Plant Phenomics Indexed in SCIE!
The journal has been indexed in Web of Science - Science Citation Index Expanded and is expected to receive its first Journal Impact Factor in 2022.See full indexing coverage
The open access journal Plant Phenomics, published in association with NAU, publishes novel research that advances plant phenotyping and connects phenomics with other research domains.
Plant Phenomics' editorial board is led by Seishi Ninomiya (University of Tokyo), Frédéric Baret (French National Research Institute for Agriculture, Food and Environment), and Zong-Ming Cheng (Nanjing Agricultural University/University of Tennessee) and is comprised of leading experts in the field.
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Robust High-Throughput Phenotyping with Deep Segmentation Enabled by a Web-Based Annotator
The abilities of plant biologists and breeders to characterize the genetic basis of physiological traits are limited by their abilities to obtain quantitative data representing precise details of trait variation, and particularly to collect this data at a high-throughput scale with low cost. Although deep learning methods have demonstrated unprecedented potential to automate plant phenotyping, these methods commonly rely on large training sets that can be time-consuming to generate. Intelligent algorithms have therefore been proposed to enhance the productivity of these annotations and reduce human efforts. We propose a high-throughput phenotyping system which features a Graphical User Interface (GUI) and a novel interactive segmentation algorithm: Semantic-Guided Interactive Object Segmentation (SGIOS). By providing a user-friendly interface and intelligent assistance with annotation, this system offers potential to streamline and accelerate the generation of training sets, reducing the effort required by the user. Our evaluation shows that our proposed SGIOS model requires fewer user inputs compared to the state-of-art models for interactive segmentation. As a case study of the use of the GUI applied for genetic discovery in plants, we present an example of results from a preliminary genome-wide association study (GWAS) of in planta regeneration in Populus trichocarpa (poplar). We further demonstrate that the inclusion of a semantic prior map with SGIOS can accelerate the training process for future GWAS, using a sample of a dataset extracted from a poplar GWAS of in vitro regeneration. The capabilities of our phenotyping system surpass those of unassisted humans to rapidly and precisely phenotype our traits of interest. The scalability of this system enables large-scale phenomic screens that would otherwise be time-prohibitive, thereby providing increased power for GWAS, mutant screens, and other studies relying on large sample sizes to characterize the genetic basis of trait variation. Our user-friendly system can be used by researchers lacking a computational background, thus helping to democratize the use of deep segmentation as a tool for plant phenotyping.
Evaluation of Postharvest Senescence of Broccoli via Hyperspectral Imaging
Fresh fruit and vegetables are invaluable for human health; however, their quality often deteriorates before reaching consumers due to ongoing biochemical processes and compositional changes. We currently lack any objective indices which indicate the freshness of fruit or vegetables resulting in limited capacity to improve product quality eventually leading to food loss and waste. In this conducted study, we hypothesized that certain proteins and compounds, such as glucosinolates, could be used as one potential indicator to monitor the freshness of broccoli following harvest. To support our study, glucosinolate contents in broccoli based on HPLC measurement and transcript expression of glucosinolate biosynthetic genes in response to postharvest stresses were evaluated. We found that the glucosinolate biosynthetic pathway coincided with the progression of senescence in postharvest broccoli during storage. Additionally, we applied machine learning-based hyperspectral image (HSI) analysis, unmixing, and subpixel target detection approaches to evaluate glucosinolate level to detect postharvest senescence in broccoli. This study provides an accessible approach to precisely estimate freshness in broccoli through machine learning-based hyperspectral image analysis. Such a tool would further allow significant advancement in postharvest logistics and bolster the availability of high-quality, nutritious fresh produce.
Enabling Breeding Selection for Biomass in Slash Pine Using UAV-Based Imaging
Traditional methods used to monitor the aboveground biomass (AGB) and belowground biomass (BGB) of slash pine (Pinus elliottii) rely on on-ground measurements, which are time- and cost-consuming and suited only for small spatial scales. In this paper, we successfully applied unmanned aerial vehicle (UAV) integrated with structure from motion (UAV-SfM) data to estimate the tree height, crown area (CA), AGB, and BGB of slash pine for in slash pine breeding plantations sites. The CA of each tree was segmented by using marker-controlled watershed segmentation with a treetop and a set of minimum three meters heights. Moreover, the genetic variation of these traits has been analyzed and employed to estimate heritability (). The results showed a promising correlation between UAV and ground truth data with a range of from 0.58 to 0.85 at 70 m flying heights and a moderate estimate of for all traits ranges from 0.13 to 0.47, where site influenced the value of slash pine trees, where in site 1 ranged from 0.13~0.25 lower than that in site 2 (range: 0.38~0.47). Similar genetic gains were obtained with both UAV and ground truth data; thus, breeding selection is still possible. The method described in this paper provides faster, more high-throughput, and more cost-effective UAV-SfM surveys to monitor a larger area of breeding plantations than traditional ground surveys while maintaining data accuracy.
