Modern western medicine typically focuses on treating specific symptoms or diseases,and traditional Chinese medicine(TCM)emphasizes the interconnections of the body’s various systems under external environment and ta...Modern western medicine typically focuses on treating specific symptoms or diseases,and traditional Chinese medicine(TCM)emphasizes the interconnections of the body’s various systems under external environment and takes a holistic approach to preventing and treating diseases.Phenomics was initially introduced to the field of TCM in 2008 as a new discipline that studies the laws of integrated and dynamic changes of human clinical phenomes under the scope of the theories and practices of TCM based on phenomics.While TCM Phenomics 1.0 has initially established a clinical phenomic system centered on Zhenghou(a TCM definition of clinical phenome),bottlenecks remain in data standardization,mechanistic interpretation,and precision intervention.Here,we systematically elaborates on the theoretical foundations,technical pathways,and future challenges of integrating digital medicine with TCM phenomics under the framework of“TCM phenomics 2.0”,which is supported by digital medicine technologies such as artificial intelligence,wearable devices,medical digital twins,and multi-omics integration.This framework aims to construct a closed-loop system of“Zhenghou–Phenome–Mechanism–Intervention”and to enable the digitization,standardization,and precision of disease diagnosis and treatment.The integration of digital medicine and TCM phenomics not only promotes the modernization and scientific transformation of TCM theory and practice but also offers new paradigms for precision medicine.In practice,digital tools facilitate multi-source clinical data acquisition and standardization,while AI and big data algorithms help reveal the correlations between clinical Zhenghou phenomes and molecular mechanisms,thereby improving scientific rigor in diagnosis,efficacy evaluation,and personalized intervention.Nevertheless,challenges persist,including data quality and standardization issues,shortage of interdisciplinary talents,and insufficiency of ethical and legal regulations.Future development requires establishing national data-sharing platforms,strengthening international collaboration,fostering interdisciplinary professionals,and improving ethical and legal frameworks.Ultimately,this approach seeks to build a new disease identification and classification system centered on phenomes and to achieve the inheritance,innovation,and modernization of TCM diagnostic and therapeutic patterns.展开更多
Traditional Chinese medicine(TCM)has demonstrated unique advantages in the prevention and treatment of chronic diseases such as glycolipid metabolism disorder.However,its widespread application has been hindered by th...Traditional Chinese medicine(TCM)has demonstrated unique advantages in the prevention and treatment of chronic diseases such as glycolipid metabolism disorder.However,its widespread application has been hindered by the unclear biological essence of TCM syndromes and therapeutic mechanisms.As an emerging interdisciplinary field,phenomics integrates multi-dimensional data including genome,transcriptome,proteome,metabolome,and microbiome.When combined with TCM's holistic philosophy,it forms TCM phenomics,providing novel approaches to reveal the biological connotation of TCM syndromes and the mechanisms of herbal medicine.Taking glycolipid metabolism disorder as an example,this paper explores the application of TCM phenomics in glycolipid metabolism disorder.By analyzing molecular characteristics of related syndromes,TCM phenomics identifies differentially expressed genes,metabolites,and gut microbiota biomarkers to elucidate the dynamic evolution patterns of syndromes.Simultaneously,it deciphers the multi-target regulatory networks of herbal formulas,demonstrating their therapeutic effects through mechanisms including modulation of insulin signaling pathways,improvement of gut microbiota imbalance,and suppression of inflammatory responses.Current challenges include the subjective nature of syndrome diagnosis,insufficient standardization of animal models,and lack of integrated multi-omics analysis.Future research should employ machine learning,multimodal data integration,and cross-omics longitudinal studies to establish quantitative diagnostic systems for syndromes,promote the integration of precision medicine in TCM and western medicine,and accelerate the modernization of TCM.展开更多
Advances in gene editing and natural genetic variability present significant opportunities to generate novel alleles and select natural sources of genetic variation for horticulture crop improvement.The genetic improv...Advances in gene editing and natural genetic variability present significant opportunities to generate novel alleles and select natural sources of genetic variation for horticulture crop improvement.The genetic improvement of crops to enhance their resilience to abiotic stresses and new pests due to climate change is essential for future food security.The field of genomics has made significant strides over the past few decades,enabling us to sequence and analyze entire genomes.However,understanding the complex relationship between genes and their expression in phenotypes-the observable characteristics of an organism-requires a deeper understanding of phenomics.Phenomics seeks to link genetic information with biological processes and environmental factors to better understand complex traits and diseases.Recent breakthroughs in this field include the development of advanced imaging technologies,artificial intelligence algorithms,and large-scale data analysis techniques.These tools have enabled us to explore the relationships between genotype,phenotype,and environment in unprecedented detail.This review explores the importance of understanding the complex relationship between genes and their expression in phenotypes.Integration of genomics with efficient high throughput plant phenotyping as well as the potential of machine learning approaches for genomic and phenomics trait discovery.展开更多
Traditional Chinese medicine (TCM) with its millenniaold wisdom rooted in the principles of holistic Yin-Yang balance and “Bianzheng Lunzhi”[辨证论治, Zhenghou(证候) differentiation and treatment], has long offered ...Traditional Chinese medicine (TCM) with its millenniaold wisdom rooted in the principles of holistic Yin-Yang balance and “Bianzheng Lunzhi”[辨证论治, Zhenghou(证候) differentiation and treatment], has long offered a unique lens to understand human health and disease.However, the modern scientific interpretation of TCM remains at the stage of “knowing that it works, but not knowing why it works”.展开更多
Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships betwe...Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships between the genomic variabilities and the current organ-or system-based definition and classification of disease in Western medi⁃cine.The major challenges in the effort to establish and develop precision medicine are how diseases should be defined and classified in an integrated systemic or omic scale and also on an individualized basis.The phenomics approach to the understanding of diseases will allow the transition from focused phenotype/genotype studies to a systemic largescale phenome and genome,proteome,metabolome approach and the identification of a systemically integrated setof biomarkers for diagnosis and prognosis of disease phenome(or Zhenghou).Phenome-wide associated study(PheWAS)may soon lead the field of medical research and provide insightful and novel clues for redefinition of the disease phenome and its clinical classifications and personalized treatment and ultimately precision medicine.Pharma⁃cophenomics is to characterize the phenomes of drug response and also to identify the corresponding therapeutic targets at the level of systems biology.As a complement of pharmacogenomics/proteomics/metabolomics,pharmacoph⁃enomics offers a suite of new technologies and platforms for the transition from focused phenotype-genotype study to a systematic phenome-genome approach and refine drug research with systematically-defined drug response and thera⁃peutic targets.Therefore,pharmacophenomics will provide a new paradigm for the study of drug response including effects and toxicities at the level of systems biology and will identify the corresponding therapeutic targets and principles for combination treatment and prevention of disease using Fangji or Fufang that takes into account individual variability in genes,environment,and lifestyle for each person.展开更多
Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart cultivation.Despite this advancement,the lack of standards for the cre-ation and u...Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart cultivation.Despite this advancement,the lack of standards for the cre-ation and usage of crop phenomics technology and equipment has become a bottleneck,limiting the industry’s high-quality development.This paper begins with an overview of the crop phenotyping indus-try and presents an industrial mapping of technology and equipment for big data in crop phenomics.It analyzes the necessity and current state of constructing a standard framework for crop phenotyping.Furthermore,this paper proposes the intended organizational structure and goals of the standard frame-work.It details the essentials of the standard framework in the research and development of hardware and equipment,data acquisition,and the storage and management of crop phenotyping data.Finally,it discusses promoting the construction and evaluation of the standard framework,aiming to provide ideas for developing a high-quality standard framework for crop phenotyping.展开更多
Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most mod...Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal resolutions.Such multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop breeding.Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.展开更多
Over the past decade,plant phenomics has emerged as a powerful discipline for high-throughput measurement of plant traits across genotypic and environmental contexts.By leveraging advanced imaging and sensor technolog...Over the past decade,plant phenomics has emerged as a powerful discipline for high-throughput measurement of plant traits across genotypic and environmental contexts.By leveraging advanced imaging and sensor technologies,it enables nondestructive,continuous monitoring of plant growth,development,and stress responses at scale(Zhang et al.,2023).However,the exponential growth of phenotypic data,coupled with the increasing need to holistically model plant–environment systems,calls for a transition to post-phenomics(Figure 1A).This emerging paradigm focuses on dynamic,multiscale systems modeling and actionable decision-making,ultimately enabling the development of crops better adapted to climate change.展开更多
Wine typicity,defined by the unique sensory profiles and chemical compositions that are linked to a specific region,is greatly influenced by the“terroir”-a complex interplay of environmental and biological factors i...Wine typicity,defined by the unique sensory profiles and chemical compositions that are linked to a specific region,is greatly influenced by the“terroir”-a complex interplay of environmental and biological factors in which the microbiota plays a pivotal role.However,the standardization of methods and the usage of commercial microorganisms removed or restricted typicity and regionality in winemaking.Therefore,to regain this lost typicity,this study biochemically characterized 14 native yeast strains,previously isolated by our group from the DOC Douro region.The strains-Saccharomyces cerevisiae,Torulaspora delbrueckii,Lachancea thermotolerans,and Metschnikowia pulcherrima-exhibited diverse stress tolerance profiles,with S.cerevisiae being more tolerant to ethanol and sulphur dioxide,and non-Saccharomyces yeasts showing greater resilience to copper sulphate and osmotic stress.Enzymatic activities varied significantly,with the selected strains demonstrating highβ-glycosidase andβ-lyase activities.Notably,the low BA production observed,apart from M.pulcherrima,highlights the safety of these yeasts for winemaking.Fermentative performance assessments revealed robust glucose consumption and ethanol production by S.cerevisiae,and medium ethanol production by non-Saccharomyces yeasts.Acetic acid production was significantly variable and glycerol production was low for all the strains.In particular,the isolate SL195 T.delbrueckii produced the highest levels of acetic acid and showed no glycerol production.These findings highlight the potential of native yeasts to preserve and enhance regional wine characteristics,providing an avenue to counteract the increase homogenization of wine profiles in modern viticulture.展开更多
Dissecting the mechanism of drought resistance(DR)and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change.Here,we selected a typical droughtavoidant(DA)variet...Dissecting the mechanism of drought resistance(DR)and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change.Here,we selected a typical droughtavoidant(DA)variety,IRAT109,and a drought-tolerant(DT)variety,Hanhui15,as parents to develop a stable recombinant inbred line(RIL)population(F8,1262 lines).The de novo assembled genomes of both parents were released.By resequencing of the RIL population,a set of 1189216 reliable SNPs were obtained and used to construct a dense genetic map.Using above-and belowground phenomic platforms and multimodal cameras,we captured 139040 image-based traits(i-traits)of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32586 drought-responsive quantitative trait loci(QTLs),including 2097 unique QTLs.QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8,and QTLs associated with leaf i-traits occurred more than 800 times on the 50 end of chromosome 3,indicating the potential effects of these QTLs on plant phenotypes.We selected three candidate genes(OsMADS50,OsGhd8,OsSAUR11)related to leaf,panicle,and root traits,respectively,and verified their functions in DR.OsMADS50 was found to negatively regulate DR by modulating leaf dehydration,grain size,and downward root growth.A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments,and the composite QTL regions showed substantial overlap(76.9%)with known DR gene regions.Based on three candidate DR genes,we proposed a haplotype design suitable for different environments and breeding objectives.This study provides a valuable reference for multimodal and time-series phenomic analyses,deciphers the genetic mechanisms of DA and DT rice varieties,and offers a molecular navigation map for breeding of DR varieties.展开更多
