Plant Phenomics最新文献

{"title":"A Multiscale Point-Supervised Network for Counting Maize Tassels in the Wild.","authors":"Haoyu Zheng,&nbsp;Xijian Fan,&nbsp;Weihao Bo,&nbsp;Xubing Yang,&nbsp;Tardi Tjahjadi,&nbsp;Shichao Jin","doi":"10.34133/plantphenomics.0100","DOIUrl":"10.34133/plantphenomics.0100","url":null,"abstract":"<p><p>Accurate counting of maize tassels is essential for monitoring crop growth and estimating crop yield. Recently, deep-learning-based object detection methods have been used for this purpose, where plant counts are estimated from the number of bounding boxes detected. However, these methods suffer from 2 issues: (a) The scales of maize tassels vary because of image capture from varying distances and crop growth stage; and (b) tassel areas tend to be affected by occlusions or complex backgrounds, making the detection inefficient. In this paper, we propose a multiscale lite attention enhancement network (MLAENet) that uses only point-level annotations (i.e., objects labeled with points) to count maize tassels in the wild. Specifically, the proposed method includes a new multicolumn lite feature extraction module that generates a scale-dependent density map by exploiting multiple dilated convolutions with different rates, capturing rich contextual information at different scales more effectively. In addition, a multifeature enhancement module that integrates an attention strategy is proposed to enable the model to distinguish between tassel areas and their complex backgrounds. Finally, a new up-sampling module, UP-Block, is designed to improve the quality of the estimated density map by automatically suppressing the gridding effect during the up-sampling process. Extensive experiments on 2 publicly available tassel-counting datasets, maize tassels counting and maize tassels counting from unmanned aerial vehicle, demonstrate that the proposed MLAENet achieves marked advantages in counting accuracy and inference speed compared to state-of-the-art methods. The model is publicly available at https://github.com/ShiratsuyuShigure/MLAENet-pytorch/tree/main.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10545326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41156724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotyping of <i>Salvia miltiorrhiza</i> Roots Reveals Associations between Root Traits and Bioactive Components.","authors":"Junfeng Chen,&nbsp;Yun Wang,&nbsp;Peng Di,&nbsp;Yulong Wu,&nbsp;Shi Qiu,&nbsp;Zongyou Lv,&nbsp;Yuqi Qiao,&nbsp;Yajing Li,&nbsp;Jingfu Tan,&nbsp;Weixu Chen,&nbsp;Ma Yu,&nbsp;Ping Wei,&nbsp;Ying Xiao,&nbsp;Wansheng Chen","doi":"10.34133/plantphenomics.0098","DOIUrl":"https://doi.org/10.34133/plantphenomics.0098","url":null,"abstract":"<p><p>Plant phenomics aims to perform high-throughput, rapid, and accurate measurement of plant traits, facilitating the identification of desirable traits and optimal genotypes for crop breeding. <i>Salvia miltiorrhiza</i> (Danshen) roots possess remarkable therapeutic effect on cardiovascular diseases, with huge market demands. Although great advances have been made in metabolic studies of the bioactive metabolites, investigation for <i>S</i>. <i>miltiorrhiza</i> roots on other physiological aspects is poor. Here, we developed a framework that utilizes image feature extraction software for in-depth phenotyping of <i>S</i>. <i>miltiorrhiza</i> roots. By employing multiple software programs, <i>S. miltiorrhiza</i> roots were described from 3 aspects: agronomic traits, anatomy traits, and root system architecture. Through <i>K</i>-means clustering based on the diameter ranges of each root branch, all roots were categorized into 3 groups, with primary root-associated key traits. As a proof of concept, we examined the phenotypic components in a series of randomly collected <i>S</i>. <i>miltiorrhiza</i> roots, demonstrating that the total surface of root was the best parameter for the biomass prediction with high linear regression correlation (<i>R</i>² = 0.8312), which was sufficient for subsequently estimating the production of bioactive metabolites without content determination. This study provides an important approach for further grading of medicinal materials and breeding practices.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2023-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10545446/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41176981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crop/Plant Modeling Supports Plant Breeding: II. Guidance of Functional Plant Phenotyping for Trait Discovery.","authors":"Pengpeng Zhang,&nbsp;Jingyao Huang,&nbsp;Yuntao Ma,&nbsp;Xiujuan Wang,&nbsp;Mengzhen Kang,&nbsp;Youhong Song","doi":"10.34133/plantphenomics.0091","DOIUrl":"https://doi.org/10.34133/plantphenomics.0091","url":null,"abstract":"<p><p>Observable morphological traits are widely employed in plant phenotyping for breeding use, which are often the external phenotypes driven by a chain of functional actions in plants. Identifying and phenotyping inherently functional traits for crop improvement toward high yields or adaptation to harsh environments remains a major challenge. Prediction of whole-plant performance in functional-structural plant models (FSPMs) is driven by