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Tandem repeats (TRs) are genomic regions that tandemly change in repeat number, which are often multiallelic. Their characteristics and contributions to gene expression and quantitative traits in rice are largely unknown. Here, we survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph. We identify 227,391 multiallelic TR loci, including 54,416 TR variations that are absent from the Nipponbare reference genome. Only 1/3 TR variations show strong linkage with nearby bi-allelic variants (SNPs, Indels and PAVs). Using 193 panicle and 202 leaf transcriptomic data, we reveal 485 and 511 TRs act as QTLs independently of other bi-allelic variations to nearby gene expression, respectively. Using plant height and grain width as examples, we identify and validate TRs contributions to rice agronomic trait variations. These findings would enhance our understanding of the functions of multiallelic variants and facilitate rice molecular breeding.
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Alelos , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Oryza , Locos de Características Quantitativas , Sequências de Repetição em Tandem , Oryza/genética , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Sequências de Repetição em Tandem/genética , Mapeamento Cromossômico , Polimorfismo de Nucleotídeo Único , Fenótipo , Variação GenéticaRESUMO
Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.
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Rare earth ions with d-f transitions (Ce3+, Eu2+) have emerged as promising candidates for electroluminescence applications due to their abundant emission spectra, high light conversion efficiency, and excellent stability. However, directly injecting charge into 4f orbitals remains a significant challenge, resulting in unsatisfied external quantum efficiency and high operating voltage in rare earth light-emitting diodes. Herein, we propose a scheme to solve the difficulty by utilizing the energy transfer process. X-ray photoelectron spectroscopy and transient absorption spectra suggest that the Cs3CeI6 luminescence process is primarily driven by the energy transfer from the I2-based self-trapped exciton to the Ce-based Frenkel exciton. Furthermore, energy transfer efficiency is largely improved by enhancing the spectra overlap between the self-trapped exciton emission and the Ce-based Frenkel exciton excitation. When implemented as an active layer in light-emitting diodes, they show the maximum brightness and external quantum efficiency of 1073 cd m-2 and 7.9%, respectively.
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Alternative splicing (AS) plays crucial roles in regulating various biological processes in plants. However, the genetic mechanisms underlying AS and its role in controlling important agronomic traits in rice (Oryza sativa) remain poorly understood. In this study, we explored AS in rice leaves and panicles using the rice minicore collection. Our analysis revealed a high level of transcript isoform diversity, with approximately one fifth of potential isoforms acting as major transcripts in both tissues. Regarding the genetic mechanism of AS, we found that the splicing of 833 genes in the leaf and 1,230 genes in the panicle was affected by cis-genetic variation. Twenty-one percent of these AS events could only be explained by large structural variations. Approximately 77.5% of genes with significant splicing quantitative trait loci (sGenes) exhibited tissue-specific regulation, and AS can cause 26.9% (leaf) and 23.6% (panicle) of sGenes to have altered, lost or gained functional domains. Additionally, through splicing-phenotype association analysis, we identified phosphate-starvation induced RING-type E3 ligase (OsPIE1; LOC_Os01g72480), whose splicing ratio was significantly associated with plant height. In summary, this study provides an understanding of AS in rice and its contribution to the regulation of important agronomic traits.
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For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610 expression quantitative trait loci associated with the expression of 7787 and 9361 eGenes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5-a major salt-tolerant locus known as qSTS5. Intriguingly, STG5 is required for maintaining Na+/K+ homeostasis by directly regulating the transcription of multiple members of the OsHKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.
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The d-f transition rare earth complexes have recently emerged as a promising candidate for display applications due to the parity-allowed transition, high photoluminescence quantum yield (PLQY), short excited lifetime, and tunable emissions. Besides, inkjet printing has been regarded as an important technique for realizing full-color display. However, inkjet-printed d-f transition rare earth complexes have not been investigated. Herein, for the first time, we explored d-f transition cerium(III) complex 2-Me as the luminescent material by inkjet printing. With 1,2-dichlorobenzene as solvent and polystyrene as an additive, 2-Me film exhibits a similar emission peak and excited-state lifetime with 2-Me powder and a high PLQY of 45%, demonstrating the excellent stability of 2-Me ink. Finally, we suppressed the coffee ring effect and prepared the first inkjet-printed pattern ''HUST'' composed of d-f transition rare earth complex ink with uniform blue fluorescence. Our pioneering work provides a promising alternative for inkjet printing inks.
