Review
Biochemistry & Molecular Biology
Minsu Kim, Chaewon Lee, Subin Hong, Song Lim Kim, Jeong-Ho Baek, Kyung-Hwan Kim
Summary: Understanding plant responses to drought stress is crucial, and high-throughput phenotyping (HTP) has emerged as a promising method to address the limitations in genomic and phenomic studies. HTP provides researchers with a non-destructive and accurate way to analyze large-scale phenotypic data, making it an increasingly popular tool in studying plant traits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Sayantan Sarkar, Alexandre-Brice Cazenave, Joseph Oakes, David McCall, Wade Thomason, Lynn Abbott, Maria Balota
Summary: This study introduces novel models for rapid estimation of peanut leaf area index (LAI) and lateral growth (LG) using UAV-collected leaf reflectance data, and for predicting pod yield. The models are effective in identifying phenotypic differences among genotypes and can be used for selecting peanut varieties with desirable LAI, LG, and yield.
SCIENTIFIC REPORTS
(2021)
Article
Environmental Sciences
Mariam K. Al-Lami, Dane Nguyen, Nadege Oustriere, Joel G. Burken
Summary: Historical hard-rock mine activities have left almost half a million mining-impacted sites across the US, with phytostabilization being a cost-effective method. Utilizing PlantCV technology in greenhouse studies can identify potential native species for restoration of mine-impacted sites.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Plant Sciences
Mia Ruppel, Sven K. Nelson, Grace Sidberry, Madison Mitchell, Daniel Kick, Shawn K. Thomas, Katherine E. Guill, Melvin J. Oliver, Jacob D. Washburn
Summary: Higher temperatures causing more frequent and severe droughts have negative impacts on agricultural crops. RootBot, an automated high-throughput phenotyping robot, provides an efficient solution for studying root growth under drought conditions, aiding in understanding drought tolerance mechanisms and identifying targets for crop breeding and genetic engineering.
APPLICATIONS IN PLANT SCIENCES
(2023)
Article
Plant Sciences
David Eyland, Nathalie Luchaire, Llorenc Cabrera-Bosquet, Boris Parent, Steven B. Janssens, Rony Swennen, Claude Welcker, Francois Tardieu, Seabstien C. Carpentier
Summary: This study evaluated genotype-dependent transpiration responses in banana wild relatives and found that they contain useful drought tolerance traits. The research highlights the importance of conserving these wild relatives and their potential for use in breeding programs.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Priyanka Dwivedi, Naleeni Ramawat, Dhandapani Raju, Gaurav Dhawan, S. Gopala Krishnan, Viswanathan Chinnusamy, Prolay Kumar Bhowmick, K. K. Vinod, Madan Pal, Mariappan Nagarajan, Ranjith Kumar Ellur, Haritha Bollinedi, Ashok K. Singh
Summary: This study utilized state-of-the-art image-based phenotyping techniques to evaluate drought tolerance in rice, providing a new approach to tackle reproductive stage drought stress. The research identified specific quantitative trait loci that play a key role in improving rice's drought tolerance and identified near-isogenic lines with higher drought tolerance. The findings suggest that selection criteria based on phenomics traits can assess rice's drought tolerance at an early stage.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Nathan T. Hein, Ignacio A. Ciampitti, S. V. Krishna Jagadish
Summary: The flowering and grain-filling stages of crops are sensitive to heat and drought stress, affecting yields. Remote sensing offers low-cost, high-throughput phenotyping methods to enhance crop resilience to stress.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Agronomy
Habtamu Demelash, Taye Tadesse, Temesgen Menamo, Ahadu Menzir
Summary: Sorghum bicolor is an important cereal crop in Ethiopia, but its productivity is hindered by drought. This study assessed the genetic variability of 214 sorghum genotypes for root and shoot traits, finding that Ethiopian Biodiversity and ICRISAT genotypes displayed more genetic diversity in root system architecture traits. Phenotypic and genotypic coefficient variations varied among traits, with broad sense heritability ranging from 40% to 94.18%. The findings can help identify promising genotypes with suitable root traits for potential breeding under specific environmental conditions.
