Dear Editor, Eukaryotic transcriptional regulation networks are extremely complex. Usually, multiple transcription factors (TFs) bind to the promoter region of a gene and cooperate to control gene expression precisely...Dear Editor, Eukaryotic transcriptional regulation networks are extremely complex. Usually, multiple transcription factors (TFs) bind to the promoter region of a gene and cooperate to control gene expression precisely. Identifying cooperative TFs remains a major challenge in modem biological research. Various types of data, including genomic sequences, expression profiles, ChiP-chip data and protein-protein interactions, have been used to identify mechanisms of cooperative transcriptional regulation.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
1碳达峰与碳中和研究的紧迫性1975年,Broecker[1]在Science上发表一篇文章“Climat change:Are we on the brink of a pronounced global warming?”使得大气中CO_(2)增加导致气候变暖的概念第一次走进人们的视野.大气CO_(2)增加主要是...1碳达峰与碳中和研究的紧迫性1975年,Broecker[1]在Science上发表一篇文章“Climat change:Are we on the brink of a pronounced global warming?”使得大气中CO_(2)增加导致气候变暖的概念第一次走进人们的视野.大气CO_(2)增加主要是由于人类对化石能源的利用及人类活动导致的土地利用改变[2].目前,大气CO_(2)浓度约为415 ppm(1 ppm=1μmol/mol,Global Carbon Budget 2020,https://www.globalcarbonproject.org/carbonbudget/index.htm)。展开更多
C_(4) photosynthesis evolved from ancestral C_(3) photosynthesis by recruiting pre-existing genes to fulfill new functions.The enzymes and transporters required for the C_(4) metabolic pathway have been intensively st...C_(4) photosynthesis evolved from ancestral C_(3) photosynthesis by recruiting pre-existing genes to fulfill new functions.The enzymes and transporters required for the C_(4) metabolic pathway have been intensively studied and well documented;however,the transcription factors(TFs)that regulate these C_(4) metabolic genes are not yet well understood.In particular,how the TF regulatory network of C_(4) metabolic genes was rewired during the evolutionary process is unclear.Here,we constructed gene regulatory networks(GRNs)for four closely evolutionarily related species from the genus Flaveria,which represent four different evolutionary stages of C_(4) photosynthesis:C_(3)(F.robusta),type Ⅰ C_(3)-C_(4)(F.sonorensis),type Ⅱ C_(3)-C_(4)(F.ramosissima),and C_(4)(F.trinervia).Our results show that more than half of the co-regulatory relationships between TFs and core C_(4) metabolic genes are species specific.The counterparts of the C_(4) genes in C_(3) species were already co-regulated with photosynthesis-related genes,whereas the required TFs for C_(4) photosynthesis were recruited later.The TFs involved in C_(4) photosynthesis were widely recruited in the type Ⅰ C_(3)-C_(4) species;nevertheless,type Ⅱ C_(3)-C_(4) species showed a divergent GRN from C_(4) species.In line with these findings,a ^(13)CO_(2) pulse-labeling experiment showed that the CO_(2) initially fixed into C_(4) acid was not directly released to the Calvin–Benson–Bassham cycle in the type Ⅱ C_(3)-C_(4) species.Therefore,our study uncovered dynamic changes in C_(4) genes and TF co-regulation during the evolutionary process;furthermore,we showed that the metabolic pathway of the type Ⅱ C_(3)-C_(4) species F.ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C_(3)-C_(4) intermediate species.展开更多
Background： The increase in global population, climate change and stagnancy in crop yield on unit land area basis in recent decades urgently call for a new approach to support contemporary crop improvements, ePlant i...Background： The increase in global population, climate change and stagnancy in crop yield on unit land area basis in recent decades urgently call for a new approach to support contemporary crop improvements, ePlant is a mathematical model of plant growth and development with a high level of mechanistic details to meet this challenge. Results： ePlant integrates modules developed for processes occurring at drastically different temporal （10-8-106 seconds） and spatial （10-10-10 meters） scales, incorporating diverse physical, biophysical and biochemical processes including gene regulation, metabolic reaction, substrate transport and diffusion, energy absorption, transfer and conversion, organ morphogenesis, plant environment interaction, etc. Individual modules are developed using a divide-and-conquer approach; modules at different temporal and spatial scales are integrated through transfer variables. We further propose a supervised learning procedure based on information geometry to combine model and data for both knowledge discovery and model extension or advances. We finally discuss the recent formation of a global consortium, which includes experts in plant biology, computer science, statistics, agronomy, phenomics, etc. aiming to expedite the development and application of ePlant or its equivalents by promoting a new model development paradigm where models are developed as a community effort instead of driven mainly by individual labs＇ effort. Conclusions： ePlant, as a major research tool to support quantitative and predictive plant science research, will play a crucial role in the future model guided crop engineering, breeding and agronomy.展开更多
