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Background Pembrolizumab has been approved by the Food and Drug Administration (FDA) for the first-line treatment of locally advanced or metastatic esophageal cancer. This study investigated the efficacy and safety of pembrolizumab combined with paclitaxel and platinum for the treatment of locally advanced and potentially resectable esophageal squamous cell carcinoma (ESCC). Methods In this retrospective, single-center, three-arm study, patients with locally advanced and potentially resectable ESCC received pembrolizumab (200 mg on day 1) in combination with paclitaxel (135 mg/m2 on day 1) and nedaplatin (100 mg/m2 on day 1) as induction therapy once every 3 weeks. After 4 cycles of systemic therapy in the first stage, patients who chose to undergo radical surgery were divided into group A, patients who underwent radical radiotherapy were divided into group B, and patients who did not undergo any radical therapy were divided into group C. Maintenance treatment with pembrolizumab was performed in all 3 groups. The efficacy and safety of pembrolizumab were evaluated through clinical data, such as the objective response rate (ORR), progression-free survival (PFS), and safety assessment. Results From August 2019 to June 2022, a total of 39 patients were included in this study. After immune response evaluation in the first stage, 34 (87.2%) patients achieved immune partial response (iPR), and 5 (12.8%) patients achieved immune stable disease (iSD). The ORR was 87.1% (27/31), and the disease control rate (DCR) was 100%. Twenty-two patients in group A underwent surgery, and all patients underwent R0 resection. The major pathological response (MPR) rate was 68.2% (15/22), and the pathological complete response (pCR) rate was 45.5% (10/22). Nine patients in group B chose radiotherapy as the radical therapeutic method after the tumors had shrunk significantly. Eight patients in group C did not undergo any radical therapy. All patients received maintenance treatment with pembrolizumab, and the median period of pembrolizumab therapy was 8 cycles (4–22 cycles). The median follow-up time was 16.6 months (6–34 months), and the median overall survival (OS) and PFS times were not reached in either groups A or B. The incidence of severe adverse events (AEs) (grade ≥ 3) was 15.4% (6/39), and the main treatment-related AEs were rash and hypothyroidism. One patient stopped treatment after 4 cycles of induction therapy due to a severe rash. There was no significant difference in the incidence of AEs between groups A and B. Conclusions Pembrolizumab in combination with paclitaxel and platinum as induction therapy for locally advanced and potentially resectable ESCC has a high ORR, high surgical conversion, MPR, pCR, and R0 resection rates, and tolerable AEs in the operation group. For patients unwilling to undergo surgical treatment, pembrolizumab could provide good benefits in sequential treatment with radical radiotherapy or maintenance therapy. This treatment model in different clinical scenarios is worth further exploration in the field of immunotherapy for locally advanced and potentially resectable ESCC.

Rice resistance proteins share a conserved defense signal transduction pathway to confer resistance to rice blast disease., Resistance (R) proteins are important components of plant innate immunity. Most known R proteins are nucleotide-binding site leucine-rich repeat (NLR) proteins. Although a number of signaling components downstream of NLRs have been identified, we lack a general understanding of the signaling pathways. Here, we used the interaction between rice (Oryza sativa) and Magnaporthe oryzae to study signaling of rice NLRs in response to blast infection. We found that in blast resistance mediated by the NLR PIRICULARIA ORYZAE RESISTANCE IN DIGU 3 (PID3), the guanine nucleotide exchange factor OsSPK1 works downstream of PID3. OsSPK1 activates the small GTPase OsRac1, which in turn transduces the signal to the transcription factor RAC IMMUNITY1 (RAI1). Further investigation revealed that the three signaling components also play important roles in disease resistance mediated by the distantly related NLR protein Pi9, suggesting that the OsSPK1–OsRac1–RAI1 signaling pathway could be conserved across rice NLR-induced blast resistance. In addition, we observed changes in RAI1 levels during blast infection, which led to identification of OsRPT2a, a subunit of the 19S regulatory particle of the 26S proteasome. OsRPT2a seemed to be responsible for RAI1 turnover in a 26S proteasome-dependent manner. Collectively, our results suggest a defense signaling route that might be common to NLR proteins in response to blast infection.