Review
Agronomy
Daniel T. Smith, Andries B. Potgieter, Scott C. Chapman
Summary: High-throughput phenotyping (HTP) and envirotyping technologies can address challenges brought by climate change in crop breeding, enabling rapid and accurate assessment of large breeding populations by measuring the morphological, biochemical, and physiological traits of vegetation to breed varieties that are adapted to specific environments.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Andrea Genangeli, Giovanni Avola, Marco Bindi, Claudio Cantini, Francesco Cellini, Stefania Grillo, Angelo Petrozza, Ezio Riggi, Alessandra Ruggiero, Stephan Summerer, Anna Tedeschi, Beniamino Gioli
Summary: Recent developments in low-cost imaging hyperspectral cameras have opened up new possibilities for high-throughput phenotyping. This study integrated a low-cost hyperspectral camera into an HTP platform to evaluate the drought stress resistance and physiological response of four tomato genotypes. The study collected over 120 gigabytes of hyperspectral data and developed an innovative segmentation method to reduce the dataset. The results showed the better capacity of the hyperspectral index to describe the dynamic of drought stress trend compared to optical indices, while the selected optical indices were capable of describing structural changes during plant growth.
Article
Plant Sciences
Long Chen, Matthias Daub, Hans-Georg Luigs, Marcus Jansen, Martin Strauch, Dorit Merhof
Summary: This study introduces a high-throughput system based on computer vision for quantifying beet cyst nematode infestation and measuring cyst phenotypic traits. The computer vision approach accurately counts and segments nematode cysts, allowing for the identification of phenotypic differences between nematode populations in different soils and planting periods.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Environmental Sciences
Tom De Swaef, Wouter H. Maes, Jonas Aper, Joost Baert, Mathias Cougnon, Dirk Reheul, Kathy Steppe, Isabel Roldan-Ruiz, Peter Lootens
Summary: This study demonstrates the potential of UAV-based remote sensing to complement or replace traditional visual breeder scoring, allowing for high-throughput field phenotyping applications. The use of thermal sensors provides complementary information to visual-based indices, enabling the analysis of ecophysiological mechanisms under drought stress. Variability in drought tolerance among different species/types of forage grasses confirms the potential for selection within these groups.
Article
Plant Sciences
Judith Scharte, Sebastian Hassa, Cornelia Herrfurth, Ivo Feussner, Giuseppe Forlani, Engelbert Weis, Antje von Schaewen
Summary: This study investigated the basis for the improved performance of transgenic tobacco plants with G6PDH-isoenzyme replacement. The results showed that these plants had accelerated defense responses against a pathogen, mainly through metabolic adjustments involving increased levels of soluble sugars, starch, and lipids. The transgenic plants also exhibited increased seed yields, enhanced tolerance to abiotic stress, and improved photosynthetic efficiency.
Article
Plant Sciences
Pedro M. P. Correia, Jesper Cairo Westergaard, Anabela Bernardes da Silva, Thomas Roitsch, Elizabete Carmo-Silva, Jorge Marques da Silva
Summary: Interannual and local fluctuations in wheat crop yield are primarily influenced by abiotic constraints such as heatwaves and drought. This study aimed to identify phenotypic traits that contribute to adaptive stress responses in wheat under water deficit and high temperature conditions. High-throughput methods were used to phenotype 10 wheat genotypes, and regression machine learning models successfully predicted plant biomass based on image-extracted parameters. The study highlights the importance of transpiration efficiency and the interplay between carbohydrate metabolism and antioxidant metabolism in wheat's stress tolerance. The observed genetic differences can be utilized in breeding programs to enhance wheat resilience to climate change.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Jana Ebersbach, Nazifa Azam Khan, Ian McQuillan, Erin E. Higgins, Kyla Horner, Venkat Bandi, Carl Gutwin, Sally Lynne Vail, Steve J. Robinson, Isobel A. P. Parkin
