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Abstract Ratoon rice is resource efficient to produce economically sound and environmentally sustainable rice production. However, there is no more information on the relative impact of soil tillage practices on soil physical and chemical properties, microbial biomass, and enzymatic activity, and grain yield in a rice–ratoon rice cropping system remains to be tested. Systematic study of soil under ratooning rice model is a problem to be solved in the development of ratooning rice model. This study primarily investigated the long‐term (from 2014 to 2020) changes in soil bulk density (BD), soil organic carbon (SOC) concentration, total nitrogen (TN) concentration, microbial biomass, β‐glucosidase activity (BG), urease activity (UR), and yield under four treatments: no‐tillage (NT), no plowing tillage + rotatory tillage (RT), plowing tillage in winter + rotatory tillage (PTW), and plowing tillage in spring + rotatory tillage (PTS). NT increased BD by 9.65%–12.97%, and RT increased the 20–40 cm soil layer BD by 8.80% in 2020, compared with the baseline initial value (in 2014). Plowing tillage (PT) time had no significant effect on BD. All tillage methods decreased the SOC concentration in the 0–20 cm soil layer, and only RT increased the TN concentration. PT was the only treatment that increased the SOC and TN concentrations in the 20–40 cm soil layer. Both the main‐season rice yield and the ratoon season rice yield ranked PTW > PTS > NT > RT, in which the main‐season rice yield increased by 28.15% and the ratoon season rice yield increased by 25.19% in PTW. Overall, the PTW treatment had the highest microbial biomass, enzyme activity, and grain yield compared with the other tillage methods. In conclusion, plowing tillage in winter + rotatory tillage is a more suitable tillage method under the mode of ratooning rice.

The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.

Flue-curing of top leaves with stems is a widely applied curing technology. Owing to the presence of stems, the quality of flue-cured leaves was significantly improved. However, the contribution of stems to flue-cured leaves is still unknown. In this study, the differences in physicochemical properties and metabolomics data between separated leaves (stem(-)) and leaves with stems (stem(+)) were investigated. The metabolic profiling of stem(+) was significantly different from that of stem(-), with phytohormone indole-3-acetic acid (IAA) being one of the most differential metabolites. The presence of stems reduced the rate of water loss in leaves, which led to less ROS accumulation, higher antioxidant enzyme activities and a lower level of membrane lipid peroxidation in stem(+) than in stem(-). The presence of stems also helped maintain the cellular membrane integrity of leaf cells by preventing the accumulation of IAA in leaf cells. Better cellular membrane integrity during flue-curing means a lower risk of leaf browning. In addition, stem(+) had a lower starch content than stem(-) because of a higher level of amylase activity. In summary, these results indicated that the presence of stems caused metabolism changes in leaves, prevented flue-cured leaves from browning and enhanced starch degradation in leaves during flue-curing.

Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.

Strawberry is an economically grown horticulture crop required for fruit consumption. The ripening of its fruit is a complex biological process regulated by various hormones. Abscisic acid (ABA) is a critical phytohormone involved in fruit ripening. However, little is known about the long non-coding RNAs (LncRNAs), especially transposon-derived LncRNA (TE-lncRNA), response to hormones during fruit ripening in octoploid strawberry. In the study, the transcriptome data of developing strawberry fruits treated with ABA and its inhibitor Nordihydroguaiaretic acid (NGDA) were analyzed to identify responsive LncRNAs and coding genes. A total of 14,552 LncRNAs were identified, including 8,617 transposon-derived LncRNAs (TE-LncRNAs), 412 LncRNAs (282 TE-LncRNAs), and 382 ABA-sensitive LncRNAs (231 TE-LncRNAs). Additionally, a weighted co-expression network analysis constructed 27 modules containing coding RNAs and LncRNAs. Seven modules, including “MEdarkorange” and “MElightyellow” were significantly correlated with ABA/NDGA treatments, resulting in 247 hub genes, including 21 transcription factors and 22 LncRNAs (15 TE-LncRNAs). Gene ontology enrichment analysis further revealed that ABA/NDGA-responsive modules, including LncRNAs, were associated with various metabolic pathways involved in strawberry fruit development and ripening, including lipid metabolism, organic acid metabolism, and phenylpropanoid metabolism. The current study identifies many high-confidence LncRNAs in strawberry, with a percentage of them being ABA pathway-specific and 22 hub-responsive LncRNAs, providing new insight into strawberry or other Rosaceae crop fruit ripening.

