Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

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.

The ABA synthesis enzyme allele OsNCED2^(T)promotes dryland adaptation in upland rice

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.

Developing superior alleles of yield genes in rice by artificial mutagenesis using the CRISPR/Cas9 system

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.

Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high-throughput RNA sequencing

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.

ENERGY FEATURE EXTRACTION AND SVM CLASSIFICATION OFMOTORIMAGERY-INDUCED ELECTROENCEPHALOGRAMS

The precise classification for the electroencephalogram(EEG)in different mental tasks in the research on brain
computer interface(BCI)is the key for the design and clinical application of the system.In this paper,a new combination classification algorithm is presented and tested using the EEG data of right and left motor imagery experiments.First,to eliminate the low frequency noise in the original EEGs,the signals were decomposed by empirical mode decomposition(EMD)and then the optimal kernel parameters for support vector machine(SVM)were determined,the energy features of thefirst three intrinsic mode functions(IMFs)of every signal were extracted and used as input vectors of the employed SVM.The output of the SVM will be classification result for different mental task EEG signals.The study shows that mean identification rate of the proposed algorithm is 95%,which is much better than the present traditional algorithms.

Harpoon-shaped topological photonic crystal for on-chip beam splitter

The advancement of integrated optical communication networks necessitates the deployment of on-chip beam splitters for efficient signal interconnections at network nodes.However,the pursuit of micron-scale beam splitting with large corners and reducing the device footprint to boost connection flexibility often results in phase mismatches.These mismatches,which stem from radiation modes and backward scattering,pose significant obstacles in creating highly integrated and interference-resistant connections.To address this,we introduce a solution based on the topological valley-contrasting state generated by photonic crystals with opposing valley Chern numbers,manifested in a harpoon-shaped structure designed to steer the splitting channels.This approach enables adiabatic mode field evolution over large corners,capitalizing on the robust phase modulation capabilities and topological protection provided by the subwavelength-scale valley-contrasting state.Our demonstration reveals that beam splitters with large corners of 60°,90°,and 120°exhibit insertion loss fluctuations below 2.7 dB while maintaining a minimal footprint of 8.8μm×8.8μm.As a practical demonstration,these devices facilitate three-channel signal connections,successfully transmitting quadrature phase shift keying signals at 3.66 Tbit/s with bit error rates below the forward error correction threshold,demonstrating performance comparable to that in defects scenarios.By harnessing the unidirectional excitation feature,we anticipate significant enhancements in the capabilities of signal distribution and connection networks through a daisy chain configuration.

The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers

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.

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis

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.

Propofol-Induced Anesthesia Alters Corticocortical Functional Connectivity in the Human Brain:An EEG Source Space Analysis

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].