Summary: Phenotyping is important for crop improvement. This study assesses the feasibility of using high-throughput phenotyping, image processing, and machine learning to capture the phenotypic diversity of agronomically important traits in Brassica napus. The results demonstrate the potential of machine learning for phenotyping studies, particularly for complex traits such as drought stress resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Daniel Pflugfelder, Johannes Kochs, Robert Koller, Siegfried Jahnke, Carola Mohl, Shree Pariyar, Heike Fassbender, Kerstin A. Nagel, Michelle Watt, Dagmar van Dusschoten, Hideki Takahashi
Summary: This study investigated seedling establishment in winter wheat using MRI technology. The results showed that the timing of root and shoot emergence, as well as the length, angle, and depth of axile roots, significantly varied among different genotypes. The study also demonstrated the importance of root initiation and elongation rates for the root system architecture of wheat seedlings.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Helga Ochagavia, Tibor Kiss, Ildiko Karsai, Ana M. Casas, Ernesto Igartua
Summary: Climate change-induced rising temperatures affect cereal crop development. This study explored the developmental responses of barley to temperature increase and identified the interaction between flowering time, vernalization, and specific genes. The findings provide valuable information for breeding high-yielding cultivars adapted to future climatic conditions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Kathryn Dumschott, Nathalie Wuyts, Christian Alfaro, Dalma Castillo, Fabio Fiorani, Andres Zurita-Silva
Summary: Quinoa is a genetically diverse crop that can tolerate abiotic stresses and has gained popularity due to its high nutritional content. The coastal lowland ecotype of quinoa is of interest for cultivation in higher latitudes. A field experiment in Chile showed that some lines of coastal lowland self-pollinated (CLS) quinoa had higher yield and seed size than the commercial cultivar Regalona, even under reduced irrigation. Proximal sensing methods, such as thermal and hyperspectral imaging, were used to estimate plant water use and differences in photosynthesis among the lines.
Article
Plant Sciences
Miriam Fernandez-Calleja, Francisco J. Ciudad, Ana M. Casas, Ernesto Igartua
Summary: This study investigates the vernalization sensitivity and phenotypic characteristics of barley in order to adapt to future climate change. The results show that the vernalization response in barley is mainly concentrated in the phase before stem elongation, and is influenced by multiple major genes. Additionally, the duration of the late reproductive phase is also affected by other genes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Essam A. Z. ElShamey, Hassan Sh Hamad, Khalid S. Alshallash, Mousa A. Alghuthaymi, Mohamed Ghazy, Raghda M. Sakran, Mahmoud E. Selim, Mahmoud A. A. ElSayed, Taher M. Abdelmegeed, Salah A. Okasha, Said Behiry, Ridha Boudiar, Elsayed Mansour
Summary: This study aimed to explore the impact of exogenous plant growth regulators on floral traits and outcrossing rates in rice CMS lines. The results showed that the combination of GA(3), IAA, and NAA significantly improved floral, growth, and yield traits in all tested CMS lines, especially for promising lines such as L2, L3, and L1.
Article
Agronomy
Miriam Fernandez-Calleja, Christophe Boutin, Emmanuelle Dyrszka, Yann Manes, Jochen C. Reif, Yusheng Zhao, Nieves Aparicio, Francisco J. Ciudad, Ana M. Casas, Ernesto Igartua
Summary: This study investigates the potential of Spanish germplasm for creating hybrids suitable for southern Europe, an untapped region for hybrid barley. A total of 140 locally adapted, advanced breeding lines from a Spanish breeding program were examined to expand the germplasm options for hybrid barley development. Through field trials and genomic predictions, lines with high general combining ability were identified for potential two-way hybrid production. The presence of brittle mutations in hybrid combinations, discovered through field trials, underscored the need for further research on heterotic patterns and proper management of brittle genes to broaden the germplasm pool for hybrid barley breeding.
