Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a princi...Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.展开更多
Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated rice.Our previous study revealed a difference in the frequency of the O...Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated rice.Our previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is unclear.In this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland conditions.OsNCED2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought tolerance.OsNCED2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland conditions.OsNCED2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice.展开更多
Rice yield is an important and complex agronomic trait controlled by multiple genes.In recent decades,dozens of yield-associated genes in rice have been cloned,many of which can increase production in the form of loss...Rice yield is an important and complex agronomic trait controlled by multiple genes.In recent decades,dozens of yield-associated genes in rice have been cloned,many of which can increase production in the form of loss or degeneration of function.However,mutations occurring randomly under natural conditions have provided very limited genetic resources for yield increases.In this study,potentially yield-increasing alleles of two genes closely associated with yield were edited artificially.The recently developed CRISPR/Cas9system was used to edit two yield genes:Grain number 1a(Gn1a)and DENSE AND ERECT PANICLE1(DEP1).Several mutants were identified by a target sequence analysis.Phenotypic analysis confirmed one mutant allele of Gn1a and three of DEP1 conferring yield superior to that conferred by other natural high-yield alleles.Our results demonstrate that favorable alleles of the Gnla and DEP1 genes,which are considered key factors in rice yield increases,could be developed by artificial mutagenesis using genome editing technology.展开更多
Plant microRNAs(miRNAs)play important roles in biological processes such as development and stress responses.Although the diverse functions of miRNAs in model organisms have been well studied,their function in wild ri...Plant microRNAs(miRNAs)play important roles in biological processes such as development and stress responses.Although the diverse functions of miRNAs in model organisms have been well studied,their function in wild rice is poorly understood.In this study,high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata.A total of 603 miRNAs,380 known rice miRNAs,72 conserved plant miRNAs,and151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes.Additionally,99 and 79 miRNAs were expressed exclusively or differentially,respectively,in the two tissues,and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes.Functional annotation of these targets suggested that transcription factors,including squamosa promoter binding proteins and auxin response factors,function in rhizome growth and development.The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR,and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets.Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′end amplification.These results provide valuable information on the composition,expression and function of miRNAs in O.longistaminata,and will aid in understanding the molecular mechanisms of rhizome development.展开更多
Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A...Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient.To fill this gap,we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas.For individual candidate among1,500,000 quantified RNA editing events,we performed diverse types of downstream functional annotations.Finally,we identified 24,236 potentially functional A-to-I RNA editing events,including the cases in APOL1,IGFBP3,GRIA2,BLCAP,and miR-589-3p.These events might play crucial roles in the scenarios of tumorigenesis,due to their tumor-related editing frequencies or probable effects on altered expression profiles,protein functions,splicing patterns,and microRNA regulations of tumor genes.Our functional A-to-I RNA editing events(https://ccsm.uth.edu/CAeditome/)will help better understand the cancer pathology from the A-to-I RNA editing aspect.展开更多
Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the g...Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery.Here,we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group.We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method,i.e.,dynamic cross-tissue(DCT)network analysis.We used one of the candidate genes,Os SPL4,whose function was previously unknown,for gene editing experimental validation of the high yield,and confirmed that Os SPL4 significantly affects panicle branching and increases the rice yield.This study,which included extensive field phenotyping,cross-tissue systems biology analyses,and functional validation,uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice.The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample.DCT can be downloaded from https://github.com/ztpub/DCT.展开更多
Dear Editor,Anesthetic-induced unconsciousness is accompanied by decreased information exchange among relevant cortical functional modular areas that support normal cognitive function[1].Using the electroencephalogram...Dear Editor,Anesthetic-induced unconsciousness is accompanied by decreased information exchange among relevant cortical functional modular areas that support normal cognitive function[1].Using the electroencephalogram(EEG)signal,evidence suggest that the feedback and feedforward connectivity among cortical regions may be asymmetrically affected during anesthetic-induced anesthesia[2].展开更多
基金supported by grants from the National Natural Science Foundation of China(32272079 and 32060474)the Yunnan Provincial Science and Technology Department,China(202101AS070001 and 202201BF070001-011)。
文摘Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.
基金This work was supported by the National Natural Science Foundation of China(U1602266,32060474,and 31601274)grants from the Yunnan Provincial Science and Technology Department(202005AF150009 and 202101AS070001).
文摘Upland rice shows dryland adaptation in the form of a deeper and denser root system and greater drought resistance than its counterpart,irrigated rice.Our previous study revealed a difference in the frequency of the OsNCED2 gene between upland and irrigated populations.A nonsynonymous mutation(C to T,from irrigated to upland rice)may have led to functional variation fixed by artificial selection,but the exact biological function in dryland adaptation is unclear.In this study,transgenic and association analysis indicated that the domesticated fixed mutation caused functional variation in OsNCED2,increasing ABA levels,root development,and drought tolerance in upland rice under dryland conditions.OsNCED2-overexpressing rice showed increased reactive oxygen species-scavenging abilities and transcription levels of many genes functioning in stress response and development that may regulate root development and drought tolerance.OsNCED2^(T)-NILs showed a denser root system and drought resistance,promoting the yield of rice under dryland conditions.OsNCED2^(T)may confer dryland adaptation in upland rice and may find use in breeding dryland-adapted,water-saving rice.