A large number of genes related to source, sink,and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This pe...A large number of genes related to source, sink,and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow;then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level,and the non-linear complex interaction between source,sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.展开更多
Engineering the C4 photosynthetic pathway into C3 crops has the potential to dramatically increase the yields of major C3 crops. The genetic control of features involved in C4 photosynthesis are still far from being u...Engineering the C4 photosynthetic pathway into C3 crops has the potential to dramatically increase the yields of major C3 crops. The genetic control of features involved in C4 photosynthesis are still far from being understood; which partially explains why we have gained little success in C4 engineering thus far. Next generation sequencing techniques and other high throughput technologies are offering an unprecedented opportunity to elucidate the developmental and evolutionary processes of C4 photosynthesis. Two contrasting hypotheses about the evolution of C4 photosynthesis exist, i.e. the master switch hypothesis and the incremental gain hypothesis. These two hypotheses demand two different research strategies to proceed in parallel to maximize the success of C4 engineering. In either case, systems biology research will play pivotal roles in identifying key regulatory elements controlling development of C4 features, identifying essential biochemical and anatomical features required to achieve high photosynthetic efficiency, elucidating genetic mechanisms underlining C4 differentiation and ultimately identifying viable routes to engineer C4 rice. As a highly interdisciplinary project, the C4 rice project will have far-reaching impacts on both basic and applied research related to agriculture in the 21st century.展开更多
This paper analyzes a mathematical model of the photosynthetic carbon metabolism, which incorporates not only the Calvin-Benson cycle, but also another two important metabolic pathways： starch synthesis and photoresp...This paper analyzes a mathematical model of the photosynthetic carbon metabolism, which incorporates not only the Calvin-Benson cycle, but also another two important metabolic pathways： starch synthesis and photorespiratory pathway. Theoretically, the paper shows the existence of steady states, stability and instability of the steady states, the effects of CO2 concentration on steady states. Especially, a critical point is found, the system has only one steady state with C02 concentration in the left neighborhood of the critical point, but has two with C02 concentration in the right neighborhood. In addition, the paper also explores the influence of C02 concentration on the efficiency of photosynthesis. These theoretical results not only provide insight to the kinetic behaviors of the photosynthetic carbon metabolism, but also can be used to help improving the efficiency of photosynthesis in plants.展开更多
Canopy photosynthesis is the sum of photosynthesis of all above-ground photosynthetic tissues.Quantitative roles of nonfoliar tissues in canopy photosynthesis remain elusive due to methodology limitations.Here,we deve...Canopy photosynthesis is the sum of photosynthesis of all above-ground photosynthetic tissues.Quantitative roles of nonfoliar tissues in canopy photosynthesis remain elusive due to methodology limitations.Here,we develop the first complete canopy photosynthesis model incorporating all above-ground photosynthetic tissues and validate this model on wheat with state-of-the-art gas exchange measurement facilities.展开更多
基金This work was supported by the National Basic Research Program of China (Grant Nos. 2009CB918404 and 2006CB910700), International S&T Cooperation Program of China (Grant No. 2007DFA31040) and the National Natural Science Foundation of China (Grant Nos. 30700154 and 31070746).
文摘Dear Editor, Eukaryotic transcriptional regulation networks are extremely complex. Usually, multiple transcription factors (TFs) bind to the promoter region of a gene and cooperate to control gene expression precisely. Identifying cooperative TFs remains a major challenge in modem biological research. Various types of data, including genomic sequences, expression profiles, ChiP-chip data and protein-protein interactions, have been used to identify mechanisms of cooperative transcriptional regulation.
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.