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Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.
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DNA Satélite , Oryza , DNA Satélite/metabolismo , Oryza/genética , Oryza/metabolismo , Sequência de Bases , Centrômero/genética , Genoma de Planta/genéticaRESUMO
Detailed knowledge of the genetic variations in diverse crop populations forms the basis for genetic crop improvement and gene functional studies. In the present study, we analyzed a large rice population with a total of 10 548 accessions to construct a rice super-population variation map (RSPVM), consisting of 54 378 986 single nucleotide polymorphisms, 11 119 947 insertion/deletion mutations and 184 736 presence/absence variations. Assessment of variation detection efficiency for different population sizes revealed a sharp increase of all types of variation as the population size increased and a gradual saturation of that after the population size reached 10 000. Variant frequency analysis indicated that â¼90% of the obtained variants were rare, and would therefore likely be difficult to detect in a relatively small population. Among the rare variants, only 2.7% were predicted to be deleterious. Population structure, genetic diversity and gene functional polymorphism of this large population were evaluated based on different subsets of RSPVM, demonstrating the great potential of RSPVM for use in downstream applications. Our study provides both a rich genetic basis for understanding natural rice variations and a powerful tool for exploiting great potential of rare variants in future rice research, including population genetics and functional genomics.
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Variação Genética , Oryza , Genética Populacional , Genômica , Oryza/genética , Polimorfismo de Nucleotídeo ÚnicoRESUMO
The elimination of seed shattering was a key step in rice (Oryza sativa) domestication. In this paper, we show that increasing the gibberellic acid (GA) content or response in the abscission region enhanced seed shattering in rice. We demonstrate that SLENDER RICE1 (SLR1), the key repressor of GA signaling, could physically interact with the rice seed shattering-related transcription factors quantitative trait locus of seed shattering on chromosome 1 (qSH1), O. sativa HOMEOBOX 15 (OSH15), and SUPERNUMERARY BRACT (SNB). Importantly, these physical interactions interfered with the direct binding of these three regulators to the lignin biosynthesis gene 4-COUMARATE: COENZYME A LIGASE 3 (4CL3), thereby derepressing its expression. Derepression of 4CL3 led to increased lignin deposition in the abscission region, causing reduced rice seed shattering. Importantly, we also show that modulating GA content could alter the degree of seed shattering to increase harvest efficiency. Our results reveal that the "Green Revolution" phytohormone GA is important for regulating rice seed shattering, and we provide an applicable breeding strategy for high-efficiency rice harvesting.
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Oryza , Oryza/genética , Oryza/metabolismo , Lignina/metabolismo , Giberelinas/metabolismo , Sementes/genética , Sementes/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismoRESUMO
Recently, perovskite light-emitting diodes (PeLEDs) have exhibited outstanding performance in next-generation high-definition display applications. However, compared with green and red PeLEDs, the development of efficient and stable blue PeLEDs to meet the requirement for a wide color gamut has been a challenge. Herein, we vacuum thermally deposited a film of the lead-free rare earth halide Rb3CeI6, which shows deep blue emission with peaks at 427â nm and 468â nm. Due to the parity-allowed 5d-4f transition of Ce(III), the excited-state lifetime is as short as 22.3â ns (427â nm) and 25â ns (468â nm), respectively. The photoluminescence quantum yield (PLQY) is optimized to 51% by regulating the nucleation and growth of Rb3CeI6 grains. In a prototype rare earth light-emitting diode (ReLED) device, a thin insulating Al2O3 layer (5â nm) is inserted between the electron transport layer (ETL) and the emitting layer (EML, Rb3CeI6) to balance the carriers and reduce the dark current. The device shows a maximum luminance and EQE of 98 cd m-2 and 0.67%, respectively, and the electroluminescence (EL) spectrum maintains stability with changes in the operating voltage. In addition, the corresponding CIE coordinate is (0.15, 0.06), which closely matches the Rec. 2020 standard (0.131, 0.046).
