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
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
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
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
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
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
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
The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent year...The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent years,significant advances have facilitated tree shrew studies,including the determination of the tree shrew genome,genetic manipulation using spermatogonial stem cells,viral vector-mediated gene delivery,and mapping of the tree shrew brain atlas.However,the limited availability of tree shrews globally remains a substantial challenge in the field.Additionally,determining the key questions best answered using tree shrews constitutes another difficulty.Tree shrew models have historically been used to study hepatitis B virus(HBV)and hepatitis C virus(HCV)infection,myopia,and psychosocial stress-induced depression,with more recent studies focusing on developing animal models for infectious and neurodegenerative diseases.Despite these efforts,the impact of tree shrew models has not yet matched that of rodent or NHP models in biomedical research.This review summarizes the prominent advancements in tree shrew research and reflects on the key biological questions addressed using this model.We emphasize that intensive dedication and robust international collaboration are essential for achieving breakthroughs in tree shrew studies.The use of tree shrews as a unique resource is expected to gain considerable attention with the application of advanced techniques and the development of viable animal models,meeting the increasing demands of life science and biomedical research.展开更多
With the rapid development of genetic analysis techniques and crop population size,phenotyping has become the bottleneck restricting crop breeding.Breaking through this bottleneck will require phenomics,defined as the...With the rapid development of genetic analysis techniques and crop population size,phenotyping has become the bottleneck restricting crop breeding.Breaking through this bottleneck will require phenomics,defined as the accurate,high-throughput acquisition and analysis of multi-dimensional phenotypes during crop growth at organism-wide levels,ranging from cells to organs,individual plants,plots,and fields.Here we offer an overview of crop phenomics research from technological and platform viewpoints at various scales,including microscopic,ground-based,and aerial phenotyping and phenotypic data analysis.We describe recent applications of high-throughput phenotyping platforms for abiotic/biotic stress and yield assessment.Finally,we discuss current challenges and offer perspectives on future phenomics research.展开更多
Fish morphological phenotypes are important resources in artificial breeding,functional gene mapping,and population-based studies in aquaculture and ecology.Traditional morphological measurement of phenotypes is rathe...Fish morphological phenotypes are important resources in artificial breeding,functional gene mapping,and population-based studies in aquaculture and ecology.Traditional morphological measurement of phenotypes is rather expensive in terms of time and labor.More importantly,manual measurement is highly dependent on operational experience,which can lead to subjective phenotyping results.Here,we developed 3DPhenoFish software to extract fish morphological phenotypes from three-dimensional(3D)point cloud data.Algorithms for background elimination,coordinate normalization,image segmentation,key point recognition,and phenotype extraction were developed and integrated into an intuitive user interface.Furthermore,18 key points and traditional 2D morphological traits,along with 3D phenotypes,including area and volume,can be automatically obtained in a visualized manner.Intuitive fine-tuning of key points and customized definitions of phenotypes are also allowed in the software.Using 3DPhenoFish,we performed high-throughput phenotyping for four endemic Schizothoracinae species,including Schizopygopsis younghusbandi,Oxygymnocypris stewartii,Ptychobarbus dipogon,and Schizothorax oconnori.Results indicated that the morphological phenotypes from 3DPhenoFish exhibited high linear correlation(>0.94)with manual measurements and offered informative traits to discriminate samples of different species and even for different populations of the same species.In summary,we developed an efficient,accurate,and customizable tool,3DPhenoFish,to extract morphological phenotypes from point cloud data,which should help overcome traditional challenges in manual measurements.3DPhenoFish can be used for research on morphological phenotypes in fish,including functional gene mapping,artificial selection,and conservation studies.3DPhenoFish is an open-source software and can be downloaded for free at https://github.com/lyh24k/3DPhenoFish/tree/master.展开更多