文摘1碳达峰与碳中和研究的紧迫性1975年,Broecker[1]在Science上发表一篇文章“Climat change:Are we on the brink of a pronounced global warming?”使得大气中CO_(2)增加导致气候变暖的概念第一次走进人们的视野.大气CO_(2)增加主要是由于人类对化石能源的利用及人类活动导致的土地利用改变[2].目前,大气CO_(2)浓度约为415 ppm(1 ppm=1μmol/mol,Global Carbon Budget 2020,https://www.globalcarbonproject.org/carbonbudget/index.htm)。
基金supported by the National Natural Science Foundation of China(32088102,31730103,31825003,32050081,and 31870218)the CAS Project for Young Scientists in Basic Research(YSBR-011)+2 种基金the Strategic Priority Research Program “Molecular Mechanism of Plant Growth and Development”of the Chinese Academy of Sciences(XDB27040207)the National Key R&D Program of China(2019YFA0904703 and 2016YFA0500502)the Young Elite Scientists Sponsorship Program by CAST(20202022QNRC001/2/3)。
基金supported by the Strategic Priority Research Program of the General Project of the Chinese Academy of Sciences(grant no.XDB27020105)by the National Research and Development Program of the Ministry of Science and Technology of the People’s Republic of China,MSTC(2019YFA0904600).
文摘C_(4) photosynthesis evolved from ancestral C_(3) photosynthesis by recruiting pre-existing genes to fulfill new functions.The enzymes and transporters required for the C_(4) metabolic pathway have been intensively studied and well documented;however,the transcription factors(TFs)that regulate these C_(4) metabolic genes are not yet well understood.In particular,how the TF regulatory network of C_(4) metabolic genes was rewired during the evolutionary process is unclear.Here,we constructed gene regulatory networks(GRNs)for four closely evolutionarily related species from the genus Flaveria,which represent four different evolutionary stages of C_(4) photosynthesis:C_(3)(F.robusta),type Ⅰ C_(3)-C_(4)(F.sonorensis),type Ⅱ C_(3)-C_(4)(F.ramosissima),and C_(4)(F.trinervia).Our results show that more than half of the co-regulatory relationships between TFs and core C_(4) metabolic genes are species specific.The counterparts of the C_(4) genes in C_(3) species were already co-regulated with photosynthesis-related genes,whereas the required TFs for C_(4) photosynthesis were recruited later.The TFs involved in C_(4) photosynthesis were widely recruited in the type Ⅰ C_(3)-C_(4) species;nevertheless,type Ⅱ C_(3)-C_(4) species showed a divergent GRN from C_(4) species.In line with these findings,a ^(13)CO_(2) pulse-labeling experiment showed that the CO_(2) initially fixed into C_(4) acid was not directly released to the Calvin–Benson–Bassham cycle in the type Ⅱ C_(3)-C_(4) species.Therefore,our study uncovered dynamic changes in C_(4) genes and TF co-regulation during the evolutionary process;furthermore,we showed that the metabolic pathway of the type Ⅱ C_(3)-C_(4) species F.ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C_(3)-C_(4) intermediate species.
基金The work in XGZ＇s lab is supported by CAS strategic leading project on designer breeding by molecular module （No. XDA08020301）, the National High Technology Development Plan of the Ministry of Science and Technology of China （2014AA101601）, the National Natural Science Foundation of China （No. C020401）, the National Key Basic Research Program of China （No. 2015CB150104）, Bill and Melinda Gates Foundation （No. OPP1060461）, CAS-CSIRO Cooperative Research Program （No. GJHZ1501）.
文摘Background： The increase in global population, climate change and stagnancy in crop yield on unit land area basis in recent decades urgently call for a new approach to support contemporary crop improvements, ePlant is a mathematical model of plant growth and development with a high level of mechanistic details to meet this challenge. Results： ePlant integrates modules developed for processes occurring at drastically different temporal （10-8-106 seconds） and spatial （10-10-10 meters） scales, incorporating diverse physical, biophysical and biochemical processes including gene regulation, metabolic reaction, substrate transport and diffusion, energy absorption, transfer and conversion, organ morphogenesis, plant environment interaction, etc. Individual modules are developed using a divide-and-conquer approach; modules at different temporal and spatial scales are integrated through transfer variables. We further propose a supervised learning procedure based on information geometry to combine model and data for both knowledge discovery and model extension or advances. We finally discuss the recent formation of a global consortium, which includes experts in plant biology, computer science, statistics, agronomy, phenomics, etc. aiming to expedite the development and application of ePlant or its equivalents by promoting a new model development paradigm where models are developed as a community effort instead of driven mainly by individual labs＇ effort. Conclusions： ePlant, as a major research tool to support quantitative and predictive plant science research, will play a crucial role in the future model guided crop engineering, breeding and agronomy.
