Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes.

The concept of pan-genome, which is the collection of all genomes from a population, has shown a great potential in genomics study, especially for crop sciences. The rice pan-genome constructed from the second-generation sequencing (SGS) data is about 270 Mb larger than Nipponbare, the rice reference genome (NipRG), but it is still disadvantaged by incompleteness and loss of genomic contexts. The third-generation sequencing (TGS) with long reads can help to construct better pan-genomes. In this paper, we report a high-quality rice pan-genome construction method by introducing a series of new steps to deal with the long-read data, including unmapped sequence block filtering, redundancy removing, and sequence block elongating. Compared to NipRG, the long-read sequencing-based pan-genome constructed from 105 rice accessions, which contains 604 Mb novel sequences, is much more comprehensive than the one constructed from ∼3000 rice genomes sequenced with short reads. The repetitive sequences are the main components of novel sequences, which partially explain the differences between the pan-genomes based on TGS and SGS. Adding six wild rice accessions, there are about 879 Mb novel sequences and 19,000 novel genes in the rice pan-genome in total. In addition, we have created high-quality reference genomes for all representative rice populations, including five gapless reference genomes. This study has made significant progress in our understanding of the rice pan-genome, and this pan-genome construction method for long-read data can be applied to accelerate a broad range of genomics studies.

PPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome.

Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .

Study on the Electrochemiluminescence Emission Mechanism of HOF-14 and Its Multimode Sensing and Imaging Application.

A novel hydrogen-bonded organic framework (HOF-14) has attracted much attention due to its excellent biocompatibility and low toxicity, but its research in the electrochemiluminescence (ECL) field has not been reported. In this work, the annihilation-type and coreactant-type ECL emission mechanisms of HOF-14 were studied systematically for the first time. It was found that the ECL quantum efficiency of HOF-14/TEA coreactant system was the highest, which was 1.82 times that of Ru(bpy)32+/TEA. Further, the ECL emission intensity of HOF-14/TEA system could achieve colorimetric (CL) imaging of mobile phone. We also discovered that HOF-14 had superior photoelectrochemical (PEC) performance. Based on the above research results, a unique HOF-14-based multimode sensing and imaging platform was constructed. The antibiotic Enrofloxacin (ENR) was selected as the detection target, and the Cu-Zn bimetallic single-atom nanozyme (Cu-Zn/SAzyme) with excellent peroxidase (POD)-like activity was used to prepare quenching probes. When the target ENR was present, Cu-Zn/SAzyme quenching probes were introduced to the surface of HOF-14 by the dual-aptamer sandwich method. Cu-Zn/SAzyme could catalyze diaminobenzidine (DAB) to produce brown precipitations to quench the ECL, PEC, and CL signals of HOF-14, realizing multimode detection of ENR. This work not only discovered excellent ECL and PEC property of new HOF-14 material but also systematically studied the ECL emission mechanism of HOF-14, and proposed a novel multimode sensing and imaging platform, which greatly improved the detection accuracy of target and showed great contributions to the field of ECL analysis.

Potential-Resolved Ratio Electrochemiluminescence Biosensor Based on Perylene Diimide-MOF and DNA Nanoflowers-CdS Quantum Dots for Detection of Dual Targets.

BRCA1 gene and carcinoembryonic antigen (CEA) are important markers of breast cancer, so accurate detection of them is significant for early detection and diagnosis of breast cancer. In this study, a potential-resolved ratio electrochemiluminescence (ECL) biosensor using perylene diimide (PDI)-metal-organic framework and DNA nanoflowers (NFs)-CdS quantum dots (QDs) was constructed for detection of BRCA1 and CEA. Specifically, PDI-MOF and CdS QDs can generate potential-resolved intense ECL signals only using one coreactant, so the detection procedure can be effectively simplified. PDI-MOF was first attached to the electrode by graphene oxide, and the dopamine (DA) probe was linked to quench the ECL signal by DNA hybridization. In the presence of target BRCA1, it can form a bipedal DNA walker, so the quenching molecules (DA) were detached from the electrode via the walker amplification process aided by Mg2+, so that the PDI signal at -0.25 V was restored for the BRCA1 assay. Moreover, CdS QDs@DNA NFs as amplified signal probes were formed by self-assembly, and the target CEA-amplified product introduced the CdS QDs@DNA NFs to the electrode, so the QD ECL signal at -1.42 V was enhanced, while the ECL signal of PDI is unchanged; thus, CEA detection was achieved by the ratio value between them. Therefore, the detection accuracy is guaranteed by detection of two cancer markers and a ratio value. This biosensor has a great contribution to the development of new ECL materials and a novel ECL technique for fast and efficient multitarget assays, showing great significance for the early monitoring and diagnosis of breast cancer.

Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice.

Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits, both determine farmers' final profit. More than one population under multiple environments may provide valuable information for breeding selection on these MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our major tasks were (1) to provide a set of reciprocal introgression lines (composed of two BC2RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test the mapping effects of different methods by using MQ-GS correlation dissection as sample case; (3) to perform genetic and breeding simulation on pyramiding favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci on average for MQ-GS traits. Notably, 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful resources for rice molecular breeding.

Highly Stretchable, Knittable, Wearable Fiberform Hydrovoltaic Generators Driven by Water Transpiration for Portable Self-Power Supply and Self-Powered Strain Sensor.

The development of excellently stretchable, highly mobile, and sustainable power supplies is of great importance for self-power wearable electronics. Transpiration-driven hydrovoltaic power generator (HPG) has been demonstrated to be a promising energy harvesting strategy with the advantages of negative heat and zero-carbon emissions. Herein, this work demonstrates a fiber-based stretchable HPG with the advantages of high output, portability, knittability, and sustainable power generation. Based on the functionalized micro-nano water diffusion channels constructed by the discarded mask straps (MSs) and oxidation-treated carbon nanomaterials, the applied water can continuously produce electricity during the spontaneous flow and diffusion. Experimentally, when a tiny 0.1 mL of water encounters one end of the proposed HPG, the centimeter-length device can yield a peak voltage of 0.43 V, peak current of 29.5 µA, and energy density of 5.833 mW h cm-3. By efficiently integrating multiple power generation units, sufficient output power can be provided to drive commercial electronic devices even in the stretched state. Furthermore, due to the reversibility of the electrical output during dynamic stretching-releasing, it can passively convert physiological activities and motion behaviors into quantifiable and processable current signals, opening up HPG's application in the field of self-powered wearable sensing.

Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics.

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.

Astaxanthin activates the Nrf2/Keap1/HO-1 pathway to inhibit oxidative stress and ferroptosis, reducing triphenyl phosphate (TPhP)-induced neurodevelopmental toxicity.

Triphenyl phosphate (TPhP) serves as a major organophosphorus flame retardant, and its induced neurodevelopmental toxicity has attracted widespread attention, but the mechanism remains unclear. In this study, we involved zebrafish to explore the new mechanism of TPhP inducing oxidative stress and ferroptosis to promote neurodevelopmental toxicity. The results suggested that TPhP affected the embryonic development, reduced the number of new neurons, and led to abnormal neural behavior in zebrafish larvae. TPhP also induced ROS accumulation, activated the antioxidant defense signal Nrf2 and Keap1, and significantly changed the activities of Acetylcholinesterase (AChE), Adenosine triphosphatase (ATPase) and glutathione S-transferase (GST). In addition, TPhP induced ferroptosis in zebrafish, which was reflected in the increase of Fe2+ content, the abnormal expression of GPX4 protein and genes related to iron metabolism (gpx4a, slc7a11, acsl4b, tfa, slc40a1, fth1b, tfr2, tfr1a, tfr1b and ncoa4). Astaxanthin intervention specifically inhibited ROS levels, and reversed SLC7A11 and GPX4 expression levels and Fe2+ metabolism thus alleviating ferroptosis induced by TPhP. Astaxanthin also partially reversed the activity of AChE, GST and the expression of neurodevelopmental-related genes (gap43, gfap, neurog1 and syn2a), so as to partially rescue the embryonic developmental abnormalities and motor behavior disorders induced by TPhP. More interestingly, the expression of mitochondrial apoptosis-related protein BAX, anti-apoptotic protein BCL-2, Caspase3 and Caspase9 was significantly altered in the TPhP exposed group, which could be also reversed by Astaxanthin intervention. In summary, our results suggested that TPhP exposure can induce oxidative stress and ferroptosis, thereby causing neurodevelopment toxicity to zebrafish, while Astaxanthin can partially reverse oxidative stress and reduce the neurodevelopmental toxicity of zebrafish larvae by activating Nrf2/Keap1/HO-1 signaling pathway.

Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice.

RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.

Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice.

Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.

Genetic architecture of seed glycerolipids in Asian cultivated rice.

