Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations.

Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.

A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance.

Rice feeds half the world's population, and rice blast is often a destructive disease that results in significant crop loss. Non-race-specific resistance has been more effective in controlling crop diseases than race-specific resistance because of its broad spectrum and durability. Through a genome-wide association study, we report the identification of a natural allele of a C2H2-type transcription factor in rice that confers non-race-specific resistance to blast. A survey of 3,000 sequenced rice genomes reveals that this allele exists in 10% of rice, suggesting that this favorable trait has been selected through breeding. This allele causes a single nucleotide change in the promoter of the bsr-d1 gene, which results in reduced expression of the gene through the binding of the repressive MYB transcription factor and, consequently, an inhibition of H2O2 degradation and enhanced disease resistance. Our discovery highlights this novel allele as a strategy for breeding durable resistance in rice.

Rice false smut virulence protein subverts host chitin perception and signaling at lemma and palea for floral infection.

The flower-infecting fungus Ustilaginoidea virens causes rice false smut, which is a severe emerging disease threatening rice (Oryza sativa) production worldwide. False smut not only reduces yield, but more importantly produces toxins on grains, posing a great threat to food safety. U. virens invades spikelets via the gap between the 2 bracts (lemma and palea) enclosing the floret and specifically infects the stamen and pistil. Molecular mechanisms for the U. virens-rice interaction are largely unknown. Here, we demonstrate that rice flowers predominantly employ chitin-triggered immunity against U. virens in the lemma and palea, rather than in the stamen and pistil. We identify a crucial U. virens virulence factor, named UvGH18.1, which carries glycoside hydrolase activity. Mechanistically, UvGH18.1 functions by binding to and hydrolyzing immune elicitor chitin and interacting with the chitin receptor CHITIN ELICITOR BINDING PROTEIN (OsCEBiP) and co-receptor CHITIN ELICITOR RECEPTOR KINASE1 (OsCERK1) to impair their chitin-induced dimerization, suppressing host immunity exerted at the lemma and palea for gaining access to the stamen and pistil. Conversely, pretreatment on spikelets with chitin induces a defense response in the lemma and palea, promoting resistance against U. virens. Collectively, our data uncover a mechanism for a U. virens virulence factor and the critical location of the host-pathogen interaction in flowers and provide a potential strategy to control rice false smut disease.

Exogenous Indole-3-Acetic Acid Suppresses Rice Infection of Magnaporthe oryzae by Affecting Plant Resistance and Fungal Growth.

Auxin is an important phytohormone that regulates diverse biologic processes, including plant growth and immunity. Indole-3-acetic acid (IAA), known as one of the main forms of auxin, is able to activate plant immunity. However, it is unknown whether IAA enhances plant resistance and/or suppresses the growth of the fungal pathogen Magnaporthe oryzae. Here, we found that IAA could induce expression levels of pathogenesis-related genes to enhance disease resistance and could control the development of blast disease through inhibiting M. oryzae infection. Exogenous IAA suppressed mycelial growth and delayed spore germination by inhibiting fungal endogenous IAA biosynthesis and impairing redox homeostasis, respectively. When applied to a field test, two IAA analogues, 1-naphthaleneacetic acid and 2,4-dichlorophenoxy acetic acid, can effectively control rice blast disease. Our study advances the understanding of IAA in controlling rice blast disease through suppressing pathogen growth and enhancing plant resistance.

Two-faced OsNAS3 influences disease resistance via nicotianamine and ethylene.

The loss and gain of OsNAS3 function both positively influence plant disease resistance. Overexpression of OsNAS3 boosts blast resistance by promoting nicotianamine accumulation, thereby enhancing blast resistance. Conversely, knockout of OsNAS3 increases ethylene biosynthesis, also contributing to improved blast resistance.

D53 represses rice blast resistance by directly targeting phenylalanine ammonia lyases.

In rice, DWARF 53 directly binds to the promoters of seven phenylalanine ammonia lyase genes, OsPAL1˜OsPAL7, and represses their expression, leading to decreased lignin accumulation and compromised resistance against Magnaporthe oryzae.

Golovinomyces cichoracearum effector-associated nuclear localization of RPW8.2 amplifies its expression to boost immunity in Arabidopsis.