基金Research funding by the CAS Strategic Leading Project (XDA08020301)National Natural Science Foundation of China (31501240)+4 种基金the open funding from State Key Laboratory of Hybrid Rice (2016KF06)the CAS-CSIRO collaboration grant (GJHZ1501)National Key Research and Development Program of China (2017YFD0301502)the project of Hunan Provincial Natural Science Foundation of China (2018JJ2286)the project of Hunan Academy of Agricultural Sciences (2017JC04)
文摘A large number of genes related to source, sink,and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow;then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level,and the non-linear complex interaction between source,sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.
基金supported by the Bill and Melinda Gates FoundationShanghai PuJiang Talent ProgramSIBS President's special grant for Dry-lab and Wet-lab collaboration,Max PlanckSociety,and Chinese Academy of Sciences.
文摘Engineering the C4 photosynthetic pathway into C3 crops has the potential to dramatically increase the yields of major C3 crops. The genetic control of features involved in C4 photosynthesis are still far from being understood; which partially explains why we have gained little success in C4 engineering thus far. Next generation sequencing techniques and other high throughput technologies are offering an unprecedented opportunity to elucidate the developmental and evolutionary processes of C4 photosynthesis. Two contrasting hypotheses about the evolution of C4 photosynthesis exist, i.e. the master switch hypothesis and the incremental gain hypothesis. These two hypotheses demand two different research strategies to proceed in parallel to maximize the success of C4 engineering. In either case, systems biology research will play pivotal roles in identifying key regulatory elements controlling development of C4 features, identifying essential biochemical and anatomical features required to achieve high photosynthetic efficiency, elucidating genetic mechanisms underlining C4 differentiation and ultimately identifying viable routes to engineer C4 rice. As a highly interdisciplinary project, the C4 rice project will have far-reaching impacts on both basic and applied research related to agriculture in the 21st century.
基金Supported by the National Natural Science Foundation of China(No.11071238)the Key Lab of Random Complex Structures and Data Science,CAS(No.2008DP173182)the National Center for Mathematics and interdisciplinary Sciences,CAS(N0.Y029184K51)
文摘This paper analyzes a mathematical model of the photosynthetic carbon metabolism, which incorporates not only the Calvin-Benson cycle, but also another two important metabolic pathways： starch synthesis and photorespiratory pathway. Theoretically, the paper shows the existence of steady states, stability and instability of the steady states, the effects of CO2 concentration on steady states. Especially, a critical point is found, the system has only one steady state with C02 concentration in the left neighborhood of the critical point, but has two with C02 concentration in the right neighborhood. In addition, the paper also explores the influence of C02 concentration on the efficiency of photosynthesis. These theoretical results not only provide insight to the kinetic behaviors of the photosynthetic carbon metabolism, but also can be used to help improving the efficiency of photosynthesis in plants.
基金This work was supported by the open research fund of the State Key Laboratory of Hybrid Rice(Hunan Hybrid Rice Research Center)to T.C.(2020KF01)the National Natural Science Foundation of China to T.C.(32000285)and Q.S.(31970378)+1 种基金the Chinese Academy of Science strategic lead-ing project to X.Z.(XDB27020105)the funding from the BASF Belgium Coordination Center-Innovation Center Gent to X.Z..
文摘Canopy photosynthesis is the sum of photosynthesis of all above-ground photosynthetic tissues.Quantitative roles of nonfoliar tissues in canopy photosynthesis remain elusive due to methodology limitations.Here,we develop the first complete canopy photosynthesis model incorporating all above-ground photosynthetic tissues and validate this model on wheat with state-of-the-art gas exchange measurement facilities.