The bacterium Xanthomonas oryzae pv. Oryzae (Xoo) causes blight in rice worldwide, resulting in significant crop loss. However, no gene underlying a quantitative trait locus (QTL) for resistance against Xoo has been cloned yet. Here, we report the map-based cloning of a QTL, in which the NBS8R gene confers quantitative resistance to Xoo. NBS8R encodes an NB-ARC protein, which is involved in pathogen/microbe-associated molecular pattern-triggered immunity and whose expression is regulated by non-TAL effector XopQ-inducible Osa-miR1876 through DNA methylation. Sequence analysis of NBS8R in wild rice species and rice cultivars suggests that the Osa-miR1876 binding sites in the 5′ UTR of NBS8R are inserted by chance and have undergone variations with Osa-miR1876 throughout evolution. The interaction between NBS8R and XopQ-inducible Osa-miR1876 is partially in keeping with the zigzag model, revealing that quantitative genes may also follow this model to control the innate immune response or basal disease resistance, and may prove valuable in utilizing the existing landraces that harbor the NBS8R gene but with no Osa-miR1876 binding site in rice breeding for bacterial blight resistance.

Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders., Hybrid rice cultivars are widely planted around the world. Here, the authors resequence 1,143 indica accessions, focusing on the parents of superior hybrid rice lines in China, and reveal genetic loci that are associated with heterosis via measuring frequency of parental variation difference (FPVD).

Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.

The enhancement of rice production numbers can be achieved by using quality rice cultivars and fertilizers. The double rice cropping model has given rise to an important rice production system in southern China. Exploring the possibility of whether hybrid vigor could make a substantial contribution to early and late season rice production, and how the heterosis expression of hybrid rice functions under different levels of fertilizer application is of great significance. The objective of this study was to evaluate the grain yield and associated plant traits of popular hybrid and inbred rice varieties with large–scale promotion under conditions of customary (high) and combined (low) fertilization in the early and late seasons of 2017–18 in Changsha County, Hunan Province, China. We found that hybrid rice varieties displayed their respective advantages in the early and late rice seasons, but the advantages in their relative yield traits varied. The leading advantages of early season rice were effective panicle number per hill (EPN), 1000–grain weight (KGW), harvest index (HI), yield, and nitrogen use efficiency (NUE), whereas in late season rice, the foremost advantages were grain number per panicle (GNP), HI, yield, and NUE. The EPN was the prime advantage of early season hybrid rice with a short growth period, and the GNP was the main advantage of late season hybrid rice with a long growth period. Notably, the main yield advantage of hybrid rice was stronger under combined (low) fertilization than under customary (high) fertilization. Hence, high yield can be achieved by selecting the best hybrid rice varieties supported by combined fertilization (lower fertilizer use with higher efficiency).

Map-based cloning of plant disease resistance (R) genes is time-consuming. Here, we reported the isolation of blast R gene Pid4 using comparative transcriptomic profiling and genome-wide sequence analysis. Pid4 encodes a coiled-coil nucleotide-binding site leucine-rich repeat (CC-NBS-LRR) protein and is constitutively expressed at diverse developmental stages in the rice variety Digu. The Pid4 protein is localized in both the nucleus and cytoplasm. Introduction of Pid4 into susceptible rice cultivars confers race-specific resistance to leaf and neck blast. Amino acid sequence comparison and blast resistance spectrum tests showed that Pid4 is a novel R gene, different from the previously reported R genes located in the same gene cluster. A Pid4 Indel marker was developed to facilitate the identification of Pid4 in different rice varieties. We demonstrated that a plant R gene can be quickly isolated using transcriptomic profiling coupled with genome-wide sequence analysis.

Additional file 3: Fig. S1. PCR-based genotyping for the 28-bp deletion in indica accessions (partially). M: DL2000 DNA marker; lane 1–24: IR64, Nipponbare, Bing 1A, Digu, Yuetai A, 9311, Zhenxian 97A, Fengyuan A, Mianhui 725, II-32A, Tianfeng A, Fenghuazan, Yuanhui 2 hao, Yuetai B, IR36, Gui 99, Fengyuan A, Shuhui 498, Miyang 46, IR64, D62A, G46A, CDR22, Wufeng A. Fig. S2. Pfam motifs of HIS1 and amino acid variation of haplotypes. The shaded parts are predicted amino acids due to the 28-bp deletion in H5. Fig. S3. Protein sequence alignment of 2OGDs. (A) Protein sequence alignment and conserved site analysis of 91 experimentally characterized 2OGDs in plants. (B) Protein sequence alignment and conserved site analysis of 114 putative 2OGDs in rice. Fig. S4. RNA expression of HIS1 in some accessions harboring H1, H2, H3, and H5. The qRT-PCR results were normalized with the actin reference gene. Error bars represent the standard error of the mean (SEM) of three replicates. Fig. S5. The T1510G mutation is completely co-segregated with the susceptibility to BBC (partially). Rice accessions Nongxiang42 and Xianhui207 carry HIS1 haplotypes H2 and H3, respectively. The upper electrophoretic band represents the PCR products of HIS1, and the lower band shows the PCR products treated with the restriction enzyme Dde1. Fig. S6. BBC is effective when the seeds are mixed. (A). BBC can effectively kill hybrid sterile lines (MingS) without harming hybrids (Mingliangyou143). The red arrow indicates the sterile line that was killed. (B). Random selection of 10 normal and severely affected seedlings. Through the detection of 28-bp deletion primers, it was found that the normal materials were all in a heterozygous state, and the sterile line materials lacking 28-bp were killed.