Panicle architecture is an important agronomic trait in rice that affects rice yields and quality. The GRAIN SIZE 3 (GS3) locus has been identified as a major quantitative trait locus (QTL) affecting grain length and weight. The current understanding of the function of the GS3 gene, especially concerning the regulatory mechanism of panicle development, is still in its infancy. In this study, we generated GS3 near-isogenic lines (NILs) by successive crossing and backcrossing of TD70 (large grain) with Kasalath (small grain), using Kasalath as the recurrent parent. To identify potential transcription dynamic changes in rice panicle formation and grain shape, we deeply analyzed transcriptional profiles for the NILs (NIL-GS3 and NIL-gs3) at three different panicle developmental stages (S, M, and L). A total of 887, 1,768, and 1,478 differentially expressed genes (DEGs) were identified at stages S, M, and L, respectively. We also found 542 differential expressed long non-coding RNAs (lncRNAs). Co-expression analysis further revealed significant clusters associated with different development periods in NIL-gs3 lines. Gene Ontology and KEGG enrichment analysis revealed G-protein signaling and hormones pathway were successively activated at the M and L stages of NIL-gs3, which indicated activation of the G-protein signaling pathway might trigger the down-streaming hormone signaling transduction. we found that other hormones such ABA, Auxin, CK were significantly enriched in the L stage in the NIL-gs3. We highlighted the synergistic interplay of G-protein and multiple hormones signaling pathways and their essential roles in regulating rice panicle formation and the grain shape. Our study provides an invaluable resource for further molecular mechanistic studies that affect rice grain size and provide new insight for directed selection by marker-assisted backcross breeding.

Potassium (K) is the essential element for plant growth. It is one of the critical factors that determine crop yield, quality, and especially leaf development in tobacco. However, the molecular mechanism of potassium use efficiency (KUE), especially non-coding RNA, is still unknown. In this study, tobacco seedlings were employed, and their hydro-cultivation with K treatments of low and sufficient concentrations was engaged. Physiological analysis showed that low potassium treatment could promote malondialdehyde (MDA) accumulation and antioxidant enzyme activities such as peroxidase (POD), ascorbate-peroxidase (APX). After transcriptomic analysis, a total of 10,585 LncRNA transcripts were identified, and 242 of them were significantly differently expressed under potassium starvation. Furthermore, co-expression networks were constructed and generated 78 potential regulation modules in which coding gene and LncRNAs are involved and functional jointly. By further module-trait analysis and module membership (MM) ranking, nine modules, including 616 coding RNAs and 146 LncRNAs, showed a high correlation with K treatments, and 20 hub K-responsive LncRNAs were finally predicted. Following gene ontology (GO) analysis, the results showed potassium starvation inducing the pathway of antioxidative stress which is consistent with the physiology result mentioned above. Simultaneously, a part of detected LncRNAs, such as MSTRG.6626.1, MSTRG.11330.1, and MSTRG.16041.1, were co-relating with a bench of MYB, C3H, and NFYC transcript factors in response to the stress. Overall, this research provided a set of LncRNAs that respond to K concentration from starvation and sufficient supply. Simultaneously, the regulation network and potential co-functioning genes were listed as well. This massive dataset would serve as an outstanding clue for further study in tobacco and other plant species for nutrient physiology and molecular regulation mechanism.