plant growth algorithms based on organ scale wrapped up with micro-environments. In particular, the models are flexible for scaling down or up through specific functions at the organ nexus, allowing the prediction of crop system behaviors from the genome to the field. As such, by virtue of FSPMs, model parameters that determine organogenesis, development, biomass production, allocation, and morphogenesis from a molecular to the whole plant level can be profiled systematically and made readily available for phenotyping. FSPMs can provide rich functional traits representing biological regulatory mechanisms at various scales in a dynamic system, e.g., Rubisco carboxylation rate, mesophyll conductance, specific leaf nitrogen, radiation use efficiency, and source-sink ratio apart from morphological traits. High-throughput phenotyping such traits is also discussed, which provides an unprecedented opportunity to evolve FSPMs. This will accelerate the co-evolution of FSPMs and plant phenomics, and thus improving breeding efficiency. To expand the great promise of FSPMs in crop science, FSPMs still need more effort in multiscale, mechanistic, reproductive organ, and root system modeling. In summary, this study demonstrates that FSPMs are invaluable tools in guiding functional trait phenotyping at various scales and can thus provide abundant functional targets for phenotyping toward crop improvement.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41125528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits.","authors":"Rahul Chandnani,&nbsp;Tongfei Qin,&nbsp;Heng Ye,&nbsp;Haifei Hu,&nbsp;Karim Panjvani,&nbsp;Mutsutomo Tokizawa,&nbsp;Javier Mora Macias,&nbsp;Alma Armenta Medina,&nbsp;Karine Bernardino,&nbsp;Pierre-Luc Pradier,&nbsp;Pankaj Banik,&nbsp;Ashlyn Mooney,&nbsp;Jurandir V Magalhaes,&nbsp;Henry T Nguyen,&nbsp;Leon V Kochian","doi":"10.34133/plantphenomics.0097","DOIUrl":"10.34133/plantphenomics.0097","url":null,"abstract":"<p><p>Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (<i>DOF1-like</i> zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10538525/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41145487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Protocol of Ultrasonic Backscatter Measurements of Musculoskeletal Properties","authors":"Dongsheng Bi, Lingwei Shi, Boyi Li, Ying Li, Chengcheng Liu, Lawrence H. Le, Jingchun Luo, Sijia Wang, Dean Ta","doi":"10.1007/s43657-023-00122-0","DOIUrl":"https://doi.org/10.1007/s43657-023-00122-0","url":null,"abstract":"","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135536266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening of Ginkgo Individuals with Superior Growth Structural Characteristics in Different Genetic Groups Using Terrestrial Laser Scanning (TLS) Data.","authors":"Wen Gao,&nbsp;Xiaoming Yang,&nbsp;Lin Cao,&nbsp;Fuliang Cao,&nbsp;Hao Liu,&nbsp;Quan Qiu,&nbsp;Meng Shen,&nbsp;Pengfei Yu,&nbsp;Yuhua Liu,&nbsp;Xin Shen","doi":"10.34133/plantphenomics.0092","DOIUrl":"10.34133/plantphenomics.0092","url":null,"abstract":"<p><p>With the concept of sustainable management of plantations, individual trees with excellent characteristics in plantations have received attention from breeders. To improve and maintain long-term productivity, accurate and high-throughput access to phenotypic characteristics is essential when establishing breeding strategies. Meanwhile, genetic diversity is also an important issue that must be considered, especially for plantations without seed source information. This study was carried out in a ginkgo timber plantation. We used simple sequence repeat (SSR) markers for genetic background analysis and high-density terrestrial laser scanning for growth structural characteristic extraction, aiming to provide a possibility of applying remote sensing approaches for forest breeding. First, we analyzed the genetic diversity and population structure, and grouped individual trees according to the genetic distance. Then, the growth structural characteristics (height, diameter at breast height, crown width, crown area, crown volume, height to living crown, trunk volume, biomass of all components) were extracted. Finally, individual trees in each group were comprehensively evaluated and the best-performing ones were selected. Results illustrate that terrestrial laser scanning (TLS) point cloud data can provide nondestructive estimates of the growth structural characteristics at fine scale. From the ginkgo plantation containing high genetic diversity (average polymorphism information content index was 0.719) and high variation in growth structural characteristics (coefficient of variation ranged from 21.822% to 85.477%), 11 excellent individual trees with superior growth were determined. Our study guides the scientific management of plantations and also provides a potential for applying remote sensing technologies to accelerate forest breeding.