Phenomics is a new branch of science that provides high-throughput quantification of plant and animal traits at systems level.The last decade has witnessed great successes in high-throughput phenotyping of numerous mo...Phenomics is a new branch of science that provides high-throughput quantification of plant and animal traits at systems level.The last decade has witnessed great successes in high-throughput phenotyping of numerous morphological traits,yet major challenges still exist in precise phenotyping of physiological traits such as transpiration and photosynthesis.Due to the highly dynamic nature of physiological traits in responses to the environment,appropriate selection criteria and efficient screening systems at the physiological level for abiotic stress tolerance have been largely absent in plants.In this review,the current status of phenomics techniques was briefly summarized in horticultural plants.Specifically,the emerging field of high-throughput physiology-based phenotyping,which is referred to as“physiolomics”,for drought stress responseswas highlighted.In addition to analyzing the advantages of physiology-based phenotyping overmorphology-based approaches,recent examples that applied high-throughput physiological phenotyping to model and non-model horticultural plants were revisited and discussed.Based on the collective findings,we propose that high-throughput,non-destructive,and automatic physiological assays can and should be used as routine methods for phenotyping stress response traits in horticultural plants.展开更多
Objective: This study aimed to explore the experiences of women in the process of formula feeding their infants. The World Health Organization has emphasized the importance of breastfeeding for infant health. After de...Objective: This study aimed to explore the experiences of women in the process of formula feeding their infants. The World Health Organization has emphasized the importance of breastfeeding for infant health. After decades of breastfeeding promotions,breastfeeding rates in Hong Kong have been rising consistently; however, the low continuation rate is alarming. This study explores women's experiences with formula feeding their infants, including factors affecting their decision to do so.Methods: A qualitative approach using an interpretative phenomenological analysis(IPA) was adopted as the study design. Data were collected from 2014 to 2015 through individual in-depth unstructured interviews with 16 women, conducted between 3 and 12 months after the birth of their infant. Data were analyzed using IPA.Results: Three main themes emerged as follows:(1) self-struggle, with the subthemes of feeling like a milk cow and feeling trapped;(2) family conflict, with the subtheme of sharing the spotlight; and(3) interpersonal tensions, with the subthemes of embarrassment,staring, and innocence. Many mothers suffered various stressors and frustrations during breastfeeding. These findings suggest a number of pertinent areas that need to be considered in preparing an infant feeding campaign.Conclusions: The findings of this study reinforce our knowledge of women's struggles with multiple sources of pressure, such as career demands, childcare demands, and family life after giving birth. All mothers should be given assistance in making informed decisions about the optimal approach to feeding their babies given their individual situation and be provided with support to pursue their chosen feeding method.展开更多
An emerging area of interest in understanding disease phenotypes is systems genomics.Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations.A wide num...An emerging area of interest in understanding disease phenotypes is systems genomics.Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations.A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful,but understanding the candidate genes harboring those mutations is an unmet goal.In this perspective,using systems genomic approaches,we highlight the application of phenome-interactome networks in diabetes and provide deep insights.LINC01128,which we previously described as candidate for diabetes,is shown as an example to discuss the approach.展开更多
Despite the skin microbiome has been linked to skin health and diseases,its role in modulating human skin appearance remains understudied.Using a total of 1244 face imaging phenomes and 246 cheek metagenomes,we first ...Despite the skin microbiome has been linked to skin health and diseases,its role in modulating human skin appearance remains understudied.Using a total of 1244 face imaging phenomes and 246 cheek metagenomes,we first established three skin age indices by machine learning,including skin phenotype age(SPA),skin microbiota age(SMA),and skin integration age(SIA)as surrogates of phenotypic aging,microbial aging,and their combination,respectively.Moreover,we found that besides aging and gender as intrinsic factors,skin microbiome might also play a role in shaping skin imaging phenotypes(SIPs).Skin taxonomic and functionalαdiversity was positively linked to melanin,pore,pigment,and ultraviolet spot levels,but negatively linked to sebum,lightening,and porphyrin levels.Furthermore,certain species were correlated with specific SIPs,such as sebum and lightening levels negatively correlated with Corynebacterium matruchotii,Staphylococcus capitis,and Streptococcus sanguinis.Notably,we demonstrated skin microbial potential in predicting SIPs,among which the lightening level presented the least error of 1.8%.Lastly,we provided a reservoir of potential mechanisms through which skin microbiome adjusted the SIPs,including the modulation of pore,wrinkle,and sebum levels by cobalamin and heme synthesis pathways,predominantly driven by Cutibacterium acnes.This pioneering study unveils the paradigm for the hidden links between skin microbiome and skin imaging phenome,providing novel insights into how skin microbiome shapes skin appearance and its healthy aging.展开更多