Background Benzobicyclon (BBC) is a β-triketone herbicide (bTH) used in rice paddy fields. It has the advantages of high efficiency, low toxicity, high crop safety, and good environmental compatibility, and shows efficacy against paddy weeds resistant to other types of herbicides. However, as some important indica rice varieties are susceptible to BBC, BBC is currently only registered and applied in japonica rice cultivation areas. Results By analyzing haplotypes of the bTHs broad-spectrum resistance gene HIS1 and phenotypes for BBC in 493 major indica rice accessions in China, we identified a novel non-functional allelic variant of HIS1 in addition to the previously reported 28-bp deletion. Through detection with markers specific to the two non-functional mutations, it was clear that 25.4% of indica conventional varieties, 59.9% of fertility restorers, and 15.9% of sterile lines were susceptible to BBC. In addition, due to natural allelic variations of the HIS1 gene in the sterile and restorer lines, some two-line hybrid sterile lines were sensitive to bTHs, and the corresponding restorers were resistant. We showed the potential effectiveness of using bTHs to address the issue of two-line hybrid rice seed purity stemming from the self-crossing of sterile lines during hybrid rice seed production. Finally, allelic variations of the HIS1 gene may also play an important role in the mechanized seed production of hybrid rice. Conclusions Our findings offer guidance for the application of BBC in indica rice areas and provide a non-transgenic approach to address the seed purity issue of two-line hybrid rice.

Many pathogenic fungi depend on the development of specialized infection structures called appressoria to invade their hosts and cause disease. Impairing the function of fungal infection structures therefore provides a potential means by which diseases could be prevented. In spite of this extraordinary potential, however, relatively few anti-penetrant drugs have been developed to control fungal diseases, of either plants or animals. In the present study, we report the identification of compounds that act specifically to prevent fungal infection. We found that the organization of septin GTPases, which are essential for appressorium-mediated infection in the rice blast fungus Magnaporthe oryzae, requires very-long-chain fatty acids (VLCFAs), which act as mediators of septin organization at membrane interfaces. VLCFAs promote septin recruitment to curved plasma membranes and depletion of VLCFAs prevents septin assembly and host penetration by M. oryzae. We observed that VLCFA biosynthesis inhibitors not only prevent rice blast disease, but also show effective, broad-spectrum fungicidal activity against a wide range of fungal pathogens of maize, wheat and locusts, without affecting their respective hosts. Our findings reveal a mechanism underlying septin-mediated infection structure formation in fungi and provide a class of fungicides to control diverse diseases of plants and animals.

Increasing rice production by using genetically improved rice cultivars and fertilizer application has been the main objective of rice farming. The double rice-cropping system has been an important rice production system in the middle and lower reaches of the Yangtze River in China since the 1950s. It is of great significance to determine whether hybrid vigor can make a substantial contribution to early- and late-season rice production, and how the heterosis expression of hybrid rice functions under different level of fertilization application. The objective of this study was to evaluate the grain yield and associated plant traits of popular hybrid and inbred rice varieties with large-scale promotion under conditions of customary (high) and combined (low) fertilization in the early and late seasons of 2017-18 in Changsha County, Hunan Province, central Southern China. We found that hybrid rice varieties displayed their respective advantages in the early- and late-rice seasons, but the advantages in their relative yield traits varied. The main advantages of early-season rice were effective panicle number per hill (EPN), 1000-grain weight (KGW), harvest index (HI), yield, and nitrogen use efficiency (NUE). Whereas in late-season rice, the major advantages were grain number per panicle (GNP), HI, yield, and NUE. The EPN was the main advantage of early-season hybrid rice with a short-growth period, and the GNP was the main advantage of late-season hybrid rice with a long-growth period. The main yield advantage of hybrid rice was stronger under combined (low) fertilization than under customary (high) fertilization. Hence, high yield can be achieved by selecting good hybrid rice varieties and by using combined fertilization (lower fertilizer use with higher efficiency). This work is contributive for rice growers, extension specialists, and fertilizer producers, as it provides data that can be used to maximize yields with reduced fertilizer and pesticide inputs.