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10515975/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41138847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Circulating Lipoproteins Mediate the Association Between Cardiovascular Risk Factors and Cognitive Decline: A Community-Based Cohort Study","authors":"Jialin Li, Qingxia Huang, Yingzhe Wang, Mei Cui, Kelin Xu, Chen Suo, Zhenqiu Liu, Yanpeng An, Li Jin, Huiru Tang, Xingdong Chen, Yanfeng Jiang","doi":"10.1007/s43657-023-00120-2","DOIUrl":"https://doi.org/10.1007/s43657-023-00120-2","url":null,"abstract":"","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136155655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plasma-Free Blood as a Potential Alternative to Whole Blood for Transcriptomic Analysis","authors":"Qingwang Chen, Xiaorou Guo, Haiyan Wang, Shanyue Sun, He Jiang, Peipei Zhang, Erfei Shang, Ruolan Zhang, Zehui Cao, Quanne Niu, Chao Zhang, Yaqing Liu, Leming Shi, Ying Yu, Wanwan Hou, Yuanting Zheng","doi":"10.1007/s43657-023-00121-1","DOIUrl":"https://doi.org/10.1007/s43657-023-00121-1","url":null,"abstract":"Abstract RNA sequencing (RNAseq) technology has become increasingly important in precision medicine and clinical diagnostics, and emerged as a powerful tool for identifying protein-coding genes, performing differential gene analysis, and inferring immune cell composition. Human peripheral blood samples are widely used for RNAseq, providing valuable insights into individual biomolecular information. Blood samples can be classified as whole blood (WB), plasma, serum, and remaining sediment samples, including plasma-free blood (PFB) and serum-free blood (SFB) samples that are generally considered less useful byproducts during the processes of plasma and serum separation, respectively. However, the feasibility of using PFB and SFB samples for transcriptome analysis remains unclear. In this study, we aimed to assess the suitability of employing PFB or SFB samples as an alternative RNA source in transcriptomic analysis. We performed a comparative analysis of WB, PFB, and SFB samples for different applications. Our results revealed that PFB samples exhibit greater similarity to WB samples than SFB samples in terms of protein-coding gene expression patterns, detection of differentially expressed genes, and immunological characterizations, suggesting that PFB can serve as a viable alternative to WB for transcriptomic analysis. Our study contributes to the optimization of blood sample utilization and the advancement of precision medicine research.","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135689436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of the Immune Response by Standardized Whole-Blood Stimulation with Metabolism Modulation","authors":"Jialin Zhao, Xuling Han, Helian Li, Yali Luo, Yan Fang, Yun Wang, Jian Gao, Yiran Zhao, Jingxuan Han, Feng Qian","doi":"10.1007/s43657-023-00114-0","DOIUrl":"https://doi.org/10.1007/s43657-023-00114-0","url":null,"abstract":"","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135830259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of Poly(ADP-ribose) Polymerase 9 (PARP9) as a Potent Suppressor for <i>Mycobacterium tuberculosis</i> Infection.","authors":"Zhenyu Zhu, Shufeng Weng, Fen Zheng, Qi Zhao, Ying Xu, Jiaxue Wu","doi":"10.1007/s43657-023-00112-2","DOIUrl":"10.1007/s43657-023-00112-2","url":null,"abstract":"<p><p>ADP-ribosylation is a reversible and dynamic post-translational modification mediated by ADP-ribosyltransferases (ARTs). Poly(ADP-ribose) polymerases (PARPs) are an important family of human ARTs. ADP-ribosylation and PARPs have crucial functions in host-pathogen interaction, especially in viral infections. However, the functions and potential molecular mechanisms of ADP-ribosylation and PARPs in <i>Mycobacterium</i> infection remain unknown. In this study, bioinformatics analysis revealed significantly changed expression levels of several PARPs in tuberculosis patients compared to healthy individuals. Moreover, the expression levels of these PARPs returned to normal following tuberculosis treatment. Then, the changes in the expression levels of PARPs during <i>Mycobacterium</i> infection were validated in Tohoku Hospital Pediatrics-1 (THP1)-induced differentiated macrophages infected with <i>Mycobacterium</i> model strains bacillus Calmette-Guérin (BCG) and in human lung adenocarcinoma A549 cells infected with <i>Mycobacterium smegmatis</i> (Ms), respectively. The mRNA levels of PARP9, PARP10, PARP12, and PARP14 were most significantly increased during infection, with corresponding increases in protein levels, indicating the possible biological functions of these PARPs during <i>Mycobacterium</i> infection. In addition, the biological function of host PARP9 in <i>Mycobacterium</i> infection was further studied. PARP9 deficiency significantly increased the infection efficiency and intracellular proliferation ability of Ms, which was reversed by the reconstruction of PARP9. Collectively, this study updates the understanding of changes in PARP expression during <i>Mycobacterium</i> infection and provides evidence supporting PARP9 as a potent suppressor for <i>Mycobacterium</i> infection.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s43657-023-00112-2.</p>","PeriodicalId":20318,"journal":{"name":"Plant Phenomics","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2023-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11169154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80910798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}