, also provide comparable benchmark to evaluate its dynamic development at the different grow...

Authors: Ying Zhang, Liming Ma, Jinglu Wang, Xiaodong Wang, Xinyu Guo and Jianjun Du

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics

Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment...

Authors: Paul G. Nevill, Xiao Zhong, Julian Tonti-Filippini, Margaret Byrne, Michael Hislop, Kevin Thiele, Stephen van Leeuwen, Laura M. Boykin and Ian Small

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

In the original publication [1], the copyright line was incorrectly published as “© The Author(s) 2019”. The corrected copyright line should read as “© Her Majesty the Queen in Right of Canada as represented b...

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

PI-Plat: a high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits

Recent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which pr...

Authors: Jaspreet Sandhu, Feiyu Zhu, Puneet Paul, Tian Gao, Balpreet K. Dhatt, Yufeng Ge, Paul Staswick, Hongfeng Yu and Harkamal Walia

Structural parameters for X-ray micro-computed tomography (μCT) and their relationship with the breakage rate of maize varieties

High grain breakage rate is the main limiting factor encountered in the mechanical harvest of maize grain. X-ray micro-computed tomography (μCT) scanning technology could be used to obtain the three-dimensiona...

Authors: Junfeng Hou, Ying Zhang, Xiuliang Jin, Pengfei Dong, Yanan Guo, Keru Wang, Yinghu Fan and Shaokun Li

An efficient RGB-UAV-based platform for field almond tree phenotyping: 3-D architecture and flowering traits

Almond is an emerging crop due to the health benefits of almond consumption including nutritional, anti-inflammatory, and hypocholesterolaemia properties. Traditional almond producers were concentrated in Cali...

Authors: Francisca López-Granados, Jorge Torres-Sánchez, Francisco M. Jiménez-Brenes, Octavio Arquero, María Lovera and Ana I. de Castro

Detection of white head symptoms of panicle blast caused by Pyricularia oryzae using cut-flower dye

Breeding of rice with panicle resistance to rice blast disease caused by Pyricularia oryzae is a challenge towards sustainable rice production. Methods for accurate estimation of disease severity can support bree...

Authors: Keiko Hayashi, Tomofumi Yoshida and Yuriko Hayano-Saito

Optimal long-term seed storage conditions for the endangered seagrass Zostera japonica: implications for habitat conservation and restoration

Seagrass meadows are recognized as critical and among the most vulnerable habitats on the planet. The alarming rates of decline in seagrass meadows have attracted the attention globally. There is an urgent nee...

Authors: Shidong Yue, Yu Zhang, Yi Zhou, Shaochun Xu, Shuai Xu, Xiaomei Zhang and Ruiting Gu

Virus-induced gene silencing (VIGS) in Cannabis sativa L.

The raised demand of cannabis as a medicinal plant in recent years led to an increased interest in understanding the biosynthetic routes of cannabis metabolites. Since there is no established protocol to gener...

Authors: Julia Schachtsiek, Tajammul Hussain, Khadija Azzouhri, Oliver Kayser and Felix Stehle

Fluctuating light experiments and semi-automated plant phenotyping enabled by self-built growth racks and simple upgrades to the IMAGING-PAM

Over the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under f...

Authors: Dominik Schneider, Laura S. Lopez, Meng Li, Joseph D. Crawford, Helmut Kirchhoff and Hans-Henning Kunz

Dynamic biospeckle analysis, a new tool for the fast screening of plant nematicide selectivity

Plant feeding, free-living nematodes cause extensive damage to plant roots by direct feeding and, in the case of some trichodorid and longidorid species, through the transmission of viruses. Developing more en...

Authors: Felicity E. O’Callaghan, Roy Neilson, Stuart A. MacFarlane and Lionel X. Dupuy

A high-throughput quantification of resin and rubber contents in Parthenium argentatum using near-infrared (NIR) spectroscopy

Guayule (Parthenium argentatum A. Gray), a plant native to semi-arid regions of northern Mexico and southern Texas in the United States, is an alternative source for natural rubber (NR). Rapid screening tools are...

Authors: Zinan Luo, Kelly R. Thorp and Hussein Abdel-Haleem

X-ray microtomography and linear discriminant analysis enable detection of embolism-related acoustic emissions

Acoustic emission (AE) sensing is in use since the late 1960s in drought-induced embolism research as a non-invasive and continuous method. It is very well suited to assess a plant’s vulnerability to dehydrati...

Authors: Niels J. F. De Baerdemaeker, Michiel Stock, Jan Van den Bulcke, Bernard De Baets, Luc Van Hoorebeke and Kathy Steppe

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

In the original publication of the article [1], a few errors were identified.

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

A protocol for laser microdissection (LMD) followed by transcriptome analysis of plant reproductive tissue in phylogenetically distant angiosperms

Plant development is controlled by the action of many, often connected gene regulatory networks. Differential gene expression controlled by internal and external cues is a major driver of growth and time speci...

Authors: Kimmo Kivivirta, Denise Herbert, Matthias Lange, Knut Beuerlein, Janine Altmüller and Annette Becker

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