Abstract Circularly polarized light (CPL) detection has emerged as a key technology for various optoelectronics. Chiral hybrid perovskites (CHPs) that combine CPL‐sensitive absorption induced by chiral organic ligands and superior photoelectric properties of perovskites are promising candidates for direct CPL detection. To date, most of the CHP detectors are made up of polycrystalline thin‐film, which results in a rather limited discrimination of CPL due to the existence of redundant impurities and intrinsic defect states originating from rapid crystallization process. Here, it is developed a direct CPL detector with high photocurrent and polarization selectivity based on low‐defect CHP single‐crystal nanowire arrays. Large‐scale CHP nanowires are obtained through a micropillar template‐assisted capillary‐bridge rise approach. Thanks to the high crystallinity and ordered crystallographic alignment of these arrays, a CPL photodetector with high light on/off ratio of 1.8 × 104, excellent responsivity of 1.4 A W−1, and an outstanding anisotropy factor of 0.24 for photocurrent has been achieved. These results would provide useful enlightenment for direct CPL detection in high‐performance chiral optoelectronics.

Alternative splicing (AS) occurs extensively in eukaryotes as an essential mechanism for regulating transcriptome complexity and diversity, but the AS landscape regulating potassium (K) use efficiency in plants is unclear. In this study, we performed high-throughput transcriptome sequencing of roots and shoots from allopolyploid Nicotiana tabacum under K+ deficiency. Preliminary physiological analysis showed that root system architecture was dramatically changed due to potassium deficiency and that IAA content was significantly reduced in root and shoot. AS analysis showed that a total of 28,179 genes exhibited 54,457 AS events, and 1,510 and 1,732 differentially alternatively spliced (DAS) events were identified in shoots and roots under low K+ stress. Nevertheless, only 120 DAS events occurred in both shoots and roots, implying that most DAS events were tissue-specific. Both in shoot and the root, the proportion of DAS genes in differentially expressed (DE) genes equaled that in non-DE genes, which indicated that AS might play a unique regulatory role in response to low potassium. Gene ontology analysis further indicated that transcription regulation and AS modulation worked independently in response to low K+ stress in tobacco, as their target biological processes were different. Totally 45 DAS transcription factors (TFs) were found, which were involved in 18 TF families. Five Auxin response factor (ARF) TFs were significantly DAS in root, suggesting that response to auxin was probably subject to AS regulation in the tobacco root. Our study shows that AS variation occurs extensively and has a particular regulatory mechanism under K+ deficiency in tobacco. The study also links changes in root system architecture with the changes in AS of ARF TFs, which implied the functional significance of these AS events for root growth and architecture.

Secondary wall-associated NAC (SWN) genes are a subgroup of NAC (NAM, ATAF, and CUC) transcription factors (TF) that play a key role in regulating secondary cell wall biosynthesis in plants. However, this gene family has not been systematically characterized, and their potential roles in response to hormones are unknown in Nicotiana tabacum. In this study, a total of 40 SWN genes, of which 12 from Nicotiana tomentosiformis, 13 from Nicotiana sylvestris, and 15 from Nicotiana tabacum, were successfully identified. The 15 SWNs from Nicotiana tabacum were further classified into three groups, namely, vascular-related NAC domain genes (NtVNDs), NAC secondary wall thickening promoting factor genes (NtNSTs), and secondary wall-associated NAC domain genes (NtSNDs). The protein characteristic, gene structure, and chromosomal location of 15 NtSWNs (also named Nt1 to Nt15) were also analyzed. The NtVND and NtNST group genes had five conserved subdomains in their N-terminal regions and a motif (LP[Q/x] L[E/x] S[P/A]) in their diverged C- terminal regions. Some hormones, dark and low-temperature related cis-acting elements, were significantly enriched in the promoters of NtSWN genes. A comprehensive expression profile analysis revealed that Nt4 and Nt12 might play a role in vein development. Others might be important for stem development. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) revealed that in the NtNST group, genes such as Nt7, Nt8, and Nt13 were more sensitive than the genes in NtVND and NtSND groups under abiotic stress conditions. A transactivation assay further suggested that Nt7, Nt8, and Nt13 showed a significant transactivation activity. Overall, SWN genes were finally identified and characterized in diploid and tetraploid tobacco, revealing new insights into their evolution, variation, and homology relationships. Transcriptome, cis-acting element, qRT-PCR, and transactivation assay analysis indicated the roles in hormonal and stress responses, which provided further resources in molecular mechanism and genetic improvement.