Glycerolipids are essential for rice development and grain quality but its genetic regulation remains unknown. Here we report its genetic base using metabolite-based genome-wide association study and metabolite-based quantitative traits locus (QTL) analyses based on lipidomic profiles of seeds from 587 Asian cultivated rice accessions and 103 chromosomal segment substitution lines, respectively. We found that two genes encoding phosphatidylcholine (PC):diacylglycerol cholinephosphotransferase (OsLP1) and granule-bound starch synthase I (Waxy) contribute to variations in saturated triacylglycerol (TAG) and lyso-PC contents, respectively. We demonstrated that allelic variation in OsLP1 sequence between indica and japonica results in different enzymatic preference for substrate PC-16:0/16:0 and different saturated TAG levels. Further evidence demonstrated that OsLP1 also affects heading date, and that co-selection of OsLP1 and a flooding-tolerant QTL in Aus results in the abundance of saturated TAGs associated with flooding tolerance. Moreover, we revealed that the sequence polymorphisms in Waxy has pleiotropic effects on lyso-PC and amylose content. We proposed that rice seed glycerolipids have been unintentionally shaped during natural and artificial selection for adaptive or import seed quality traits. Collectively, our findings provide valuable genetic resources for rice improvement and evolutionary insights into seed glycerolipid variations in rice.

The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress.

BACKGROUND: Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars. METHODS AND RESULTS: In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data. CONCLUSION: These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.

The basic helix-loop-helix transcription factor gene, OsbHLH38, plays a key role in controlling rice salt tolerance.

The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination. The considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian (indica) and Geng (japonica) subspecies and between the upland-Geng and lowland-Geng ecotypes. The upland-Geng accessions were most sensitive to ABA. Genome-wide association analyses identified four major quantitative trait loci containing 21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene, OsbHLH38, was the most important for ABA sensitivity. Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses. Overexpression of OsbHLH38 increased seedling salt tolerance, while knockout of OsbHLH38 increased sensitivity to salt stress. A salt-responsive transcription factor, OsDREB2A, interacted with OsbHLH38 and was directly regulated by OsbHLH38. Moreover, OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones, transcription factor genes, and many downstream genes with diverse functions, including photosynthesis, redox homeostasis, and abiotic stress responsiveness. These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.

Auxin signaling module OsSK41-OsIAA10-OsARF regulates grain yield traits in rice.

Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin (OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic lines. Based on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling pathways. We also suggested rice auxin response factor (OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the 'best' gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.

The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice.

Grain size is one of the essential determinants of rice yield. Our previous studies revealed that ethylene plays an important role in grain-size control; however, the precise mechanism remains to be determined. Here, we report that the ethylene response factor OsERF115 functions as a key downstream regulator for ethylene-mediated grain development. OsERF115 encodes an AP2/ERF-type transcriptional factor that is specifically expressed in young spikelets and developing caryopses. Overexpression of OsERF115 significantly increases grain length, width, thickness and weight by promoting longitudinal elongation and transverse division of spikelet hull cells, as well as enhancing grain-filling activity, whereas its knockout mutations lead to the opposite effects, suggesting that OsERF115 positively regulates grain size and weight. OsERF115 transcription is strongly induced by ethylene, and OsEIL1 directly binds to the promoter to activate its expression. OsERF115 acts as a transcriptional repressor to directly or indirectly modulate a set of grain-size genes during spikelet growth and endosperm development. Importantly, haplotype analysis reveals that the SNP variations in the EIN3-binding sites of OsERF115 promoter are significantly associated with the OsERF115 expression levels and grain weight, suggesting that natural variations in the OsERF115 promoter contribute to grain-size diversity. In addition, the OsERF115 orthologues are identified only in grass species, implying a conserved and unique role in the grain development of cereal crops. Our results provide insights into the molecular mechanism of ethylene-mediated grain-size control and a potential strategy based on the OsEIL1-OsERF115-target gene regulatory module for genetic improvement of rice yield.

Advancement on target ranging and tracking by single-point photon counting lidar.

