Article
Agronomy
Lejun Yu, Jiawei Shi, Chenglong Huang, Lingfeng Duan, Di Wu, Debao Fu, Changyin Wu, Lizhong Xiong, Wanneng Yang, Qian Liu
Summary: Rice panicle phenotyping is crucial in rice breeding, allowing for the evaluation of spikelet and kernel traits using X-ray and RGB scanning to improve accuracy and speed of analysis, benefiting rice breeding efforts.
Review
Biochemistry & Molecular Biology
Elizabeth A. Kellogg
Summary: This review focuses on the genetic and regulatory mechanisms of inflorescence branching in grasses, primarily based on data from rice and maize. The placement and development of primary branches are controlled by conserved auxin regulatory genes, while subtending bracts are repressed by a network of genes including TASSELSHEATH4. Axillary branch meristems are regulated by signaling centers adjacent to the meristems themselves. The production of spikelets is governed by gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators.
Review
Plant Sciences
Robert D. Hall, John C. D'Auria, Antonio C. Silva Ferreira, Yves Gibon, Dariusz Kruszka, Puneet Mishra, Rick van de Zedde
Summary: High-throughput plant phenotyping approaches are rapidly developing and helping bridge the genotype-phenotype gap. Metabolites play a crucial role in defining key physiological and agronomic traits in plants. Despite challenges, novel technological innovations have the potential to fully integrate metabolomics approaches into plant phenotyping pipelines in the near future.
TRENDS IN PLANT SCIENCE
(2022)
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)
Review
Plant Sciences
Alebel Mekuriaw Abebe, Younguk Kim, Jaeyoung Kim, Song Lim Kim, Jeongho Baek
Summary: Plant phenotyping plays a vital role in plant breeding programs by selecting genotypes with desirable traits. The current techniques for phenotyping are time-consuming and destructive. However, the development of imaging platforms and sensors has revolutionized high-throughput phenotyping studies. This review focuses on the trends and applications of image-based phenotyping methods in horticultural crops, highlighting the advantages and limitations of different imaging platforms and techniques. It also emphasizes the potential of high-throughput phenotyping in discovering new phenotypic traits for future exploration.
Article
Plant Sciences
Guofang Zhang, Jinzhi Zhou, Yan Peng, Zengdong Tan, Yuting Zhang, Hu Zhao, Dongxu Liu, Xiao Liu, Long Li, Liangqian Yu, Cheng Jin, Shuai Fang, Jiawei Shi, Zedong Geng, Shanjing Yang, Guoxing Chen, Kede Liu, Qingyong Yang, Hui Feng, Liang Guo, Wanneng Yang
Summary: Salt stress affects the survival and growth of crops, and understanding the genetic resources related to salt stress tolerance in Brassica napus is important. This study quantified the salt stress tolerance of B. napus using a high-throughput phenotyping platform and identified candidate genes associated with salt stress response through genome-wide association study and linkage analysis.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Agronomy
Liang Gong, Xiaofeng Du, Kai Zhu, Ke Lin, Qiaojun Lou, Zheng Yuan, Guoqiang Huang, Chengliang Liu
Summary: Automated measurement of crop phenotypic parameters is important for quantitative crop growth research. However, segmentation of crop spike-shaped point clouds faces various challenges. This study introduces a 3D point cloud convolutional neural network model called Panicle-3D, which achieves higher segmentation accuracy at multiple scales and is suitable for different crop point cloud segmentation tasks.
Article
Agronomy
Junfeng Chen, Yun Wang, Peng Di, Yulong Wu, Shi Qiu, Zongyou Lv, Yuqi Qiao, Yajing Li, Jingfu Tan, Weixu Chen, Ma Yu, Ping Wei, Ying Xiao, Wansheng Chen
Summary: Plant phenomics aims to accurately measure plant traits for crop breeding. In this study, a framework utilizing image feature extraction software was developed to analyze the phenotypic components of Salvia miltiorrhiza roots, providing an important approach for grading medicinal materials and breeding practices.