Abstract Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

Quinoa is a gluten-free food crop that contains all the essential amino acids and vitamins. The selection of proper housekeeping and tissue-specific genes is the crucial prerequisite for gene expression analysis using the common approach, real-time quantitative PCR (RT-qPCR). In this study, we identified 40 novel candidate housekeeping genes by the minimum transcript per million (TPM), coefficient of variation (CV) and maximum fold change (MFC) methods and 19 candidate tissue-specific genes by the co-expression network method based on an RNA-seq dataset that included 53 stem, leaf, flower and seed samples, as well as additional shoot and root samples under different stresses. The expression stability of 12 housekeeping and tissue-specific genes, as well as that of another two traditionally used housekeeping genes, was further evaluated using qPCR and ranked using NormFinder, BestKeeper and the comparative delta-Ct method. The results demonstrated that MIF, RGGA, VATE and UBA2B were ranked as the top four most stable candidate housekeeping genes. qPCR analysis also revealed three leaf-specific genes and five root-specific genes, but no stem-specific gene was identified. Gene Ontology (GO) enrichment analysis identified that housekeeping genes were mainly enriched in the small molecule metabolic process, organonitrogen compound metabolic process, NAD binding and ligase activity. In addition, tissue-specific genes are closely associated with the major functions of a specific tissue. Specifically, GO terms “photosynthesis” and “thylakoid” were most significantly overrepresented in candidate leaf-specific genes. The novel housekeeping and tissue-specific genes in our study will enable better normalization and quantification of transcript levels in quinoa.

High N loss and low N use efficiency (NUE), caused by high N fertilizer inputs and inappropriate fertilization patterns, have become important issues in the rice (Oryza sativa L.) growing regions of southern China. Changing current farmer fertilizer practice (FFP, 225 kg ha-1 N as three applications, 40% as basal fertilizer, 30% as tillering fertilizer and 30% as jointing fertilizer) to one-time root-zone fertilization (RZF, 225 kg ha-1 N applied once into 10 cm deep holes positioned 5 cm from the rice root as basal fertilizer) will address this problem. A two-year field experiment covering two rice growing regions was conducted to investigate the effect of urea one-time RZF on rice growth, nutrient uptake, and NUE. The highest NH4+-N content for RZF at fertilizer point at 30 d and 60 d after fertilization were 861.8 and 369.9 mg kg-1 higher than FFP, respectively. Rice yield and total N accumulation of RZF increased by 4.3-44.9% and 12.7-111.2% compared to FFP, respectively. RZF reduced fertilizer-N loss by 56.3-81.9% compared to FFP. The NUEs following RZF (mean of 65.8% for the difference method and 43.7% for the labelled method) were significantly higher than FFP (mean of 35.7% for the difference method and 14.4% for the labelled method). In conclusion, RZF maintained substantial levels of fertilizer-N in the root-zone, which led to enhanced rice biomass and N uptake during the early growth stages, increased fertilizer-N residual levels and reduced fertilizer-N loss at harvest. RZF produced a higher yield increment and showed an increased capacity to resist environmental threats than FFP in sandy soils. Therefore, adopting suitable fertilizer patterns plays a key role in enhancing agricultural benefits.

Highly fluorescent CdTe quantum dots (Q-dots) stabilized by 3-mercaptopropionic acid (MPA)were prepared by an aqueous solution approach and used as fluorescent labels in detectinga cancer marker, carcinoembryonic antigen (CEA), expressed on human colon carcinomacell line LS 180. Nonspecific adsorptions of CdTe Q-dots on carcinoma cells were observedand effectively eliminated by replacing MPA with a thiolated PEG (poly(ethylene glycol),Mn = 750) synthesized according to literature. It was unexpectedly found out that thePEG-coated CdTe Q-dots exhibited very strong and specific affinity to anti-CEAmonoclonal antibody rch 24 (rch 24mAb). The resultant CdTe–(rch 24mAb) conjugateswere successfully used in detections of CEA expressed on the surface of cell lineLS 180. Further experiments demonstrated that the fluorescent CdTe Q-dotsexhibited much better photostability and a brighter fluorescence than FITC,which consequently led to a higher efficiency in the cancer marker detection. [ABSTRACT FROM AUTHOR]