Two‐line hybrid rice with high efficiency and yield was successfully and widely being planted in China. HHZ is an elite inbred rice which is widely cultivated in Southern China. The latest developed engineered hybrid is promising for the future of hybrid rice breeding and production. In order to explore its heterosis performance, the main yield traits of two different groups of hybrid rice varieties and a inbred variety were investigated, specifically: (1) a large‐scale extension of high‐yield varieties of two‐line hybrid rice and their parents (restorer lines), (2) a new generation of hybrid rice created by genetic engineered with HHZ as a background genome and its parental lines, and (3) a inbred indica rice variety, HHZ. We postulate that the performance of the main yield traits of genetically engineered hybrid rice may be better than that of commercial high‐yielding hybrid rice in the same paddy field. To test our assumption, field experiments were conducted to investigate the performance of the main yield traits in the different types of hybrid rice and to compare and analyze the differences of the yield heterosis traits. The hybrid rice varieties showed obvious high‐parent heterosis for effective panicle number (EPN) per hill, grain number per panicle (GNP), seed set rate (SSR), and harvest index (HI), but high‐parent heterosis for the 1000‐grain weight (KGW) was negative. Standard heterosis for GNP and KGW was found in the hybrid rice varieties, and the standard heterosis for EPN, SSR, and HI was negative. The grain number per panicle (GNP) is the largest contributor to heterotic performance. The genetically engineered hybrid rice showed similar heterotic performance to but not greater than that of two‐line hybrid rice varieties. This study provides important insights for the breeding, cultivation, and popularization of different types of hybrid rice varieties.

Salicylic acid (SA) is a key natural component that mediates local and systemic resistance to pathogens in many dicotyledonous species. However, its function is controversial in disease resistance in rice plants. Here, we show that the SA signaling is involved in both pathogen-associated-molecular-patterns triggered immunity (PTI) and effector triggered immunity (ETI) to Xanthomonas oryzae pv. Oryzae (Xoo) mediated by the recessive gene xa5, in which OsNPR3.3 plays an important role through interacting with TGAL11. Rice plants containing homozygous xa5 gene respond positively to exogenous SA, and their endogenous SA levels are also especially induced upon infection by the Xoo strain, PXO86. Depletion of endogenous SA can significantly attenuate plant resistance to PXO86, even to 86∆HrpXG (mutant PXO86 with a damaged type III secretion system). These results indicated that SA plays an important role in disease resistance in rice plants, which can be clouded by high levels of endogenous SA and the use of particular rice varieties.

This paper introduces the concept of cyberspace search engine, and makes a deep survey on 5 well-known search engines, say Shodan, Censys, BinaryEdge, ZoomEye and Fofa, by querying official websites, analyzing APIs, and making academic research. We discuss the following items in details: Supporting internet protocols, Total amounts of detected devices, Device information, Scanning frequency, System architecture, The third party databases, Probes distribution, etc. We give a comprehensive comparison of the detecting abilities and working principles of the cyberspace search engines.

Natural antisense long noncoding RNAs (lncRNAs) are widespread in many organisms. However, their biological functions remain largely unknown, particularly in plants. We report the identification and characterization of an endogenous lncRNA, TWISTED LEAF (TL), which is transcribed from the opposite strand of the R2R3 MYB transcription factor gene locus, OsMYB60, in rice (Oryza sativa). TL and OsMYB60 were found to be coexpressed in many different tissues, and the expression level of TL was higher than that of OsMYB60. Downregulation of TL by RNA interference (RNAi) and overexpression of OsMYB60 resulted in twisted leaf blades in transgenic rice. The expression level of OsMYB60 was significantly increased in TL-RNAi transgenic plants. This suggests that TL may play a cis-regulatory role on OsMYB60 in leaf morphological development. We also determined that the antisense transcription suppressed the sense gene expression by mediating chromatin modifications. We further discovered that a C2H2 transcription factor, OsZFP7, is an OsMYB60 binding partner and involved in leaf development. Taken together, these findings reveal that the cis-natural antisense lncRNA plays a critical role in maintaining leaf blade flattening in rice. Our study uncovers a regulatory mechanism of lncRNA in plant leaf development.