Machine learning models for crop image analysis and phenomics are highly important for precision agriculture and breeding and have been the subject of intensive research.However,the lack of publicly available high-qua...Machine learning models for crop image analysis and phenomics are highly important for precision agriculture and breeding and have been the subject of intensive research.However,the lack of publicly available high-quality image datasets with detailed annotations has severely hindered the development of these models.In this work,we present a comprehensive multicultivar and multiview rice plant image dataset(CVRP)created from 231 landraces and 50 modern cultivars grown under dense planting in paddy fields.The dataset includes images capturing rice plants in their natural environment,as well as indoor images focusing specifically on panicles,allowing for a detailed investigation of cultivar-specific differences.A semiautomatic annotation process using deep learning models was designed for annotations,followed by rigorous manual curation.We demonstrated the utility of the CVRP by evaluating the performance of four state-of-the-art(SOTA)semantic segmentation models.We also conducted 3D plant reconstruction with organ segmentation via images and annotations.The database not only facilitates general-purpose image-based panicle identification and segmentation but also provides valuable re-sources for challenging tasks such as automatic rice cultivar identification,panicle and grain counting,and 3D plant reconstruction.The database and the model for image annotation are available at.展开更多
The continuous advancement of remote sensing technology and artificial intelligence has led to the development of UAV(unmanned aerial vehicle)-based crop phenotyping technology,which is becoming increasingly significa...The continuous advancement of remote sensing technology and artificial intelligence has led to the development of UAV(unmanned aerial vehicle)-based crop phenotyping technology,which is becoming increasingly significant in agricultural research.The hardware,algorithms and application contexts associated with UAV phenotyping technology were comprehensively reviewed as well as its future developments.The characteristics of sensors mounted on UAVs and the types of images they capture were introduced,including RGB(red,gueen,blue),infrared,multispectral and fluorescence imaging sensors.The working principles of these sensors and their applications in phenotyping research were subsequently outlined.For example,RGB imaging sensors were utilized for monitoring plant growth status,while infrared sensors were employed for thermal imaging surveillance.Furthermore,the detailed review of the applications of UAV technology in assessing crop field performance were conducted,estimating plant biomass,addressing biotic and abiotic stresses.In conjunction with UAV technology and genome-wide association study(GWAS),the potential for advancing genetic breeding were explored by identifying genes associated with specific crop traits.Finally,the shortcomings of current UAV technology and propose future prospects and recommendations were concluded to enhance its reliability and effectiveness in supporting agricultural production and research.展开更多
Canopy photosynthesis,rather than leaf photosynthesis,is highly related to plant biomass and yield formation.Studying canopy photosynthesis and identifying the parameters that control it can help optimize agricultural...Canopy photosynthesis,rather than leaf photosynthesis,is highly related to plant biomass and yield formation.Studying canopy photosynthesis and identifying the parameters that control it can help optimize agricultural management and achieve crop yield potential.Compared with traditional parameters,canopy occupation volume(COV)offers an integrative parameter on canopy architecture related to canopy photosynthetic rates.In this study,we developed a high-throughput method to derive COV for different rice varieties.We first used multi-perspective two-dimensional imaging to reconstruct three-dimensional point clouds of rice plants and developed a suite of pipelines to calculate plant height,leaf number,tiller number,and biomass,with R^(2) values of 91.8%,95.9%,82.3%,and 94.3%,respectively.We further employed point cloud data to reconstruct the surfaces of rice plants and construct a virtual canopy model of the rice population.Light distribution was simulated using a ray-tracing algorithm and canopy photosynthetic rates were simulated via photosynthetic rate-incident light intensity curve fitting.Furthermore,we systematically explored the relationships between canopy phenotypes and photosynthetic rates,and found that COV was the most effective predictor of canopy photosynthesis,achieving an R^(2) value of 92.1%.Adjustment in atmospheric transmittance showed that COV strongly correlated with canopy photosynthesis under different light conditions,with higher accuracy observed under diffuse light.Variations in planting density confirmed that this correlation remained strong at the community level.In summary,this study demonstrates that COV is closely linked to simulated canopy photosynthesis and the developed pipeline can support future agronomic and breeding research.展开更多
High epicuticular wax(Ewax)content on leaves is a key trait for drought and heat stress tolerance in plants.One hundred diverse rice germplasm lines from the 3K-IRRI collection were screened for leaf Ewax content unde...High epicuticular wax(Ewax)content on leaves is a key trait for drought and heat stress tolerance in plants.One hundred diverse rice germplasm lines from the 3K-IRRI collection were screened for leaf Ewax content under open field conditions during the monsoon season of 2023,and for their nocturnal transpiration during the summer season of 2024.Using a novel drought-simulator phenomics platform,we identified a balance between cuticular and stomatal transpiration at night,with wax modulating these processes under varying night temperatures.展开更多
Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one o...Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies.Nevertheless,recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years.In this article,we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades.We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies.Finally,we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap.It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.展开更多
Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotypi...Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits.Proximal and remote sensing(PRS)techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis.Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications.This progress covers most aspects of PRS application in PP,including patterns of global spatial distribution and temporal dynamics,specific PRS technologies,phenotypic research fields,working environments,species,and traits.Subsequently,we demonstrate how to link PRS to multi-omics studies,including how to achieve multi-dimensional PRS data acquisition and processing,how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance,and how to link PP to multi-omics association analysis.Finally,we identify three future perspectives for PRS-based PP:(1)strengthening the spatial and temporal consistency of PRS data,(2)exploring novel phenotypic traits,and(3)facilitating multi-omics communication.展开更多