Article
Environmental Sciences
Anjin Chang, Jinha Jung, Junho Yeom, Juan Landivar
Summary: This study developed a method for detecting and characterizing individual sorghum panicles using a 3D point cloud derived from UAV images, and proposed strategies to estimate panicle volumes. Experimental results showed a high correlation between UAV-derived panicle parameters and ground measurements, providing important information for studying genetic diversity and yield estimation in sorghum.
Article
Fisheries
Milena Freitas, Celma G. Lemos, Raquel B. Ariede, John F. G. Agudelo, Rubens R. O. Neto, Carolina H. S. Borges, Vito A. Mastrochirico-Filho, Fabio Porto-Foresti, Rogerio L. Iope, Fabricio M. Batista, Jose R. F. Brega, Diogo T. Hashimoto
Summary: This study developed a computer vision system (CVS) using deep learning to predict body shape in fish. Through the analysis of pacu, it was found that morphotypes vary according to the environment, sex, and age. The genetic parameters for body shape indicate that this trait is moderately controlled by genetics and can be altered through selection.
Article
Plant Sciences
Yanwei Li, Xinyi Wu, Wenzhao Xu, Yudong Sun, Ying Wang, Guojing Li, Pei Xu
Summary: Phenomics is a new branch of science that quantifies plant and animal traits at the systems level, with challenges remaining in precise phenotyping of physiological traits. High-throughput physiology-based phenotyping, or physiolomics, for drought stress responses is highlighted in this review, emphasizing the need for routine physiological assays for phenotyping stress response traits in horticultural plants.
HORTICULTURAL PLANT JOURNAL
(2021)
Article
Ecology
Moritz D. Luerig
Summary: Digital images are widely used by biologists to capture and analyze organismal phenotypes. phenopype is a high-throughput phenotyping pipeline for Python that aims to extract high-dimensional phenotypic data from digital images efficiently. It provides functions for image preprocessing, segmentation, data extraction, visualization, and data export, facilitating scientific image analysis for biologists with little coding experience. This software helps in increasing the speed and reproducibility of data collection, making it a valuable tool for researchers in ecological, evolutionary, and developmental biology.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Review
Cell Biology
Stephan Handschuh, Martin Gloesmann
Summary: Microscopic X-ray computed tomography (microCT) is a non-destructive imaging technique that provides high-resolution 3D images of biological samples. Staining with X-ray dense contrast agents allows for high-contrast imaging of whole embryos and specific organ systems. This technique has significant applications in qualitative and quantitative phenotyping of mouse development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Agronomy
Yinglun Li, Weiliang Wen, Jiangchuan Fan, Wenbo Gou, Shenghao Gu, Xianju Lu, Zetao Yu, Xiaodong Wang, Xinyu Guo
Summary: This study collected high-throughput, time-series raw data of field maize populations using a field rail-based phenotyping platform with LiDAR and an RGB camera. The orthorectified images and LiDAR point clouds were aligned using the direct linear transformation algorithm, and time-series point clouds were registered using time-series image guidance. The cloth simulation filter algorithm was then used to remove ground points, and individual plants and plant organs were segmented from the maize population. The plant heights obtained using the multi-source fusion data were highly correlated with manual measurements (R2 = 0.98), demonstrating the effectiveness of multi-source data fusion in improving the accuracy of time series phenotype extraction.
Article
Agronomy
Jidong Wang, Yinglong Chen, Yongen Zhang, Yongchun Zhang, Yuchun Ai, Yupeng Feng, David Moody, Art Diggle, Paul Damon, Zed Rengel
Summary: Barley is an important cereal crop, but its sustainable production is hindered by various edaphic stresses. Studying the variability in root morphological traits among different barley genotypes is crucial for breeding cultivars better adapted to stress environments. This study identified phenotypic variability in root morphological traits in barley genotypes in the early growth stage, providing a basis for selecting breeding lines with optimal root properties for efficient soil resource acquisition and stress adaptation.