基金the Department of Sciences and Technology of Yunnan Province (2016BB001)the National Basic Research Program of China (2013CB835200)a Key Grant of Yunnan Provincial Science and Technology Department (2013GA004)
文摘Rice yield is an important and complex agronomic trait controlled by multiple genes.In recent decades,dozens of yield-associated genes in rice have been cloned,many of which can increase production in the form of loss or degeneration of function.However,mutations occurring randomly under natural conditions have provided very limited genetic resources for yield increases.In this study,potentially yield-increasing alleles of two genes closely associated with yield were edited artificially.The recently developed CRISPR/Cas9system was used to edit two yield genes:Grain number 1a(Gn1a)and DENSE AND ERECT PANICLE1(DEP1).Several mutants were identified by a target sequence analysis.Phenotypic analysis confirmed one mutant allele of Gn1a and three of DEP1 conferring yield superior to that conferred by other natural high-yield alleles.Our results demonstrate that favorable alleles of the Gnla and DEP1 genes,which are considered key factors in rice yield increases,could be developed by artificial mutagenesis using genome editing technology.
基金supported by the National Natural Science Foundation of China(31271694 and U1302264)
文摘Plant microRNAs(miRNAs)play important roles in biological processes such as development and stress responses.Although the diverse functions of miRNAs in model organisms have been well studied,their function in wild rice is poorly understood.In this study,high-throughput small RNA sequencing was performed to characterize tissue-specific transcriptomes in Oryza longistaminata.A total of 603 miRNAs,380 known rice miRNAs,72 conserved plant miRNAs,and151 predicted novel miRNAs were identified as being expressed in aerial shoots and rhizomes.Additionally,99 and 79 miRNAs were expressed exclusively or differentially,respectively,in the two tissues,and 144 potential targets were predicted for the differentially expressed miRNAs in the rhizomes.Functional annotation of these targets suggested that transcription factors,including squamosa promoter binding proteins and auxin response factors,function in rhizome growth and development.The expression levels of several miRNAs and target genes in the rhizomes were quantified by RT-PCR,and the results indicated the existence of complex regulatory mechanisms between the miRNAs and their targets.Eight target cleavage sites were verified by RNA ligase-mediated rapid 5′end amplification.These results provide valuable information on the composition,expression and function of miRNAs in O.longistaminata,and will aid in understanding the molecular mechanisms of rhizome development.
基金supported by the National Natural Science Foundation of China(Grant No.62002270)the Fundamental Research Funds for the Central Universities,the Natural Science Foundation of Shaanxi Province of China(Grant No.2020JQ-332)+3 种基金the China Postdoctoral Science Foundation(Grant No.2018M643583)the National Natural Science Foundation of China(Grant No.82227802)the National Key R&D Program of China(Grant No.2017YFA0205202)partially funded by the National Natural Science Foundation of China(Grant No.61672422).
文摘Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse cancers.However,the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient.To fill this gap,we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas.For individual candidate among1,500,000 quantified RNA editing events,we performed diverse types of downstream functional annotations.Finally,we identified 24,236 potentially functional A-to-I RNA editing events,including the cases in APOL1,IGFBP3,GRIA2,BLCAP,and miR-589-3p.These events might play crucial roles in the scenarios of tumorigenesis,due to their tumor-related editing frequencies or probable effects on altered expression profiles,protein functions,splicing patterns,and microRNA regulations of tumor genes.Our functional A-to-I RNA editing events(https://ccsm.uth.edu/CAeditome/)will help better understand the cancer pathology from the A-to-I RNA editing aspect.
基金the National Basic Research Program of China(Grant No.2013CB835200)the National Key R&D Program of China(Grant No.2017YFA0505500)+4 种基金the Key Grant of Yunnan Provincial Science and Technology Department(Grant No.2013GA004)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB13040700)the National Natural Science Foundation of China(Grant Nos.11871456 and 31771476)the Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01)the Open Research Fund of State Key Laboratory of Hybrid Rice(Wuhan University,Grant No.KF201806),China。
文摘Significantly increasing crop yield is a major and worldwide challenge for food supply and security.It is well-known that rice cultivated at Taoyuan in Yunnan of China can produce the highest yield worldwide.Yet,the gene regulatory mechanism underpinning this ultrahigh yield has been a mystery.Here,we systematically collected the transcriptome data for seven key tissues at different developmental stages using rice cultivated both at Taoyuan as the case group and at another regular rice planting place Jinghong as the control group.We identified the top 24 candidate high-yield genes with their network modules from these well-designed datasets by developing a novel computational systems biology method,i.e.,dynamic cross-tissue(DCT)network analysis.We used one of the candidate genes,Os SPL4,whose function was previously unknown,for gene editing experimental validation of the high yield,and confirmed that Os SPL4 significantly affects panicle branching and increases the rice yield.This study,which included extensive field phenotyping,cross-tissue systems biology analyses,and functional validation,uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice.The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample.DCT can be downloaded from https://github.com/ztpub/DCT.
基金the National Natural Science Foundation of China(81701787,81671778,31271063 and U1401255)the Natural Science Basic Research Plan in Shaanxi Province,China(2019JQ-138)。
文摘Dear Editor,Anesthetic-induced unconsciousness is accompanied by decreased information exchange among relevant cortical functional modular areas that support normal cognitive function[1].Using the electroencephalogram(EEG)signal,evidence suggest that the feedback and feedforward connectivity among cortical regions may be asymmetrically affected during anesthetic-induced anesthesia[2].