The systematicness of phenomics and Traditional Chinese Medicine(TCM)enable these two disciplines to interlink with each other.This article discussed the similarity in theory and application between TCM and phenomics ...The systematicness of phenomics and Traditional Chinese Medicine(TCM)enable these two disciplines to interlink with each other.This article discussed the similarity in theory and application between TCM and phenomics and illustrates their respective advantages in diagnosis and treatment of diseases,forming a new discipline eventually.Chinese medicine phe-nomics(Chinmedphenomics)is built on classic TCM,combined with phenomics technology,and the development of which needs the mega cohort with TCM syndrome and the characteristics of precision medicine as well as multi-disciplinary coop-eration,which is personalized,precise and promising,providing unique scientific insights into understanding human health.展开更多
Phenomics explores the complex interactions among genes,epigenetics,symbiotic microorganisms,diet,and environmental exposure based on the physical,chemical,and biological characteristics of individuals and groups.Incr...Phenomics explores the complex interactions among genes,epigenetics,symbiotic microorganisms,diet,and environmental exposure based on the physical,chemical,and biological characteristics of individuals and groups.Increasingly efficient and comprehensive phenotyping techniques have been integrated into modern phenomics-related research.Multicolor flow cytometry technology provides more measurement parameters than conventional flow cytometry.Based on detailed descriptions of cell phenotypes,rare cell populations and cell subsets can be distinguished,new cell phenotypes can be discovered,and cell apoptosis characteristics can be detected,which will expand the potential of cell phenomics research.Based on the enhancements in multicolor flow cytometry hardware,software,reagents,and method design,the present review summarizes the recent advances and applications of multicolor flow cytometry in cell phenomics,illuminating the potential of applying phenomics in future studies.展开更多
Background:The advancement of genomics has progressed in lightning speed over the past two decades.Numerous large-scale genome sequencing initiatives were announced,along with the rise of the holistic precision medici...Background:The advancement of genomics has progressed in lightning speed over the past two decades.Numerous large-scale genome sequencing initiatives were announced,along with the rise of the holistic precision medicine approach.However,the field of genomic medicine has now come to a bottleneck since genomic-phenomic interactions are not fully comprehended due to the complexity of the human systems biology and environmental influence,hence the emergence of human phenomics.Results:This review attempts to provide an overview of the potential advantages of investigating the human phenomics of indigenous populations and the challenges ahead.Conclusion:We believe that the indigenous populations serve as an ideal model to excavate our understanding of genomic-environmental-phenomics interactions.展开更多
With thousands of years of application history,traditional Chinese medicine(TCM)has unique advantages in the prevention of various chronic diseases,and in recent years,the development of TCM has presented a situation ...With thousands of years of application history,traditional Chinese medicine(TCM)has unique advantages in the prevention of various chronic diseases,and in recent years,the development of TCM has presented a situation where opportunities and challenges coexist.Phenomics is an emerging area of life science research,which has numerous similarities to the cognitive perspective of TCM.Thus,how to carry out the interdisciplinary research between TCM and phenomics deserves in-depth discussion.Diabetes is one of the most common chronic non-communicable diseases around the world,and TCM plays an important role in all stages of diabetes treatment,but the molecular mechanisms are difficult to elucidate.Phenomics research can not only reveal the hidden scientific connotations of TCM,but also provide a bridge for the confluence and complementary between TCM and Western medicine.Facing the challenges of the TCM phenomics research,we suggest applying the State-target theory(STT)to overall plan relevant researches,namely,focusing on the disease development,change trends,and core targets of each stage,and to deepen the understanding of TCM disease phenotypes and the therapeutic mechanisms of herbal medicine.展开更多
基金Science and Technology strategic cooperation Programs of Luzhou Municipal People’s Government and Southwest Medical University (2019LZXNYD-P01DUAN)National Key R&D Program of China (2024YFC3505400)Regional Key R&D Program of Ningxia Hui Autonomous Region (2024BEG01003)。
文摘Modern western medicine typically focuses on treating specific symptoms or diseases,and traditional Chinese medicine(TCM)emphasizes the interconnections of the body’s various systems under external environment and takes a holistic approach to preventing and treating diseases.Phenomics was initially introduced to the field of TCM in 2008 as a new discipline that studies the laws of integrated and dynamic changes of human clinical phenomes under the scope of the theories and practices of TCM based on phenomics.While TCM Phenomics 1.0 has initially established a clinical phenomic system centered on Zhenghou(a TCM definition of clinical phenome),bottlenecks remain in data standardization,mechanistic interpretation,and precision intervention.Here,we systematically elaborates on the theoretical foundations,technical pathways,and future challenges of integrating digital medicine with TCM phenomics under the framework of“TCM phenomics 2.0”,which is supported by digital medicine technologies such as artificial intelligence,wearable devices,medical digital twins,and multi-omics integration.This framework aims to construct a closed-loop system of“Zhenghou–Phenome–Mechanism–Intervention”and to enable the digitization,standardization,and precision of disease diagnosis and treatment.The integration of digital medicine and TCM phenomics not only promotes the modernization and scientific transformation of TCM theory and practice but also offers new paradigms for precision medicine.In practice,digital tools facilitate multi-source clinical data acquisition and standardization,while AI and big data algorithms help reveal the correlations between clinical Zhenghou phenomes and molecular mechanisms,thereby improving scientific rigor in diagnosis,efficacy evaluation,and personalized intervention.Nevertheless,challenges persist,including data quality and standardization issues,shortage of interdisciplinary talents,and insufficiency of ethical and legal regulations.Future development requires establishing national data-sharing platforms,strengthening international collaboration,fostering interdisciplinary professionals,and improving ethical and legal frameworks.Ultimately,this approach seeks to build a new disease identification and classification system centered on phenomes and to achieve the inheritance,innovation,and modernization of TCM diagnostic and therapeutic patterns.