Review
Plant Sciences
Marcus Griffiths, Benjamin M. Delory, Vanessica Jawahir, Kong M. Wong, G. Cody Bagnall, Tyler G. Dowd, Dmitri A. Nusinow, Allison J. Miller, Christopher N. Topp
Summary: Roots play a central role in the interaction between plants and soil, contributing to multiple ecosystem processes. Cover crops can be used to restore soil health and provide ecosystem services. However, breeding for improved root traits in these crops has been limited, resulting in variations in the effectiveness of their ecosystem services. Advancements in root phenotyping and genetic tools are crucial in enhancing agricultural sustainability through improving cover crop root traits.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Plant Sciences
Keith E. Duncan, Kirk J. Czymmek, Ni Jiang, August C. Thies, Christopher N. Topp
Summary: This study presents technical advances in using lab-based X-ray microscopy for high-resolution 3D imaging of plant samples at multiple scales. Serial imaging and improved sample preparation methods allow for the generation of sub-micron 3D volumes co-registered with lower magnification scans, providing explicit contextual reference. This method bridges the imaging gap between light and electron microscopy and can be applied to various economically and scientifically important plant systems.
Article
Plant Sciences
Kevin L. Cox, Sai Guna Ranjan Gurazada, Keith E. Duncan, Kirk J. Czymmek, Christopher N. Topp, Blake C. Meyers
Summary: Plant cells communicate through transcriptional regulation and gene networks to control development and respond to external stresses. Acquiring high resolution, multi-dimensional spatial transcriptomic data and placing it within a cellular and organismal context is crucial for understanding gene regulation across plant tissues and organs. Combining spatial transcriptomics with 3D imaging technologies can provide insights into how genes are regulated in a multi-dimensional space.
Article
Plant Sciences
Watchara Arthan, Vanezza Morales-Fierro, Maria S. Vorontsova, Elizabeth A. Kellogg, Jonathan Mitchley, Caroline E. R. Lehmann
Summary: This study investigates the habitat preferences of grassland/savanna and wetland species within the Heteropogon-Themeda clade by describing bioclimatic niche characteristics, functional traits, and evolutionary history. The unique bioclimatic niche of wetland species and differences in functional traits between wetland and grassland/savanna species were highlighted. Climatic factors alone do not fully explain the geographic distributions of species.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Plant Sciences
Robert J. Soreng, Paul M. Peterson, Fernando O. Zuloaga, Konstantin Romaschenko, Lynn G. Clark, Jordan K. Teisher, Lynn J. Gillespie, Patricia Barbera, Cassiano A. D. Welker, Elizabeth A. Kellogg, De-Zhu Li, Gerrit Davidse
Summary: This article presents an updated worldwide phylogenetic classification of the Poaceae family, including detailed information on species numbers, genera, tribes, and subfamilies, as well as proposing new names and combinations.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Plant Sciences
Timothy J. Gallaher, Paul M. Peterson, Robert J. Soreng, Fernando O. Zuloaga, De-Zhu Li, Lynn G. Clark, Christopher D. Tyrrell, Cassiano A. D. Welker, Elizabeth A. Kellogg, Jordan K. Teisher
Summary: Grasses are widely distributed and have significant impacts on Earth's climate, geochemistry, and biodiversity. By using DNA sequence data and fossil records, we can reassess the origins, timing, geographic spread, and diversification drivers of the grass family.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Review
Multidisciplinary Sciences
Paula McSteen, Elizabeth A. Kellogg
Summary: Grasses have been cultivated by humans for various purposes for thousands of years. They have adapted and diversified into approximately 12,000 species, with different genes and traits selected in different crop species. Research on the molecular, cellular, and developmental bases of grain yield and dispersal in grasses is ongoing, and with increasing genomic resources, we expect to gain more insights into their ecological and economic success.