Article
Plant Sciences
Gianluca Bretani, Salar Shaaf, Alessandro Tondelli, Luigi Cattivelli, Stefano Delbono, Robbie Waugh, William Thomas, Joanne Russell, Hazel Bull, Ernesto Igartua, Ana M. M. Casas, Pilar Gracia, Roberta Rossi, Alan H. H. Schulman, Laura Rossini
Summary: In this study, a total of 261 barley accessions were phenotyped for culm diameter and culm wall thickness using an image analysis-based protocol. Genome-wide association studies revealed 192 quantitative trait loci (QTLs) associated with these traits, including 21 loci that impact lodging without affecting plant height. This research provides insights into the genetic control of culm morphology in barley and highlights the potential for improving lodging resistance and yield stability.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Green & Sustainable Science & Technology
Ridha Boudiar, Khalid S. Alshallash, Khadiga Alharbi, Salah A. Okasha, Mohammed Fenni, Abdelhamid Mekhlouf, Bilal Fortas, Keirieddine Hamsi, Kamel Nadjem, Abdennour Belagrouz, Elsayed Mansour, Mahfoud Mekhlouf
Summary: Conservation agriculture can improve soil nutrient content, but it may lead to increased soil bulk density and decreased water infiltration rate. Different cropping systems have an impact on soil properties and agronomic performance, with lower soil nutrient content in continuous cropping systems and mono-cropping systems under conventional tillage.
Article
Plant Sciences
Laura Schmidt, Kerstin A. Nagel, Anna Galinski, Wiebke Sannemann, Klaus Pillen, Andreas Maurer
Summary: This study analyzed the genetic control of root system architecture in a winter wheat population under different nitrogen treatments. The research found that 60 quantitative trait loci were specific to nitrogen treatments. Additionally, this study revealed a disparity in the genetic control of root development under low and high nitrogen supply, suggesting the need for targeted gene selection in breeding wheat varieties with improved nitrogen uptake efficiency.
Review
Plant Sciences
Gustavo A. Slafer, Ana M. Casas, Ernesto Igartua
Summary: This article reviews the contrasting meaning of photoperiod insensitivity for wheat and barley, examines its molecular bases, and provides recommendations for managing this trait in research.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Agronomy
Nahid A. A. Morsi, Omnia S. M. Hashem, Mohamed A. Abd El-Hady, Yasser M. M. Abd-Elkrem, Mohamed E. E. El-temsah, Elhussin G. G. Galal, Khaled I. I. Gad, Ridha Boudiar, Cristina Silvar, Salah El-Hendawy, Elsayed Mansour, Mohamed A. A. Abdelkader
Summary: Drought is a major abiotic stress that affects canola growth, production, and quality. Developing drought-tolerant and high-yielding canola genotypes is critical for sustaining production and ensuring global food security. This study evaluated ten canola genotypes under different irrigation regimes and found that certain tissue-cultured and exotic genotypes performed better than commercial cultivars under water-deficit conditions.
Article
Plant Sciences
Mohamed E. El-temsah, Yasser M. Abd-Elkrem, Yasser A. El-Gabry, Mohamed A. Abdelkader, Nahid A. A. Morsi, Noura M. Taha, Shaimaa H. Abd-Elrahman, Fadl A. E. Hashem, Mostafa G. Shahin, Gomaa A. Abd El-Samad, Ridha Boudiar, Cristina Silvar, Salah El-Hendawy, Elsayed Mansour, Mohamed A. Abd El-Hady
Summary: This study assessed the effects of different calcium fertilizers on the growth, yield, and quality traits of peanuts. The results showed that foliar-applied nano-calcium combined with calcium nitrate or calcium sulfate had superior effects on peanut growth and yield. Additionally, the peanut cultivar Giza-6 exhibited better performance compared to the other cultivars. The research highlights the importance of calcium application for peanut cultivation, particularly in sandy soil with high pH.
Article
Biotechnology & Applied Microbiology
Bruno Contreras-Moreira, Shradha Saraf, Guy Naamati, Ana M. Casas, Sandeep S. Amberkar, Paul Flicek, Andrew R. Jones, Sarah Dyer
Summary: This study proposes a crop pangenome approach using individual cultivar assemblies to access conserved genes more easily. However, the variability in genome content and inconsistent identifiers have hindered exploration. To overcome these challenges, the concept of pangenes is introduced to summarize a species coding potential and link back to original annotations. The protocol get_pangenes utilizes whole genome alignments to identify syntenic gene models based on coordinate overlaps. Benchmark tests with both small and large plant genomes demonstrate that pangenes accurately recapitulate phylogeny-based orthologies and generate complete soft-core gene sets.