基金National Natural Science Foundation of China(82474323)High Level Chinese Medical Hospital Promotion Project(HLCMHPP20230CZ40907)China Academy of Chinese Medical Sciences Outstanding Young Scientific and Technological Talents Program(ZZ13-YQ-026).
文摘Traditional Chinese medicine(TCM)has demonstrated unique advantages in the prevention and treatment of chronic diseases such as glycolipid metabolism disorder.However,its widespread application has been hindered by the unclear biological essence of TCM syndromes and therapeutic mechanisms.As an emerging interdisciplinary field,phenomics integrates multi-dimensional data including genome,transcriptome,proteome,metabolome,and microbiome.When combined with TCM's holistic philosophy,it forms TCM phenomics,providing novel approaches to reveal the biological connotation of TCM syndromes and the mechanisms of herbal medicine.Taking glycolipid metabolism disorder as an example,this paper explores the application of TCM phenomics in glycolipid metabolism disorder.By analyzing molecular characteristics of related syndromes,TCM phenomics identifies differentially expressed genes,metabolites,and gut microbiota biomarkers to elucidate the dynamic evolution patterns of syndromes.Simultaneously,it deciphers the multi-target regulatory networks of herbal formulas,demonstrating their therapeutic effects through mechanisms including modulation of insulin signaling pathways,improvement of gut microbiota imbalance,and suppression of inflammatory responses.Current challenges include the subjective nature of syndrome diagnosis,insufficient standardization of animal models,and lack of integrated multi-omics analysis.Future research should employ machine learning,multimodal data integration,and cross-omics longitudinal studies to establish quantitative diagnostic systems for syndromes,promote the integration of precision medicine in TCM and western medicine,and accelerate the modernization of TCM.
基金supported this research through the National Research Foundation of Korea(NRF),funded by the Ministry of Education(2019R1A6A1A11052070)。
文摘Advances in gene editing and natural genetic variability present significant opportunities to generate novel alleles and select natural sources of genetic variation for horticulture crop improvement.The genetic improvement of crops to enhance their resilience to abiotic stresses and new pests due to climate change is essential for future food security.The field of genomics has made significant strides over the past few decades,enabling us to sequence and analyze entire genomes.However,understanding the complex relationship between genes and their expression in phenotypes-the observable characteristics of an organism-requires a deeper understanding of phenomics.Phenomics seeks to link genetic information with biological processes and environmental factors to better understand complex traits and diseases.Recent breakthroughs in this field include the development of advanced imaging technologies,artificial intelligence algorithms,and large-scale data analysis techniques.These tools have enabled us to explore the relationships between genotype,phenotype,and environment in unprecedented detail.This review explores the importance of understanding the complex relationship between genes and their expression in phenotypes.Integration of genomics with efficient high throughput plant phenotyping as well as the potential of machine learning approaches for genomic and phenomics trait discovery.
文摘Traditional Chinese medicine (TCM) with its millenniaold wisdom rooted in the principles of holistic Yin-Yang balance and “Bianzheng Lunzhi”[辨证论治, Zhenghou(证候) differentiation and treatment], has long offered a unique lens to understand human health and disease.However, the modern scientific interpretation of TCM remains at the stage of “knowing that it works, but not knowing why it works”.
文摘Recent fast advance in biomedical research at the“omic”levels has led to an explosion of big data for the understanding the molecular makeup of diseases,which have revealed the intimate unmatched relationships between the genomic variabilities and the current organ-or system-based definition and classification of disease in Western medi⁃cine.The major challenges in the effort to establish and develop precision medicine are how diseases should be defined and classified in an integrated systemic or omic scale and also on an individualized basis.The phenomics approach to the understanding of diseases will allow the transition from focused phenotype/genotype studies to a systemic largescale phenome and genome,proteome,metabolome approach and the identification of a systemically integrated setof biomarkers for diagnosis and prognosis of disease phenome(or Zhenghou).Phenome-wide associated study(PheWAS)may soon lead the field of medical research and provide insightful and novel clues for redefinition of the disease phenome and its clinical classifications and personalized treatment and ultimately precision medicine.Pharma⁃cophenomics is to characterize the phenomes of drug response and also to identify the corresponding therapeutic targets at the level of systems biology.As a complement of pharmacogenomics/proteomics/metabolomics,pharmacoph⁃enomics offers a suite of new technologies and platforms for the transition from focused phenotype-genotype study to a systematic phenome-genome approach and refine drug research with systematically-defined drug response and thera⁃peutic targets.Therefore,pharmacophenomics will provide a new paradigm for the study of drug response including effects and toxicities at the level of systems biology and will identify the corresponding therapeutic targets and principles for combination treatment and prevention of disease using Fangji or Fufang that takes into account individual variability in genes,environment,and lifestyle for each person.
基金supported by the National Key R&D Program of China(2022YFD2002300)the Construction of Collaborative Innovation Center of Beijing Academy of Agricultural and Forestry Sciences(KJCX20240406)+1 种基金the National Natural Science Foundation of China(32071891)the earmarked fund(CARS-02 and CARS-054).
文摘Crop phenomics has rapidly progressed in recent years due to the growing need for crop functional geno-mics,digital breeding,and smart cultivation.Despite this advancement,the lack of standards for the cre-ation and usage of crop phenomics technology and equipment has become a bottleneck,limiting the industry’s high-quality development.This paper begins with an overview of the crop phenotyping indus-try and presents an industrial mapping of technology and equipment for big data in crop phenomics.It analyzes the necessity and current state of constructing a standard framework for crop phenotyping.Furthermore,this paper proposes the intended organizational structure and goals of the standard frame-work.It details the essentials of the standard framework in the research and development of hardware and equipment,data acquisition,and the storage and management of crop phenotyping data.Finally,it discusses promoting the construction and evaluation of the standard framework,aiming to provide ideas for developing a high-quality standard framework for crop phenotyping.