Arabidopsis RESISTANCE TO POWDERY MILDEW 8.2 (RPW8.2) is specifically induced by the powdery mildew (PM) fungus (Golovinomyces cichoracearum) in the infected epidermal cells to activate immunity. However, the mechanism of RPW8.2-induction is not well understood. Here, we identify a G. cichoracearum effector that interacts with RPW8.2, named Gc-RPW8.2 interacting protein 1 (GcR8IP1), by a yeast two-hybrid screen of an Arabidopsis cDNA library. GcR8IP1 is physically associated with RPW8.2 with its REALLY INTERESTING NEW GENE finger domain that is essential and sufficient for the association. GcR8IP1 was secreted and translocated into the nucleus of host cell infected with PM. Association of GcR8IP1 with RPW8.2 led to an increase in RPW8.2 in the nucleus. In turn, the nucleus-localized RPW8.2 promoted the activity of the RPW8.2 promoter, resulting in transcriptional self-amplification of RPW8.2 to boost immunity at infection sites. Additionally, ectopic expression or host-induced gene silencing of GcR8IP1 supported its role as a virulence factor in PM. Altogether, our results reveal a mechanism of RPW8.2-dependent defense strengthening via altered partitioning of RPW8.2 and transcriptional self-amplification triggered by a PM fungal effector, which exemplifies an atypical form of effector-triggered immunity.

Hydrogen improves exercise endurance in rats by promoting mitochondrial biogenesis.

BACKGROUND: Previous studies have shown that hydrogen water has antioxidant and anti-inflammatory effects on exercise-induced fatigue; however, its molecular mechanism remains unclear. METHODS: Adult male Sprague-Dawley rats were randomly divided into a pure water drinking group (NC) and a hydrogen water drinking group (HW) (n = 7), and 2-week treadmill training was used to establish a sports model. Gut bacterial community profiling was performed using 16S rRNA gene sequencing analysis. The expression levels of mitochondrial energy metabolism-related genes and the levels of sugar metabolites and enzymes were measured. RESULTS: The exercise tolerance of rats in the HW group significantly improved, and the distribution and diversity of intestinal microbes were altered. Hydrogen significantly upregulated genes related to mitochondrial biogenesis, possibly via the Pparγ/Pgc-1α/Tfam pathway. In addition, hydrogen effectively mediated the reprogramming of skeletal muscle glucose metabolism. CONCLUSION: Our findings establish a critical role for hydrogen in improving endurance exercise performance by promoting mitochondrial biogenesis via the Pparγ/Pgc-1α/Tfam pathway.

Finding family resilience in adversity: A grounded theory of families with children diagnosed with leukaemia.

AIMS AND OBJECTIVES: To develop a conceptual framework that explores the process of building family resilience among Chinese families with children diagnosed with leukaemia. BACKGROUND: The diagnosis of childhood leukaemia has a devastating effect on the family. Nonetheless, some families were able to positively respond to the crisis. The process through which Chinese families bounce back has received little attention. DESIGN: Grounded theory. METHODS: This study used purposive and theoretical sampling to select 16 parents who agreed to participate in semistructured interviews after children were diagnosed with leukaemia. Data collection and analysis occurred simultaneously. Data were analysed through a process of open, axial and selective coding. The COREQ checklist was followed for reporting. RESULTS: A core category of 'finding family resilience in adversity' was generated. The core category was underpinned by a transition process between two fluid stages: (a) Disrupting the family system, informed by subcategories of negative emotional disturbances and challenges of the diagnosis and treatment journey; (b) Cultivating resilience in families, informed by subcategories of increasing positive attitudes; establishing new family routines; activating good support systems; and practising open family communication. CONCLUSIONS: The transition process from the disruption of the family system to the cultivation of family resilience is perceived as a complex family dynamic in response to childhood leukaemia. Our findings can form the basis for further research about resilience-based family interventions that promote family well-being during the early stages of a childhood leukaemia diagnosis. RELEVANCE TO CLINICAL PRACTICE: It is necessary for healthcare professionals to provide essential support for families to face the challenges of diagnosis and treatment to facilitate the successful transition to family resilience. By understanding the dynamic process of developing family resilience, healthcare professionals are able to focus on these families to provide holistic care that satisfies the specific demands of family members.

The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals.

Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.

OsBSK2, a putative brassinosteroid-signalling kinase, positively controls grain size in rice.

Grain size is an important trait that directly affects grain yield in rice; however, the genetic and molecular mechanisms regulating grain size remain unclear. In this study, we identified a mutant, grain length and grain weight 10 (glw10), which exhibited significantly reduced grain length and grain weight. Histological analysis demonstrated that GLW10 affects cell expansion, which regulates grain size. MutMap-based gene mapping and transgenic experiments demonstrated that GLW10 encodes a putative brassinosteroid (BR) signalling kinase, OsBSK2. OsBSK2 is a plasma membrane protein, and an N-myristoylation site is needed for both membrane localization and function. OsBSK2 directly interacts with the BR receptor kinase OsBRI1; however, genetic experiments have demonstrated that OsBSK2 may regulate grain size independent of the BR signalling pathway. OsBSK2 can form a homodimer or heterodimer with OsBSK3 and OsBSK4, and silencing OsBSK2, OsBSK3, and OsBSK4 reduce grain size. This indicates that OsBSKs seem to function as homodimers or heterodimers to positively regulate grain size in rice. OsBSK2/3/4 are all highly expressed in young panicles and spikelet hulls, suggesting that they control grain size. In summary, our results provide novel insights into the function of BSKs in rice, and identify novel targets for improving grain size during crop breeding.