Laser tracking with a cooperative target has been widely used in many fields and becomes increasingly important while the non-cooperative target tracking is still a challenge. In this article, a pure laser scanning, ranging and tracking system based on a single-point single photon detector (SP-SPD) is proposed, which can achieve a non-cooperative target real-time tracking without any other passive detection sensor. Through laboratory tracking experiment, we realized the real-time angular measurement, ranging and tracking of a small unmanned aerial vehicle (UAV) at a distance of about 38 m. The results show that the system and its tracking strategy have the ability to achieve a non-cooperative target real-time ranging and tracking in conditions of weak echo signals (a few tenths of a photoelectron), which means that the pure lidar tracking of the non-cooperative target in far distance become reality. It has important guiding significance and application value for a non-cooperative long-distance target ranging and tracking in the airspace.

Genetic basis underlying tiller angle in rice (Oryza sativa L.) by genome-wide association study.

KEY MESSAGE: Novel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis. Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. Little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association study (GWAS) on tiller angle in rice using a population of 164 japonica varieties derived from the 3 K Rice Genomes Project (3 K RGP). We detected a total of 18 QTLs using 1135519 single-nucleotide polymorphisms (SNP) based on three GWAS models (GLM, FastLMM and FarmCPU). Among them, two identified QTLs, qTA8.3 and qTA8.4, overlapped with PAY1 and TIG1, respectively, and additional 16 QTLs were identified for the first time. Combined with haplotype and expression analyses, we further revealed that PAY1 harbors one non-synonymous variation at its coding region, likely leading to variable tiller angle in the population, and that nature variations in the promoter of TIG1 significantly affect its expression, closely correlating with tiller angle phenotypes observed. Similarly, using qRT-PCR and haplotype analysis, we identified 1 and 7 candidate genes in qTA6.1 and qTA8.1 that were commonly detected by two GWAS models, respectively. In addition, we identified 3 more candidate genes in the remaining 14 novel QTLs after filtering by transcriptome analysis and qRT-PCR. In summary, this study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding.

Global N6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress.

N6-methyladenosine (m6A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m6A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m6A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m6A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m6A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m6A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m6A methylation levels only in the shoots or roots under salt stress, implying m6A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m6A modifications and gene expression changes revealed that m6A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m6A modifications on rice salt tolerance.

A flexible electrostatic nanogenerator and self-powered capacitive sensor based on electrospun polystyrene mats and graphene oxide films.

Electrostatic nanogenerators or capacitive sensors that leverage electrostatic induction for power generation or sensing, has attracted significant interests due to their simple structure, ease of fabrication, and high device stability. However, in order for such devices to work, an additional power source or a post-charging process is necessary to activate the electrostatic effect. In this work, an electrostatic nanogenerator is fabricated using electrospun polystyrene (PS) mats and dip-coated graphene oxide (GO) films as the self-charged components. The electret performances of the PS mats and GO films are characterized via the electrostatic force microscopy phase shift and surface potential measurements. With a multilayer device structure that consists of top electrodes/GO films/spacer/electrospun PS mats/bottom electrodes, the resultant device acts as an electrostatic generator that operates in the noncontact mode. The nanogenerator can output a peak voltage of ca. 6.41 V and a peak current of ca. 6.57 nA at a rate of 1 Hz of mechanical compression, and with no attenuation of electrical outputs even after 50 000 cycles over a 13 h period. Furthermore, this as-prepared device is also capable of serving as a self-powered capacitive sensor for detection of tiny mechanical impacts and measurement of human finger bending. This results of this work provides a new avenue to easily fabricate electrostatic nanogenerators with high durability and self-powered capacitive sensors for the detection of small impacts.

A sub-1V, microwatt power-consumption iontronic pressure sensor based on organic electrochemical transistors.

Wearable and implantable pressure sensors are in great demand for personalized health monitoring. Pressure sensors with low operation voltage and low power-consumption are desired for energy-saving devices. Organic iontronic devices, such as organic electrochemical transistors (OECTs), have demonstrated great potential for low power-consumption bioelectronic sensing applications. The ability to conduct both electrons and ions, in addition to their low-operation voltage has enabled the widespread use of OECTs in different biosensing fields. However, despite these merits, OECTs have not been demonstrated for pressure sensing applications. This is because most OECTs are gated with aqueous electrolyte, which fails to respond to external pressure. Here, a low power-consumption iontronic pressure sensor is presented based on an OECT, in which an ionic hydrogel is used as a solid gating medium. The resultant iontronic device operated at voltages less than 1 V, with a power-consumption between ~ 101-103 µW, while maintaining a tunable sensitivity between 1 ~ 10 kPa-1. This work places OECTs on the frontline for developing low power-consumption iontronic pressure sensors and for biosensing applications.