基金supported by National Research and Development Program of Ministry of Science and Technology of China(2020YFA0907600,2018YFA0900600,2019YFA09004600)Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27020105,XDB37020104,XDA24010203,XDA0450202)+2 种基金National Science Foundation of China(31870214)the National Key Research and Development Program of China(2023YFF1000100)STI2030eMajor Projects(2023ZD04076).
文摘Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal resolutions.Such multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop breeding.Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.
基金supported by the National Key Research and Development Program of China(China-Israel 2022YFE0198000 and 3013005724)the Basic Public Welfare Research Program of Zhejiang Province(LTGN24C130003)+1 种基金the Zhejiang Science and Technology Major Program on Agricultural New Variety(2021C02067-7 and 2021C02066-5)the National Natural Science Foundation of China(U24A20419).
文摘Over the past decade,plant phenomics has emerged as a powerful discipline for high-throughput measurement of plant traits across genotypic and environmental contexts.By leveraging advanced imaging and sensor technologies,it enables nondestructive,continuous monitoring of plant growth,development,and stress responses at scale(Zhang et al.,2023).However,the exponential growth of phenotypic data,coupled with the increasing need to holistically model plant–environment systems,calls for a transition to post-phenomics(Figure 1A).This emerging paradigm focuses on dynamic,multiscale systems modeling and actionable decision-making,ultimately enabling the development of crops better adapted to climate change.
基金supported by the“Contrato-Programa”UIDB/04050/20202020(DOI 10.54499/UIDB/04050/2020)by DOI 10.54499/DL57/2016/CP1377/CT0027 to VM+3 种基金funded by Portuguese national funds through the FCT I.Psupported by FCT and European Funds(FEDER/POCI/COMPETE2020)through the project GrapeMicrobiota(PTDC/BAA-AGR/2691/2020)Richard Breia was supported with a post-doctoral researcher contract/position within the same project.
文摘Wine typicity,defined by the unique sensory profiles and chemical compositions that are linked to a specific region,is greatly influenced by the“terroir”-a complex interplay of environmental and biological factors in which the microbiota plays a pivotal role.However,the standardization of methods and the usage of commercial microorganisms removed or restricted typicity and regionality in winemaking.Therefore,to regain this lost typicity,this study biochemically characterized 14 native yeast strains,previously isolated by our group from the DOC Douro region.The strains-Saccharomyces cerevisiae,Torulaspora delbrueckii,Lachancea thermotolerans,and Metschnikowia pulcherrima-exhibited diverse stress tolerance profiles,with S.cerevisiae being more tolerant to ethanol and sulphur dioxide,and non-Saccharomyces yeasts showing greater resilience to copper sulphate and osmotic stress.Enzymatic activities varied significantly,with the selected strains demonstrating highβ-glycosidase andβ-lyase activities.Notably,the low BA production observed,apart from M.pulcherrima,highlights the safety of these yeasts for winemaking.Fermentative performance assessments revealed robust glucose consumption and ethanol production by S.cerevisiae,and medium ethanol production by non-Saccharomyces yeasts.Acetic acid production was significantly variable and glycerol production was low for all the strains.In particular,the isolate SL195 T.delbrueckii produced the highest levels of acetic acid and showed no glycerol production.These findings highlight the potential of native yeasts to preserve and enhance regional wine characteristics,providing an avenue to counteract the increase homogenization of wine profiles in modern viticulture.
基金supported by the National Natural Science Foundation of China(32172098 and U21A20205)the Natural Science Foundation of Shanghai(23ZR1455900 and 22ZR1455200).
文摘Dissecting the mechanism of drought resistance(DR)and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change.Here,we selected a typical droughtavoidant(DA)variety,IRAT109,and a drought-tolerant(DT)variety,Hanhui15,as parents to develop a stable recombinant inbred line(RIL)population(F8,1262 lines).The de novo assembled genomes of both parents were released.By resequencing of the RIL population,a set of 1189216 reliable SNPs were obtained and used to construct a dense genetic map.Using above-and belowground phenomic platforms and multimodal cameras,we captured 139040 image-based traits(i-traits)of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32586 drought-responsive quantitative trait loci(QTLs),including 2097 unique QTLs.QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8,and QTLs associated with leaf i-traits occurred more than 800 times on the 50 end of chromosome 3,indicating the potential effects of these QTLs on plant phenotypes.We selected three candidate genes(OsMADS50,OsGhd8,OsSAUR11)related to leaf,panicle,and root traits,respectively,and verified their functions in DR.OsMADS50 was found to negatively regulate DR by modulating leaf dehydration,grain size,and downward root growth.A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments,and the composite QTL regions showed substantial overlap(76.9%)with known DR gene regions.Based on three candidate DR genes,we proposed a haplotype design suitable for different environments and breeding objectives.This study provides a valuable reference for multimodal and time-series phenomic analyses,deciphers the genetic mechanisms of DA and DT rice varieties,and offers a molecular navigation map for breeding of DR varieties.
基金supported in part by grants from Biological Breeding-National Science and Technology Major Project(Grant No.2023ZD04076)the National Natural Science Foundation of China(Grant No.32170647)+2 种基金the National Science Foundation of Jiangsu Province in China(Grant Nos.BK20212010 and BE2022383)the Jiangsu Engineering Research Center for Plant Genome Editing,Southern Japonica Rice Research and Development Co.LTDthe Jiangsu Collaborative Innovation Center for Modern Crop Production.