Significance Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease. Despite their importance, few broad-spectrum resistance loci have been reported, and the underlying mechanisms controlling the trait remain largely unknown. This report describes the identification of a gene, called “bsr-k1,” conferring broad-spectrum resistance and demonstrates that the encoded protein regulates immunity-related genes. Loss of function of BSR-K1 in rice leads to enhanced broad-spectrum resistance to two serious rice diseases with no major penalty on yield. This report provides insights into broad-spectrum resistance and offers an efficient strategy to breeding durably resistant rice., Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of pathogens. Despite their importance, only a few crop broad-spectrum resistance loci have been reported. Here, we report the identification and characterization of the rice bsr-k1 (broad-spectrum resistance Kitaake-1) mutant, which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae pv oryzae with no major penalty on key agronomic traits. Map-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats (TPRs)-containing protein, which binds to mRNAs of multiple OsPAL (OsPAL1–7) genes and promotes their turnover. Loss of function of the Bsr-k1 gene leads to accumulation of OsPAL1–7 mRNAs in the bsr-k1 mutant. Furthermore, overexpression of OsPAL1 in wild-type rice TP309 confers resistance to M. oryzae, supporting the role of OsPAL1. Our discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice.

The cereal crops (such as rice and maize) which belong to the grass family, are the most important grain crops for human beings, and the development of their flower and inflorescence architecture has attracted extensive attention. Although multiple genes involved in the regulation of floral and inflorescence organogenesis have been identified, the underlying molecular mechanisms are largely unknown. Previously, we identified rice depressed palea1 (dp1) mutants with defects in main structure of palea and its enhancer RETARDED PALEA1 (REP1). DP1 is an AT-hook protein while REP1 is a TCP transcription factor, both of which are important regulators of palea development. However, the relationship of these two proteins has not been elucidated yet. Here, we demonstrated that DP1 interacts physically with REP1 both in yeast and in rice protoplasts. Considering the close phylogenetic relationship between maize and rice, we further hypothesize that their orthologs in maize, BARREN STALK FASTIGIATE (BAF1) and BRANCH ANGLE DEFECTIVE 1 (BAD1), may interact physically. Subsequently, we verified their physical interaction, indicating that the interaction between AT-hook proteins and TCP proteins is conserved in rice and maize. Our findings may reveal a novel molecular mechanism of floral and inflorescence development in grasses.

We use dynamic nuclear polarization (DNP)-enhanced nuclear magnetic resonance (NMR) at liquid helium temperatures to directly detect hydrogen attached to the surface of silicon microparticles. The proton NMR spectrum from a dry sample of polycrystalline silicon powder (1–5 μm) shows a distinctively narrow Lorentzian-shaped resonance with a width of 6.2 kHz, indicative of a very sparse distribution of protons attached to the silicon surface. These protons are within a few atomic monolayers of the silicon surface. The high-sensitivity NMR detection of surface protons from low surface area (0.26–1.3 m2/g) particles is enabled by an overall signal enhancement of 4150 over the room-temperature NMR signal at the same field. When the particles were suspended in a solvent with 80% H2O and 20% D2O, the narrow peak was observed to grow in intensity over time, indicating growth of the sparse surface proton layer. However, when the particles were suspended in a solvent with 20% H2O and 80% D2O, the narrow bound proto...

Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) constitutes the first line of plant inducible immunity. As an important step of plant colonization, phytopathogens have to suppress PTI, and secreted effectors are therefore co-evolved and deployed. In this study, we characterized the function of MoSec62 of Magnaporthe oryzae, the causal agent of the destructive rice blast. MoSec62 encodes a homologue of Sec62p, a yeast endoplasmic reticulum (ER) membrane transporter for precursors of secretory proteins. We showed that a T-DNA insertion into the promoter region of MoSec62, causing a disturbance to the up-regulation of MoSec62 expression during blast invasion, resulted in a complete loss of blast virulence of the mutant, M1575. Both 3,3'-diaminobenzidine (DAB) staining of the infected rice leaves and expression analysis revealed that the infectious attempt by the mutant led to strong defence responses of rice. Consistently, in transcriptomic analysis of rice leaves subject to blast inoculation, a battery of defence responses was found to be induced exclusively on M1575 challenge. For further exploration, we tested the pathogenicity on a highly susceptible rice variety and detected the accumulation of Slp1, a known PTI suppressor. Both results suggested that the mutant most likely failed to overcome rice PTI. In addition, we showed that MoSec62 was able to rescue the thermosensitivity of a yeast Δsec62, and the MoSec62-GFP fusion was co-localized to the ER membrane, both suggesting the conservation of Sec62 homologues. In conclusion, our data indicate that MoSec62, probably as an ER membrane transporter, plays an essential role in antagonizing rice defence at the early stages of blast invasion.