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Lead halide perovskite nanocrystals have recently demonstrated great potential as x-ray scintillators, yet they still suffer toxicity issues, inferior light yield (LY) caused by severe self-absorption. Nontoxic bivalent europium ions (Eu2+) with intrinsically efficient and self-absorption-free d-f transition are a prospective replacement for the toxic Pb2+. Here, we demonstrated solution-processed organic-inorganic hybrid halide BA10EuI12 (BA denotes C4H9NH4+) single crystals for the first time. BA10EuI12 was crystallized in a monoclinic space group of P21/c, with photoactive sites of [EuI6]4- octahedra isolated by BA+ cations, which exhibited high photoluminescence quantum yield of 72.5% and large Stokes shift of 97 nm. These properties enable an appreciable LY value of 79.6% of LYSO (equivalent to ~27,000 photons per MeV) for BA10EuI12. Moreover, BA10EuI12 shows a short excited-state lifetime (151 ns) due to the parity-allowed d-f transition, which boosts the potential of BA10EuI12 for use in real-time dynamic imaging and computer tomography applications. In addition, BA10EuI12 demonstrates a decent linear scintillation response ranging from 9.21 µGyair s-1 to 145 µGyair s-1 and a detection limit as low as 5.83 nGyair s-1. The x-ray imaging measurement was performed using BA10EuI12 polystyrene (PS) composite film as a scintillation screen, which exhibited clear images of objects under x-ray irradiation. The spatial resolution was determined to be 8.95 lp mm-1 at modulation transfer function = 0.2 for BA10EuI12/PS composite scintillation screen. We anticipate that this work will stimulate the exploration of d-f transition lanthanide metal halides for sensitive x-ray scintillators.
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Next-generation wide color gamut displays require the development of efficient and toxic-free light-emitting materials meeting the crucial Rec. 2020 standard. With the rapid progress of green and red perovskite light-emitting diodes (PeLEDs), blue PeLEDs remain a central challenge because of the undesirable color coordinates and poor spectra stability. Here, we report Cs3CeBrxI6-x (x = 0 to 6) with the cryolite-like structure and stable and tunable color coordinates from (0.17, 0.02) to (0.15, 0.04). Further encouraged by the short exciton lifetime (26.1 ns) and high photoluminescence quantum yield (~76%), we construct Cs3CeBrxI6-x-based rare-earth LEDs via thermal evaporation. A seed layer strategy is conducted to improve the device's performance. The optimal Cs3CeI6 device achieves a maximum external quantum efficiency of 3.5% and a luminance of 470 cd m-2 with stable deep-blue color coordinates of (0.15, 0.04). Our work opens another avenue to achieving efficient and spectrally stable deep-blue LEDs.
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Yellow light-emitting diodes (LEDs) are widely utilized in high-quality lighting, light communication, indicator lamps, etc. Owing to their outstanding material properties and device performance, the metal halide perovskites have demonstrated a significant potential for LED applications. However, the performance of the yellow perovskite LEDs (PeLEDs) is inferior to that of their green and red counterparts, with the maximum external quantum efficiency (EQE) limited to â¼3.1%. Further, a majority of the yellow PeLEDs are fabricated using the spin-coating methods. The current study reports the development of the yellow CsPbBr2I PeLEDs based on an all-vacuum deposition approach, which has been widely employed in the commercial organic LEDs (OLEDs). By controlling the co-evaporation rate of CsI and PbBr2, the growth kinetics of the perovskite layer are regulated to achieve a small grain size of â¼31.8 nm. Consequently, an improved radiative recombination rate (8.04 × 10-9 cm3/s) is obtained owing to the spatial confinement effect. The PeLEDs based on the optimal perovskite film demonstrate the yellow electroluminescence (574 nm) with a maximum EQE of â¼3.7% and luminance of â¼16,200 cd/m2, thus, representing one of the most efficient and bright yellow PeLEDs. Overall, this study provides a useful guideline for realizing the efficient PeLEDs based on the thermal evaporation strategy and highlights the potential of PeLED as an efficient and bright yellow light source.