文摘Machine learning models for crop image analysis and phenomics are highly important for precision agriculture and breeding and have been the subject of intensive research.However,the lack of publicly available high-quality image datasets with detailed annotations has severely hindered the development of these models.In this work,we present a comprehensive multicultivar and multiview rice plant image dataset(CVRP)created from 231 landraces and 50 modern cultivars grown under dense planting in paddy fields.The dataset includes images capturing rice plants in their natural environment,as well as indoor images focusing specifically on panicles,allowing for a detailed investigation of cultivar-specific differences.A semiautomatic annotation process using deep learning models was designed for annotations,followed by rigorous manual curation.We demonstrated the utility of the CVRP by evaluating the performance of four state-of-the-art(SOTA)semantic segmentation models.We also conducted 3D plant reconstruction with organ segmentation via images and annotations.The database not only facilitates general-purpose image-based panicle identification and segmentation but also provides valuable re-sources for challenging tasks such as automatic rice cultivar identification,panicle and grain counting,and 3D plant reconstruction.The database and the model for image annotation are available at.
基金supported by the National Key R&D Program of China(2021YFE0101400)National Natural Science Foundation of China(31871681).
文摘The continuous advancement of remote sensing technology and artificial intelligence has led to the development of UAV(unmanned aerial vehicle)-based crop phenotyping technology,which is becoming increasingly significant in agricultural research.The hardware,algorithms and application contexts associated with UAV phenotyping technology were comprehensively reviewed as well as its future developments.The characteristics of sensors mounted on UAVs and the types of images they capture were introduced,including RGB(red,gueen,blue),infrared,multispectral and fluorescence imaging sensors.The working principles of these sensors and their applications in phenotyping research were subsequently outlined.For example,RGB imaging sensors were utilized for monitoring plant growth status,while infrared sensors were employed for thermal imaging surveillance.Furthermore,the detailed review of the applications of UAV technology in assessing crop field performance were conducted,estimating plant biomass,addressing biotic and abiotic stresses.In conjunction with UAV technology and genome-wide association study(GWAS),the potential for advancing genetic breeding were explored by identifying genes associated with specific crop traits.Finally,the shortcomings of current UAV technology and propose future prospects and recommendations were concluded to enhance its reliability and effectiveness in supporting agricultural production and research.
基金supported by the National Natural Science Foundation of China(Grant Nos.32201654 and U22A20464)National Key Research and Development Program from the Ministry of Science and Technology of China(Grant No.2020YFA0907600)the 2115 Talent Development Program of China Agricultural University.
文摘Canopy photosynthesis,rather than leaf photosynthesis,is highly related to plant biomass and yield formation.Studying canopy photosynthesis and identifying the parameters that control it can help optimize agricultural management and achieve crop yield potential.Compared with traditional parameters,canopy occupation volume(COV)offers an integrative parameter on canopy architecture related to canopy photosynthetic rates.In this study,we developed a high-throughput method to derive COV for different rice varieties.We first used multi-perspective two-dimensional imaging to reconstruct three-dimensional point clouds of rice plants and developed a suite of pipelines to calculate plant height,leaf number,tiller number,and biomass,with R^(2) values of 91.8%,95.9%,82.3%,and 94.3%,respectively.We further employed point cloud data to reconstruct the surfaces of rice plants and construct a virtual canopy model of the rice population.Light distribution was simulated using a ray-tracing algorithm and canopy photosynthetic rates were simulated via photosynthetic rate-incident light intensity curve fitting.Furthermore,we systematically explored the relationships between canopy phenotypes and photosynthetic rates,and found that COV was the most effective predictor of canopy photosynthesis,achieving an R^(2) value of 92.1%.Adjustment in atmospheric transmittance showed that COV strongly correlated with canopy photosynthesis under different light conditions,with higher accuracy observed under diffuse light.Variations in planting density confirmed that this correlation remained strong at the community level.In summary,this study demonstrates that COV is closely linked to simulated canopy photosynthesis and the developed pipeline can support future agronomic and breeding research.
基金supported by the Department of Science and Technology,Innovation in Science Pursuit for Inspired Research,India(Grant No.DST/INSPIRE/04/2022/003192)the Ad-RICCE Project,India(Grant No.IC-12012(12)/2/2022-ICD-DBT)the Dutch Research Council,the Netherlands(Grant No.482.20.202).
文摘High epicuticular wax(Ewax)content on leaves is a key trait for drought and heat stress tolerance in plants.One hundred diverse rice germplasm lines from the 3K-IRRI collection were screened for leaf Ewax content under open field conditions during the monsoon season of 2023,and for their nocturnal transpiration during the summer season of 2024.Using a novel drought-simulator phenomics platform,we identified a balance between cuticular and stomatal transpiration at night,with wax modulating these processes under varying night temperatures.
基金the National Key Research and Development Program of China(2016YFD0100101-18,2016YFD0100103)the National Natural Science Foundation of China(31770397,21800305)+2 种基金the Fundamental Research Funds for the Central Universities(2662017PY058,2662017QD044)UK-China grant BBSRC(grant no.BB/R02118X/1)the National Institute of Food and Agriculture,U.S.Department of Agriculture,Hatch project(ALA014-1-16016).