We use above-bandgap optical excitation, via a 1047 nm laser, to hyperpolarize the $^{31}$P spins in low-doped (N$_D =6\times10^{15}$ cm$^{-3}$) natural abundance silicon at 4.2 K and 6.7 T, and inductively detect the resulting NMR signal. The $30$ kHz spectral linewidth observed is dramatically larger than the 600 Hz linewidth observed from a $^{28}$Si-enriched silicon crystal. We show that the observed broadening is consistent with previous ENDOR results showing discrete isotope mass effect contributions to the donor hyperfine coupling. A secondary source of broadening is likely due to variations in the local strain, induced by the random distribution of different isotopes in natural silicon. The nuclear spin T$_1$ and the build-up time for the optically-induced $^{31}$P hyperpolarization in the natural abundance silicon sample were observed to be $178\pm47$ s and $69\pm6$ s respectively, significantly shorter than the values previously measured in $^{28}$Si-enriched samples under the same conditions. We also measured the T$_1$ and hyperpolarization build-up time for the $^{31}$P signal in natural abundance silicon at 9.4 T to be $54\pm31$ s and $13\pm2$ s respectively. The shorter build-up and nuclear spin T$_1$ times at high field are likely due to the shorter electron-spin T$_1$, which drives nuclear spin relaxation via non-secular hyperfine interactions. At 6.7 T, the phosphorus nuclear spin T$_{2}$ was measured to be $16.7\pm1.6$ ms at 4.2 K, a factor of 4 shorter than in $^{28}$Si-enriched crystals. This was observed to further shorten to $1.9\pm0.4$ ms in the presence of the infra-red laser., 5 pages

Plants depend on Resistance (R) genes, most of which encode nucleotide-binding site leucine-rich repeat (NLR) proteins, for pathogen race-specific disease resistance. However, only a few immediate downstream targets of R proteins have been characterized, and the signalling pathways for R-protein-induced immunity are largely unknown. In rice (Oryza sativa), NLR proteins serve as important immune receptors in the response to rice blast disease caused by the fungus Magnaporthe oryzae. We used site-directed mutagenesis to create an autoactive form of the NLR protein PID3 that confers blast resistance and used transgenic rice to test the resulting immunity and gene expression changes. We identified OsRac1, a known GTPase, as a signalling molecule in PID3-mediated blast resistance, implicating OsRac1 as a possible common factor downstream of rice NLR proteins. We also identified RAI1, a transcriptional activator, as a PID3 interactor required for PID3-mediated blast resistance and showed that RAI1 expression is induced by PID3 via a process mediated by OsRac1. This study describes a new signalling pathway for NLR protein-mediated blast resistance and shows that OsRac1 and RAI1 act together to play a critical role in this process.

Background Flowering time is a key trait for regional adaption and seed production in rice (Oryza sativa L.). Forward and reverse genetic studies have characterized a number of flowering-time genes. However, co-expression analysis has not been used to identify the flowering-time genes. Results We predicted a G2-like family transcription factor, OsPHL3, by co-expression networks analysis with photoperiodic flowering pathway genes. OsPHL3 contains a MYB-CC domain, and was localized in the nucleus with transcriptional activation potential. OsPHL3 was mainly expressed in the leaves and exhibited a circadian rhythmic expression pattern. Rice lines overexpressing OsPHL3 showed a delayed flowering time in the genetic background of TP309 under both long-day (Beijing) and short-day (Hainan) conditions. By contrast, the knockout rice lines of OsPHL3 by CRISPR/Cas9 technology promoted flowering time regardless of genetic backgrounds (i.e. Nipponbare and TP309) or day length. Further analysis indicated that OsPHL3 delayed flowering time by down-regulating the expression of Hd3a and RFT1 through promoting Hd1 under long-day conditions (LDs), or suppressing Ehd1/Hd1 under short-day conditions (SDs). Conclusions Our results suggested that co-expression analysis is a useful strategy for identifying novel flowering-time genes in rice. Electronic supplementary material The online version of this article (10.1186/s12870-018-1382-6) contains supplementary material, which is available to authorized users.