Review
Plant Sciences
Kurt B. Petersen, Elizabeth A. Kellogg
Summary: Grass awns, the long outgrowths of the floral bracts in a grass spikelet, have diverse forms and functions across the Poaceae family. They have been repeatedly gained and lost in evolutionary history, suggesting their potential adaptive benefit in different environments. Awns are believed to aid in dispersal, protect seeds, and even contribute to photosynthesis in some species. However, studies on awn function lack phylogenetic information and alternative hypotheses, resulting in a biased understanding of their adaptive convergent evolution.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Computer Science, Software Engineering
D. Zeng, E. Chambers, D. Letscher, T. Ju
Summary: This study presents a method for removing unwanted topological features from a sequence of nested shapes, and demonstrates its effectiveness and superiority through empirical evaluation.
COMPUTER GRAPHICS FORUM
(2022)
Article
Plant Sciences
Katherine M. Murphy, Tyler Dowd, Ahmed Khalil, Si Nian Char, Bing Yang, Benjamin J. Endelman, Patrick M. Shih, Christopher Topp, Eric A. Schmelz, Philipp Zerbe
Summary: In maize, two major groups of specialized metabolites, kauralexins and dolabralexins, are involved in defending against pathogens, herbivores, and other stressors. This study examined the dolabralexin pathway and found new metabolites and characterized their production. Genetic analysis showed that dolabralexin biosynthesis occurs mainly in primary roots and varies across different maize lines. Loss-of-function mutants for the diterpene synthase gene ZmKSL4 demonstrated deficient dolabralexin production and exhibited altered root architecture in response to water deficit. These findings suggest that maize dolabralexins play a role in plant vigor during abiotic stress.
Article
Plant Sciences
Yunqing Yu, Getu Beyene, Justin Villmer, Keith E. Duncan, Hao Hu, Toni Johnson, Andrew N. Doust, Nigel J. Taylor, Elizabeth A. Kellogg
Summary: This study investigates the shattering mechanism in E. tef and finds that it differs significantly from other cereals, as it relies on programmed cell death and fracture of the cell walls. These findings lay the groundwork for understanding grain shattering in Eragrostis and improving shattering in E. tef.
Article
Plant Sciences
Yunqing Yu, Hao Hu, Daniel F. Voytas, Andrew N. Doust, Elizabeth A. Kellogg
Summary: Abscission is regulated by abscission zone (AZ) genes, and in Setaria, a domestication gene called SH1 plays a role in abscission activation through auxin signaling. The sh1 mutant lacks shattering, and there are no observable differences in cell anatomy or cell wall components between sh1 and the wild-type until abscission occurs. Auxin distribution and expression of auxin-related genes differ between WT and sh1, indicating the requirement of SH1 for auxin signaling in Setaria.
Article
Biodiversity Conservation
Taylor AuBuchon-Elder, Patrick Minx, Bess Bookout, Elizabeth A. A. Kellogg
Summary: The rapid rate of global biodiversity loss necessitates more efficient and thorough extinction risk assessments in plants, even with limited knowledge. This study demonstrates the significance of large-scale preliminary conservation assessments in accelerating plant conservation efforts and prioritizing further investigations, using the Andropogoneae grass tribe as a case study.
PLANTS PEOPLE PLANET
(2023)
Article
Biodiversity Conservation
Maria S. Vorontsova, Kurt B. Petersen, Patrick Minx, Taylor M. Aubuchon-Elder, M. Cinta Romay, Edward S. Buckler, Elizabeth A. Kellogg
Summary: The genus Andropogon sensu lato is polyphyletic. This study adjusts its classification and reestablishes the genus Anatherum. Plastome phylogeny and morphological diversity were assessed to understand the evolutionary history and distinguishing features of Andropogon sensu lato.
SYSTEMATICS AND BIODIVERSITY
(2023)
Review
Biochemistry & Molecular Biology
Elizabeth A. Kellogg
Summary: This review focuses on the genetic and regulatory mechanisms of inflorescence branching in grasses, primarily based on data from rice and maize. The placement and development of primary branches are controlled by conserved auxin regulatory genes, while subtending bracts are repressed by a network of genes including TASSELSHEATH4. Axillary branch meristems are regulated by signaling centers adjacent to the meristems themselves. The production of spikelets is governed by gradients of SQUAMOSA-PROMOTER BINDING-like and APETALA2-like proteins and their microRNA regulators.