Plant height(PH)is an essential trait in maize(Zea mays)that is tightly associated with planting density,biomass,lodging resistance,and grain yield in the field.Dissecting the dynamics of maize plant architecture will...Plant height(PH)is an essential trait in maize(Zea mays)that is tightly associated with planting density,biomass,lodging resistance,and grain yield in the field.Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction,as the genetic basis controlling PH in maize remains largely unknown.In this study,we developed an automated high-throughput phenotyping platform(HTP)to systematically and noninvasively quantify 77 image-based traits(i-traits)and 20 field traits(f-traits)for 228 maize inbred lines across all developmental stages.Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth.An i-trait-based genome-wide association study identified 4945 traitassociated SNPs,2603 genetic loci,and 1974 corresponding candidate genes.We found that rapid growth of maize plants occurs mainly at two developmental stages,stage 2(S2)to S3 and S5 to S6,accounting for the final PH indicators.By integrating the PH-association network with the transcriptome profiles of specific internodes,we revealed 13 hub genes that may play vital roles during rapid growth.The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize.One candidate gene,ZmVATE,was functionally validated and shown to regulate PH-related traits in maize using genetic mutation.Furthermore,machine learning was used to build predictive models for final PH based on i-traits,and their performancewas assessed across developmental stages.Moderate,strong,and very strong correlations between predictions and experimental datasets were achieved from the early S4(tenth-leaf)stage.Colletively,our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH,as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.展开更多
The ISGA(International Symposium on Genetics in Aquaculture)is an important conference in the field of aquaculture genetics,which is held every three years.This year,the meeting was hosted by James Cook University,in ...The ISGA(International Symposium on Genetics in Aquaculture)is an important conference in the field of aquaculture genetics,which is held every three years.This year,the meeting was hosted by James Cook University,in Cairns.The conference sessions included biotechnology and functional genomics,sex control,genomic prediction,selective breeding and quantitative genetics,industrial use of genetics,genome technology,genetics of diseases and stress,genetics of nutrition,epigenetics,genomics and metabolomes,population genetics and ethics,food safety,as well as environmental risks.Many new and interesting unpublished data,including those for new aquaculture species,marker-assisted selection,genomic selection and genome editing using Crispr/Cas9 technologies,were reported at the conference.In this brief review,we highlight the novel and interesting researches on aquaculture genetics and genomics to give readers an overview of the current status and trends of aquaculture genetics and genomics research.展开更多
Microarray and deep sequencing technologies have provided unprecedented opportunities for mapping genome mutations,RNA transcripts,transcription factor binding,and histone modifications at high resolution at the genom...Microarray and deep sequencing technologies have provided unprecedented opportunities for mapping genome mutations,RNA transcripts,transcription factor binding,and histone modifications at high resolution at the genome-wide level.This has revolutionized the way in which transcriptomes,regulatory networks and epigenetic regulations have been studied and large amounts of heterogeneous data have been generated.Although efforts are being made to integrate these datasets unbiasedly and efficiently,how best to do this still remains a challenge.Here we review major impacts of high-throughput genome-wide data generation,their relevance to human diseases,and various bioinformatics approaches for data integration.Finally,we provide a case study on inflammatory diseases.展开更多
This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of sho...This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.展开更多
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.
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 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.
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.
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.
基金supported by the STI2030-Major Projects(2021ZD0200900 to Y.G.Y.)"Light of West China" Program of the Chinese Academy of Sciences(xbzg-zdsys-202302 to Y.G.Y.)