Estimating Photosynthetic Attributes from High-Throughput Canopy Hyperspectral Sensing in Sorghum
Sorghum, a genetically diverse C4 cereal, is an ideal model to study natural variation in photosynthetic capacity. Specific leaf nitrogen (SLN) and leaf mass per leaf area (LMA), as well as, maximal rates of Rubisco carboxylation (), phosphoenolpyruvate (PEP) carboxylation (), and electron transport (), quantified using a C4 photosynthesis model, were evaluated in two field-grown training sets ( plots including 124 genotypes) in 2019 and 2020. Partial least square regression (PLSR) was used to predict (), (), (), SLN (), and LMA () from tractor-based hyperspectral sensing. Further assessments of the capability of the PLSR models for , , , SLN, and LMA were conducted by extrapolating these models to two trials of genome-wide association studies adjacent to the training sets in 2019 ( plots including 650 genotypes) and 2020 ( plots with 634 genotypes). The predicted traits showed medium to high heritability and genome-wide association studies using the predicted values identified four QTL for and two QTL for . Candidate genes within 200 kb of the QTL were involved in nitrogen storage, which is closely associated with Rubisco, while not directly associated with Rubisco activity per se. QTL was enriched for candidate genes involved in electron transport. These outcomes suggest the methods here are of great promise to effectively screen large germplasm collections for enhanced photosynthetic capacity.
Objective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.)
Active breeding programs specifically for root system architecture (RSA) phenotypes remain rare; however, breeding for branch and taproot types in the perennial crop alfalfa is ongoing. Phenotyping in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root types. While image-based methods have been developed, translation to applied breeding is limited. This research is aimed at developing and comparing image-based RSA phenotyping methods using machine and deep learning algorithms for objective classification of 617 root images from mature alfalfa plants collected from the field to support the ongoing breeding efforts. Our results show that unsupervised machine learning tends to incorrectly classify roots into a normal distribution with most lines predicted as the intermediate root type. Encouragingly, random forest and TensorFlow-based neural networks can classify the root types into branch-type, taproot-type, and an intermediate taproot-branch type with 86% accuracy. With image augmentation, the prediction accuracy was improved to 97%. Coupling the predicted root type with its prediction probability will give breeders a confidence level for better decisions to advance the best and exclude the worst lines from their breeding program. This machine and deep learning approach enables accurate classification of the RSA phenotypes for genomic breeding of climate-resilient alfalfa.
Prediction of the Maturity of Greenhouse Grapes Based on Imaging Technology
To predict grape maturity in solar greenhouses, a plant phenotype-monitoring platform (Phenofix, France) was used to obtain RGB images of grapes from expansion to maturity. Horizontal and longitudinal diameters, compactness, soluble solid content (SSC), titratable acid content, and the SSC/acid of grapes were measured and evaluated. The color values () of the grape skin were determined and subjected to a back-propagation neural network algorithm (BPNN) to predict grape maturity. The results showed that the physical and chemical properties (PCP) of the three varieties of grapes changed significantly during the berry expansion stage and the color-changing maturity stage. According to the normalized rate of change of the PCP indicators, the ripening process of the three varieties of grapes could be divided into two stages: an immature stage (maturity coefficient ) and a mature stage (after which color changes occurred) (). When predicting grape maturity based on the color values, the as well as performed well for Drunk Incense, Muscat Hamburg, and Xiang Yue grape maturity prediction. The GPI ranked in the top three (up to 0.87) when the above indicators were used in combination with BPNN to predict the grape Mc by single-factor and combined-factor analysis. The results showed that the prediction accuracy (RG and HI) of the two-factor combination was better for Drunk Incense, Muscat Hamburg, and Xiang Yue grapes (with recognition accuracies of 79.3%, 78.2%, and 79.4%, respectively), and all of the predictive values were higher than those of the single-factor predictions. Using a confusion matrix to compare the accuracy of the Mc’s predictive ability under the two-factor combination method, the prediction accuracies were in the following order: Xiang Yue (88%) > Muscat Hamburg (81.3%) > Drunk Incense (76%). The results of this study provide an effective way to predict the ripeness of grapes in the greenhouse.