文摘Since whole-genome sequencing of many crops has been achieved,crop functional genomics studies have stepped into the big-data and high-throughput era.However,acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies.Nevertheless,recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years.In this article,we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades.We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies.Finally,we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap.It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
基金supported by the Hainan Yazhou Bay Seed Lab(no.B21HJ1005)the Fundamental Research Funds for the Central Universities(no.KYCYXT2022017)+5 种基金the Open Project of Key Laboratory of Oasis Eco-agriculture,Xinjiang Production and Construction Corps(no.202101)the Jiangsu Association for Science and Technology Independent Innovation Fund Project(no.CX(21)3107)the High Level Personnel Project of Jiangsu Province(no.JSSCBS20210271)the China Postdoctoral Science Foundation(no.2021M691490)the Jiangsu Planned Projects for Postdoctoral Research Funds(no.2021K520C)the JBGS Project of Seed Industry Revitalization in Jiangsu Province(no.JBGS[2021]007).
文摘Plant phenomics(PP)has been recognized as a bottleneck in studying the interactions of genomics and environment on plants,limiting the progress of smart breeding and precise cultivation.High-throughput plant phenotyping is challenging owing to the spatio-temporal dynamics of traits.Proximal and remote sensing(PRS)techniques are increasingly used for plant phenotyping because of their advantages in multi-dimensional data acquisition and analysis.Substantial progress of PRS applications in PP has been observed over the last two decades and is analyzed here from an interdisciplinary perspective based on 2972 publications.This progress covers most aspects of PRS application in PP,including patterns of global spatial distribution and temporal dynamics,specific PRS technologies,phenotypic research fields,working environments,species,and traits.Subsequently,we demonstrate how to link PRS to multi-omics studies,including how to achieve multi-dimensional PRS data acquisition and processing,how to systematically integrate all kinds of phenotypic information and derive phenotypic knowledge with biological significance,and how to link PP to multi-omics association analysis.Finally,we identify three future perspectives for PRS-based PP:(1)strengthening the spatial and temporal consistency of PRS data,(2)exploring novel phenotypic traits,and(3)facilitating multi-omics communication.
基金supported by National Key R&D Program of China(2018YFC1704300)National Natural Science Foundation of China(81730107,81973883)+6 种基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)Shanghai Scientific Research Project(17401971100)Shanghai TCM Medical Center of Chronic Disease(2017ZZ01010)Three Years Action to Accelerate the Development of Traditional Chinese Medicine Plan(ZY(2018-2020)-CCCX-3003)the Program for Innovative Research Team of Ministry of Education of China(IRT1270)the Program for Innovative Research Team of Ministry of Science and Technology of China(2015RA4002)Sanming Project of Medicine in Shenzhen(SZSM201808072).
文摘The systematicness of phenomics and Traditional Chinese Medicine(TCM)enable these two disciplines to interlink with each other.This article discussed the similarity in theory and application between TCM and phenomics and illustrates their respective advantages in diagnosis and treatment of diseases,forming a new discipline eventually.Chinese medicine phe-nomics(Chinmedphenomics)is built on classic TCM,combined with phenomics technology,and the development of which needs the mega cohort with TCM syndrome and the characteristics of precision medicine as well as multi-disciplinary coop-eration,which is personalized,precise and promising,providing unique scientific insights into understanding human health.
基金This work was supported by National Key Project of China(2016YFA0502201 and 2017YFA0700404)Standard Technology Management Project(2013811)+1 种基金the State Administration for Market Regulation,National Science and Technology Basic Condition Platform project(APT2001)Natural Science Foundation of Shenzhen(JCYJ20190808150009605).
文摘Phenomics explores the complex interactions among genes,epigenetics,symbiotic microorganisms,diet,and environmental exposure based on the physical,chemical,and biological characteristics of individuals and groups.Increasingly efficient and comprehensive phenotyping techniques have been integrated into modern phenomics-related research.Multicolor flow cytometry technology provides more measurement parameters than conventional flow cytometry.Based on detailed descriptions of cell phenotypes,rare cell populations and cell subsets can be distinguished,new cell phenotypes can be discovered,and cell apoptosis characteristics can be detected,which will expand the potential of cell phenomics research.Based on the enhancements in multicolor flow cytometry hardware,software,reagents,and method design,the present review summarizes the recent advances and applications of multicolor flow cytometry in cell phenomics,illuminating the potential of applying phenomics in future studies.
文摘Background:The advancement of genomics has progressed in lightning speed over the past two decades.Numerous large-scale genome sequencing initiatives were announced,along with the rise of the holistic precision medicine approach.However,the field of genomic medicine has now come to a bottleneck since genomic-phenomic interactions are not fully comprehended due to the complexity of the human systems biology and environmental influence,hence the emergence of human phenomics.Results:This review attempts to provide an overview of the potential advantages of investigating the human phenomics of indigenous populations and the challenges ahead.Conclusion:We believe that the indigenous populations serve as an ideal model to excavate our understanding of genomic-environmental-phenomics interactions.
基金supported by Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine[State Administration of Traditional Chinese Medicine of the People’s Republic of China](No.ZYYCXTD-D-202001)Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences(No.CI2021A01600,No.CI2021A01606).
文摘With thousands of years of application history,traditional Chinese medicine(TCM)has unique advantages in the prevention of various chronic diseases,and in recent years,the development of TCM has presented a situation where opportunities and challenges coexist.Phenomics is an emerging area of life science research,which has numerous similarities to the cognitive perspective of TCM.Thus,how to carry out the interdisciplinary research between TCM and phenomics deserves in-depth discussion.Diabetes is one of the most common chronic non-communicable diseases around the world,and TCM plays an important role in all stages of diabetes treatment,but the molecular mechanisms are difficult to elucidate.Phenomics research can not only reveal the hidden scientific connotations of TCM,but also provide a bridge for the confluence and complementary between TCM and Western medicine.Facing the challenges of the TCM phenomics research,we suggest applying the State-target theory(STT)to overall plan relevant researches,namely,focusing on the disease development,change trends,and core targets of each stage,and to deepen the understanding of TCM disease phenotypes and the therapeutic mechanisms of herbal medicine.