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With the rapid development of the panel display market, demand for efficient light emitters as active layers in electroluminescence (EL) devices has significantly increased. Luminescent inorganic lanthanide compounds (ILCs) with a characteristic f-d transition are particularly preferred for EL devices because of their high photoluminescent quantum yield, short excited-state lifetime, tunable emission spectra, and high thermal stability. In this Perspective, we first present an overview of inorganic lanthanide compounds with an emphasis on the mechanisms and characteristics of f-d emission. Then, the comprehensive advances of lanthanide element-doped inorganic compounds for EL study in recent decades are summarized. Moreover, the recent progress in directly employing ILCs for EL applications and rational improvement strategies in EL performance are highlighted. Last, we summarize the current challenges and opportunities of ILC-based EL devices as well as future improvement directions.
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With rapid advances of perovskite light-emitting diodes (PeLEDs), the large-scale fabrication of patterned PeLEDs towards display panels is of increasing importance. However, most state-of-the-art PeLEDs are fabricated by solution-processed techniques, which are difficult to simultaneously achieve high-resolution pixels and large-scale production. To this end, we construct efficient CsPbBr3 PeLEDs employing a vacuum deposition technique, which has been demonstrated as the most successful route for commercial organic LED displays. By carefully controlling the strength of the spatial confinement in CsPbBr3 film, its radiative recombination is greatly enhanced while the nonradiative recombination is suppressed. As a result, the external quantum efficiency (EQE) of thermally evaporated PeLED reaches 8.0%, a record for vacuum processed PeLEDs. Benefitting from the excellent uniformity and scalability of the thermal evaporation, we demonstrate PeLED with a functional area up to 40.2 cm2 and a peak EQE of 7.1%, representing one of the most efficient large-area PeLEDs. We further achieve high-resolution patterned perovskite film with 100 µm pixels using fine metal masks, laying the foundation for potential display applications. We believe the strategy of confinement strength regulation in thermally evaporated perovskites provides an effective way to process high-efficiency and large-area PeLEDs towards commercial display panels.
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Flat panel displays enjoy 100 billion-dollar markets with significant penetration in daily life, which require efficient, color-saturated blue, green, and red light-emitting diodes (LEDs). The recently emerged halide perovskites have demonstrated low-cost and outstanding performance for potential LED applications. However, the performance of blue perovskite LEDs (PeLEDs) lags far behind red and green cousins, particularly for color coordinates approaching (0.131, 0.046) that fulfill the Rec. 2020 specification for blue emitters. Here, a high-efficiency, lead-free perovskite, CsEuBr3 , is reported that exhibits bright blue exciton emission centered at 448 nm with a color coordinates of (0.15, 0.04), contributed from Eu-5dâEu-4f/Br-4p transition with an optical band gap of 2.85 eV. Further optical characterizations reveal its short excited-state lifetime of 151 ns, excellent exciton diffusion diffusivity of 0.0227 cm2 s-1 , and high quantum yield of ≈69%. Inspired by these findings, deep-blue PeLEDs based on all-vacuum processing methods, which have been demonstrated as the most successful approach for the organic LED industry, are constructed. The devices show a maximum external quantum efficiency of 6.5% with an operating half-lifetime of 50 mins at an initial brightness of 15.9 cd m-2 . It is anticipated that this work will inspire further research on lanthanide-based perovskites for next-generation LED applications.
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X-ray detection is of great significance in biomedical, nondestructive, and scientific research. Lead halide perovskites have recently emerged as one of the most promising materials for direct X-ray detection. However, the lead toxicity remains a worrisome concern for further commercial application. Great efforts have been made to search for lead-free perovskites with similar optoelectronic properties. Here, we present a lead-free oxide double perovskite material Ba2AgIO6 for X-ray detection. The lead-free, all-inorganic nature, as well as the high density of Ba2AgIO6, promises excellent prospects in X-ray applications. By employing the hydrothermal method, we successfully synthesized highly crystalline Ba2AgIO6 powder with pure phase. Furthermore, we prepared Ba2AgIO6 wafers through isostatic pressure and built X-ray detectors with Au/Ba2AgIO6 wafer/Au photo-conductive structure. The as-prepared X-ray detectors showed a sensitivity of 18.9 µC/(Gyair·cm2) at 5 V/mm, similar to commercial α-Se detectors showcasing their advantages for X-ray detection.