文摘The tree shrew(Tupaia belangeri)has long been proposed as a suitable alternative to non-human primates(NHPs)in biomedical and laboratory research due to its close evolutionary relationship with primates.In recent years,significant advances have facilitated tree shrew studies,including the determination of the tree shrew genome,genetic manipulation using spermatogonial stem cells,viral vector-mediated gene delivery,and mapping of the tree shrew brain atlas.However,the limited availability of tree shrews globally remains a substantial challenge in the field.Additionally,determining the key questions best answered using tree shrews constitutes another difficulty.Tree shrew models have historically been used to study hepatitis B virus(HBV)and hepatitis C virus(HCV)infection,myopia,and psychosocial stress-induced depression,with more recent studies focusing on developing animal models for infectious and neurodegenerative diseases.Despite these efforts,the impact of tree shrew models has not yet matched that of rodent or NHP models in biomedical research.This review summarizes the prominent advancements in tree shrew research and reflects on the key biological questions addressed using this model.We emphasize that intensive dedication and robust international collaboration are essential for achieving breakthroughs in tree shrew studies.The use of tree shrews as a unique resource is expected to gain considerable attention with the application of advanced techniques and the development of viable animal models,meeting the increasing demands of life science and biomedical research.
基金supported by the National Key Research and Development Program of China(2016YFD0100101-18,2020YFD1000904-1-3)the National Natural Science Foundation of China(31601216,31770397)Fundamental Research Funds for the Central Universities(2662019QD053,2662020ZKPY017)。
文摘With the rapid development of genetic analysis techniques and crop population size,phenotyping has become the bottleneck restricting crop breeding.Breaking through this bottleneck will require phenomics,defined as the accurate,high-throughput acquisition and analysis of multi-dimensional phenotypes during crop growth at organism-wide levels,ranging from cells to organs,individual plants,plots,and fields.Here we offer an overview of crop phenomics research from technological and platform viewpoints at various scales,including microscopic,ground-based,and aerial phenotyping and phenotypic data analysis.We describe recent applications of high-throughput phenotyping platforms for abiotic/biotic stress and yield assessment.Finally,we discuss current challenges and offer perspectives on future phenomics research.
基金supported by the National Natural Science Foundation of China(32072980)Key Research and Development Projects in Tibet(XZ202001ZY0016N,XZ201902NB02,XZNKY-2019-C-053)。
文摘Fish morphological phenotypes are important resources in artificial breeding,functional gene mapping,and population-based studies in aquaculture and ecology.Traditional morphological measurement of phenotypes is rather expensive in terms of time and labor.More importantly,manual measurement is highly dependent on operational experience,which can lead to subjective phenotyping results.Here,we developed 3DPhenoFish software to extract fish morphological phenotypes from three-dimensional(3D)point cloud data.Algorithms for background elimination,coordinate normalization,image segmentation,key point recognition,and phenotype extraction were developed and integrated into an intuitive user interface.Furthermore,18 key points and traditional 2D morphological traits,along with 3D phenotypes,including area and volume,can be automatically obtained in a visualized manner.Intuitive fine-tuning of key points and customized definitions of phenotypes are also allowed in the software.Using 3DPhenoFish,we performed high-throughput phenotyping for four endemic Schizothoracinae species,including Schizopygopsis younghusbandi,Oxygymnocypris stewartii,Ptychobarbus dipogon,and Schizothorax oconnori.Results indicated that the morphological phenotypes from 3DPhenoFish exhibited high linear correlation(>0.94)with manual measurements and offered informative traits to discriminate samples of different species and even for different populations of the same species.In summary,we developed an efficient,accurate,and customizable tool,3DPhenoFish,to extract morphological phenotypes from point cloud data,which should help overcome traditional challenges in manual measurements.3DPhenoFish can be used for research on morphological phenotypes in fish,including functional gene mapping,artificial selection,and conservation studies.3DPhenoFish is an open-source software and can be downloaded for free at https://github.com/lyh24k/3DPhenoFish/tree/master.
基金The authors wish to thank Menachem Moshelion for useful discussions.This work is supported by National Natural Science Foundation(NSFC)of China(Grant No.31772299)NSFC-Israeli Science Foundation(ISF)joint project(Grant No.31861143044)National Program for Support of Top-Notch Young Professionals(to P.X.).