Flexible growth and immune responses in rice Plants that are fighting microbial pathogens often divert resources that could be used for growth into the immune response. For crops, this translates into lower yield when plant immunity is activated. Wang et al. show that, in rice, reversible phosphorylation of a key transcription factor allows the plant to defend against fungal attack when needed but then, within days, reallocate resources back to growth (see the Perspective by Greene and Dong). Thus, both pathogen defense and crop yield can be sustained. Science , this issue p. 1026 ; see also p. 976

Table S2. The sequence of primers used in this study. (DOCX 13 kb)

Jasmonates (JAs) are rapidly induced after wounding and act as key regulators for wound induced signaling pathway. However, what perceives the wound signal and how that triggers JA biosynthesis remains poorly understood. To identify components involved in Arabidopsis wound and JA signaling pathway, we screened for mutants with abnormal expression of a luciferase reporter, which is under the control of a wound-responsive promoter of an ethylene response factor (ERF) transcription factor gene, RAP2.6 (Related to APetala 2.6). The rea1 (RAP2.6 expresser in shoot apex) mutant constitutively expressed the RAP2.6-LUC reporter gene in young leaves. Along with the typical JA phenotypes including shorter petioles, loss of apical dominance, accumulation of anthocyanin pigments and constitutive expression of JA response gene, rea1 plants also displayed cell death and accumulated high levels of JA in response to wounding. The phenotype of rea1 mutant is caused by a gain-of-function mutation in the C-terminus of a mechanosensitive ion channel MscS-like 10 (MSL10). MSL10 is localized in the plasma membrane and is expressed predominantly in root tip, shoot apex and vascular tissues. These results suggest that MSL10 is involved in the wound-triggered early signal transduction pathway and possibly in regulating the positive feedback synthesis of JA.

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.

Electrically-detected magnetic resonance (EDMR) provides a highly sensitive method for reading out the state of donor spins in silicon. The technique relies on a spin-dependent recombination (SDR) process involving dopant spins that are coupled to interfacial defect spins near the Si/SiO$_2$ interface. To prevent ionization of the donors, the experiments are performed at cryogenic temperatures and the mobile charge carriers needed are generated via optical excitation. The influence of this optical excitation on the SDR process and the resulting EDMR signal is still not well understood. Here, we use EDMR to characterize changes to both phosphorus and defect spin readout as a function of optical excitation using: a 980 nm laser with energy just above the silicon band edge at cryogenic temperatures; a 405 nm laser to generate hot surface-carriers; and a broadband white light source. EDMR signals are observed from the phosphorus donor and two distinct defect species in all the experiments. With near-infrared excitation, we find that the EDMR signal primarily arises from donor-defect pairs, while at higher photon energies there are significant additional contributions from defect-defect pairs. The optical penetration depth into silicon is also known to be strongly wavelength dependent at cryogenic temperatures. The energy of the optical excitation is observed to strongly modulate the kinetics of the SDR process. Careful tuning of the optical photon energy could therefore be used to control both the subset of spin pairs contributing to the EDMR signal as well as the dynamics of the SDR process., Comment: extensively revised version

Due to its high biomass yield, low environmental impact, and widespread adaptability to poor soils and harsh conditions, switchgrass (Panicum virgatum L.), a warm-region perennial herbaceous plant, has attracted much attention in recent years. However, little is known about microRNAs (miRNAs) and their functions in this bioenergy grass. Here, we identified and characterized a miRNA gene, Pvi-MIR319a, encoding microRNA319a in switchgrass. Transgenic rice lines generated by overexpressing the Pvi-MIR319a precursor gene exhibited broader leaves and delayed flowering compared with the control. Gene expression analysis indicated at least four putative target genes were downregulated. Additionally, we cloned a putative target gene (PvPCF5) of Pvi-MIR319a from switchgrass. PvPCF5, a TCP transcription factor, is a nuclear-localized protein with transactivation activity and control the development of leaf. Our results suggest that Pvi-MIR319a and its target genes may be used as potential genetic regulators for future switchgrass genetic improvement.