A self-starting triangular waveform and microwave signal generator based on a dual-loop optoelectronic oscillator (OEO) is proposed. In this scheme, two continuous waves (CWs) with different wavelength are emitted from two laser diodes (LDs) to form two feedback loops in an OEO system. When the oscillation is established and the modulation index of the Mach-Zehnder modulator (MZM) is set to be 0.752, a triangular waveform could be generated by the superposition of the two oscillation signal envelopes on photodetector with appropriate time delay between two wavelength channels. Although the proposed system is similar to a traditional dual-loop OEO and no more devices are required, it is not only a microwave signal source with high side-mode suppression ratio (SMSR) but a triangular waveform generator simultaneously as well. The operation principle is theoretically analyzed and stimulated. In experimental demonstration, the full-duty-cycle triangular waveform signal and high-quality microwave signal at 5 GHz can be achieved simultaneously. In addition, the experiment result shows that the variety of the modulation depth for triangular waveform generation does not influence the quality of the generated microwave signal.

A dual-wavelength rational harmonic mode-locked fiber ring laser with different repetition frequencies is theoretically analyzed and experimentally demonstrated. In this scheme, two wavelength channels are inserted into the laser loop to form two resonant cavities. By tuning the length of each channel, required rational harmonic mode-locking conditions can be achieved, and dual-frequency mode-locked signals are simultaneously generated at different wavelengths. In addition, the supermode suppression ratio is further improved due to the mode competition caused by this dual-cavity configuration. In the experimental demonstration, when the fourth-order (or fifth-order) harmonic mode-locked signal is generated in Cavity 1, the first-, second-, and third-order (or fourth-order) harmonic mode-locked signals, respectively, can be generated in Cavity 2 by tuning its length. The measured radio frequency spectra and waveforms show that the signals have high quality. Compared with a conventional rational harmonic mode-locked laser (RHMLL), more than 10 dB supermode suppression ratio improvement is obtained. Since this system can flexibly implement multiwavelength and multifrequency signal generation without adding much cost, it may have wide applications in optical communication system, photonic microwave signal generation, and optical waveform synthesizers.

A one-pot reaction process was developed to synthesize highly dispersible, superparamagnetic Fe3O4nanoflowers; the potential of these nanoflowers as MRI contrast agents was investigated. [ABSTRACT FROM AUTHOR]

The development of new types of high-performance nanoparticulate MR contrast agents with either positive (T1) or dual-contrast (both positive and negative, T1 + T2) ability is of great importance. Here we report a facile synthesis of ultrasmall PEGylated iron oxide nanoparticles for dual-contrast T1- and T2-weighted MRI. The produced superparamagnetic iron oxide nanoparticles (SPIONs) are of high crystallinity and size uniformity with an average diameter of 5.4 nm, and can be individually dispersed in the physiological buffer with high stability. The SPIONs reveal an impressive saturation magnetization of 94 emu g [?] 1 Fe3O4, the highest r1 of 19.7 mM [?] 1 s [?] 1 and the lowest r2/r1 ratio of 2.0 at 1.5 T reported so far for PEGylated iron oxide nanoparticles. T1- and T2-weighted MR images showed that the SPIONs could not only improve surrounding water proton signals in the T1-weighted image, but induce significant signal reduction in the T2-weighted image. The good contrast effect of the SPIONs as T1 + T2 dual-contrast agents might be due to its high magnetization, optimal nanoparticle size for T1 + T2 dual-contrast agents, high size monodispersity and excellent colloidal stability. In vitro cell experiments showed that the SPIONs have little effect on HeLa cell viability. [ABSTRACT FROM AUTHOR]