文摘Phenomics is a new branch of science that provides high-throughput quantification of plant and animal traits at systems level.The last decade has witnessed great successes in high-throughput phenotyping of numerous morphological traits,yet major challenges still exist in precise phenotyping of physiological traits such as transpiration and photosynthesis.Due to the highly dynamic nature of physiological traits in responses to the environment,appropriate selection criteria and efficient screening systems at the physiological level for abiotic stress tolerance have been largely absent in plants.In this review,the current status of phenomics techniques was briefly summarized in horticultural plants.Specifically,the emerging field of high-throughput physiology-based phenotyping,which is referred to as“physiolomics”,for drought stress responseswas highlighted.In addition to analyzing the advantages of physiology-based phenotyping overmorphology-based approaches,recent examples that applied high-throughput physiological phenotyping to model and non-model horticultural plants were revisited and discussed.Based on the collective findings,we propose that high-throughput,non-destructive,and automatic physiological assays can and should be used as routine methods for phenotyping stress response traits in horticultural plants.
文摘Objective: This study aimed to explore the experiences of women in the process of formula feeding their infants. The World Health Organization has emphasized the importance of breastfeeding for infant health. After decades of breastfeeding promotions,breastfeeding rates in Hong Kong have been rising consistently; however, the low continuation rate is alarming. This study explores women's experiences with formula feeding their infants, including factors affecting their decision to do so.Methods: A qualitative approach using an interpretative phenomenological analysis(IPA) was adopted as the study design. Data were collected from 2014 to 2015 through individual in-depth unstructured interviews with 16 women, conducted between 3 and 12 months after the birth of their infant. Data were analyzed using IPA.Results: Three main themes emerged as follows:(1) self-struggle, with the subthemes of feeling like a milk cow and feeling trapped;(2) family conflict, with the subtheme of sharing the spotlight; and(3) interpersonal tensions, with the subthemes of embarrassment,staring, and innocence. Many mothers suffered various stressors and frustrations during breastfeeding. These findings suggest a number of pertinent areas that need to be considered in preparing an infant feeding campaign.Conclusions: The findings of this study reinforce our knowledge of women's struggles with multiple sources of pressure, such as career demands, childcare demands, and family life after giving birth. All mothers should be given assistance in making informed decisions about the optimal approach to feeding their babies given their individual situation and be provided with support to pursue their chosen feeding method.
文摘An emerging area of interest in understanding disease phenotypes is systems genomics.Complex diseases such as diabetes have played an important role towards understanding the susceptible genes and mutations.A wide number of methods have been employed and strategies such as polygenic risk score and allele frequencies have been useful,but understanding the candidate genes harboring those mutations is an unmet goal.In this perspective,using systems genomic approaches,we highlight the application of phenome-interactome networks in diabetes and provide deep insights.LINC01128,which we previously described as candidate for diabetes,is shown as an example to discuss the approach.
基金supported by the National Natural Science Foundation of China(Grant Nos.32071465,31871334,and 31671374)the National Key R&D Program of China(Grant No.2018YFC0910502)Yuhao Zhang(Huazhong University of Science and Technology,China)to improve the analysis of this study。
文摘Despite the skin microbiome has been linked to skin health and diseases,its role in modulating human skin appearance remains understudied.Using a total of 1244 face imaging phenomes and 246 cheek metagenomes,we first established three skin age indices by machine learning,including skin phenotype age(SPA),skin microbiota age(SMA),and skin integration age(SIA)as surrogates of phenotypic aging,microbial aging,and their combination,respectively.Moreover,we found that besides aging and gender as intrinsic factors,skin microbiome might also play a role in shaping skin imaging phenotypes(SIPs).Skin taxonomic and functionalαdiversity was positively linked to melanin,pore,pigment,and ultraviolet spot levels,but negatively linked to sebum,lightening,and porphyrin levels.Furthermore,certain species were correlated with specific SIPs,such as sebum and lightening levels negatively correlated with Corynebacterium matruchotii,Staphylococcus capitis,and Streptococcus sanguinis.Notably,we demonstrated skin microbial potential in predicting SIPs,among which the lightening level presented the least error of 1.8%.Lastly,we provided a reservoir of potential mechanisms through which skin microbiome adjusted the SIPs,including the modulation of pore,wrinkle,and sebum levels by cobalamin and heme synthesis pathways,predominantly driven by Cutibacterium acnes.This pioneering study unveils the paradigm for the hidden links between skin microbiome and skin imaging phenome,providing novel insights into how skin microbiome shapes skin appearance and its healthy aging.
基金supported by the National Key Research and Development Program of China(2021YFF1000301 and 2021YFF1000304)the National Natural Science Foundation of China(32172091)+4 种基金the National Key Research and Development Program of China(2016YFD0100103)the Fundamental Research Funds for Central Non-Profit of Chinese Academy of Agricultural Sciences(CAAS-ZDRW202109 and Y2020PT06)the Innovation Program of the Chinese Academy of Agricultural Sciences(CAAS-ZDRW202004)the 2020 Research Program of Sanya Yazhou Bay Science and Technology City(SKJC-2020-02-005)the Nanfan special project of the Chinese Academy of Agricultural Sciences(YBXM15).
文摘Plant height(PH)is an essential trait in maize(Zea mays)that is tightly associated with planting density,biomass,lodging resistance,and grain yield in the field.Dissecting the dynamics of maize plant architecture will be beneficial for ideotype-based maize breeding and prediction,as the genetic basis controlling PH in maize remains largely unknown.In this study,we developed an automated high-throughput phenotyping platform(HTP)to systematically and noninvasively quantify 77 image-based traits(i-traits)and 20 field traits(f-traits)for 228 maize inbred lines across all developmental stages.Time-resolved i-traits with novel digital phenotypes and complex correlations with agronomic traits were characterized to reveal the dynamics of maize growth.An i-trait-based genome-wide association study identified 4945 traitassociated SNPs,2603 genetic loci,and 1974 corresponding candidate genes.We found that rapid growth of maize plants occurs mainly at two developmental stages,stage 2(S2)to S3 and S5 to S6,accounting for the final PH indicators.By integrating the PH-association network with the transcriptome profiles of specific internodes,we revealed 13 hub genes that may play vital roles during rapid growth.The candidate genes and novel i-traits identified at multiple growth stages may be used as potential indicators for final PH in maize.One candidate gene,ZmVATE,was functionally validated and shown to regulate PH-related traits in maize using genetic mutation.Furthermore,machine learning was used to build predictive models for final PH based on i-traits,and their performancewas assessed across developmental stages.Moderate,strong,and very strong correlations between predictions and experimental datasets were achieved from the early S4(tenth-leaf)stage.Colletively,our study provides a valuable tool for dissecting the spatiotemporal formation of specific internodes and the genetic architecture of PH,as well as resources and predictive models that are useful for molecular design breeding and predicting maize varieties with ideal plant architectures.
文摘The ISGA(International Symposium on Genetics in Aquaculture)is an important conference in the field of aquaculture genetics,which is held every three years.This year,the meeting was hosted by James Cook University,in Cairns.The conference sessions included biotechnology and functional genomics,sex control,genomic prediction,selective breeding and quantitative genetics,industrial use of genetics,genome technology,genetics of diseases and stress,genetics of nutrition,epigenetics,genomics and metabolomes,population genetics and ethics,food safety,as well as environmental risks.Many new and interesting unpublished data,including those for new aquaculture species,marker-assisted selection,genomic selection and genome editing using Crispr/Cas9 technologies,were reported at the conference.In this brief review,we highlight the novel and interesting researches on aquaculture genetics and genomics to give readers an overview of the current status and trends of aquaculture genetics and genomics research.
文摘Microarray and deep sequencing technologies have provided unprecedented opportunities for mapping genome mutations,RNA transcripts,transcription factor binding,and histone modifications at high resolution at the genome-wide level.This has revolutionized the way in which transcriptomes,regulatory networks and epigenetic regulations have been studied and large amounts of heterogeneous data have been generated.Although efforts are being made to integrate these datasets unbiasedly and efficiently,how best to do this still remains a challenge.Here we review major impacts of high-throughput genome-wide data generation,their relevance to human diseases,and various bioinformatics approaches for data integration.Finally,we provide a case study on inflammatory diseases.
基金supported by the Office of Science (BER), U.S. Department of Energy through Interagency Agreement DE-SC0001526the Australian Grain Research and Development Corporation (GRDC)
文摘This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. Higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.