Long non-coding RNA ANRIL interacts with microRNA-34a and microRNA-125a, and they all correlate with disease risk and severity of Parkinson's disease.

BACKGROUND: This study aimed to investigate the correlation of long non-coding RNA antisense non-coding RNA in the INK4 locus (lncRNA ANRIL) and its target microRNAs (microRNA-34a (miR-34a) and microRNA-125a (miR-125a)) with disease risk and severity of Parkinson's disease (PD). METHODS: Seventy-eight PD patients and 78 age-/gender-matched controls were consecutively enrolled. Their peripheral blood mononuclear cell samples were collected and proposed for the reverse-transcription quantitative polymerase chain reaction to complete lncRNA ANRIL, miR-34a, and miR-125a measurements. RESULTS: LncRNA ANRIL was upregulated, while miR-34a and miR-125a were downregulated in PD patients compared to controls (all p < 0.001). Further, they all showed certain values for PD risk identification by ROC curve analyses, among which lncRNA ANRIL showed the highest AUC (AUC: 0.879, 95% CI: 0.824-0.934). Furthermore, lncRNA ANRIL negatively correlated with miR-34a (p = 0.016) and miR-125a (p = 0.005) in PD patients, but not in controls. In addition, lncRNA ANRIL was observed to positively associate with UPDRS-I score (p = 0.029), UPDRS-III score (p = 0.006), and UPDRS-IV score (p = 0.033), while negatively correlated with MMSE score (p = 0.003). These associations were less distinct as to miR-34a and miR-125a. CONCLUSION: LncRNA ANRIL interacts with miR-34a and miR-125a in PD patients, and they all correlate with disease risk and severity of PD.

Chemosensory proteins confer adaptation to the ryanoid anthranilic diamide insecticide cyantraniliprole in Aphis gossypii glover.

Chemosensory proteins (CSPs) are a class of small transporter proteins expressed only in arthropods with various functions beyond chemoreception. Previous studies have been reported that CSPs are involved in the insecticide resistance. In this study, we found that AgoCSP1, AgoCSP4, and AgoCSP5 were constitutively overexpressed in an insecticide-resistant strain of Aphis gossypii and showed higher expression in broad body tissue (including fat bodies) than in the midgut but without tissue specificity. However, the function of these three upregulated AgoCSPs remains unknown. Here, we investigated the function of AgoCSPs in resistance to the diamide insecticide cyantraniliprole. Suppression of AgoCSP1, AgoCSP4 and AgoCSP5 transcription by RNAi significantly increased the sensitivity of resistant aphids to cyantraniliprole. Molecular docking and competitive binding assays indicated that these AgoCSPs bind moderate with cyantraniliprole. Transgenic Drosophila melanogaster expressing these AgoCSPs in the broad body or midgut showed higher tolerance to cyantraniliprole than control flies with the same genetic background; AgoCSP4 was more effective in broad body tissue, and AgoCSP1 and AgoCSP5 were more effective in the midgut, indicating that broad body and midgut tissues may be involved in the insecticide resistance mediated by the AgoCSPs examined. The present results strongly indicate that AgoCSPs participate in xenobiotic detoxification by sequestering and masking toxic insecticide molecules, providing insights into new factors involved in resistance development in A. gossypii.

Functional analysis of cyantraniliprole tolerance ability mediated by ATP-binding cassette transporters in Aphis gossypii glover.

Cyantraniliprole, a second-generation anthranilic diamide insecticide, is widely used to control chewing and sucking pests. ATP-binding cassette transporters (ABCs) are a ubiquitous family of membrane proteins that play important roles in insect detoxification mechanisms. However, the potential effects of ABCs on cyantraniliprole-resistance remain unclear. In the present study, synergism bioassays revealed that verapamil, an ABC inhibitor, increased the toxicity of cyantraniliprole by 2.00- and 12.25-fold in the susceptible and cyantraniliprole-resistant strains of Aphis gossypii. Based on transcriptome data, the expression levels of ABCB4, ABCB5, ABCD1, ABCG4, ABCG7, ABCG13, ABCG16, ABCG17, ABCG26 and MRP12 were upregulated 1.56-, 1.32-, 1.51-, 2.03-, 1.65-, 1.50-, 4.18-, 6.07-, 4.68- and 4.69-fold, respectively, in the cyantraniliprole-resistant strain (CyR) compared to the susceptible strain (SS), as determined using RT-qPCR. Drosophila melanogaster ectopically overexpressing ABCB5, ABCG4, ABCG7, ABCG16, ABCG17, ABCG26 and MRP12 exhibited significantly increased tolerance to cyantraniliprole by 11.71-, 2.39-, 4.85-, 2.06-, 3.75-, 4.20- and 3.50-fold, respectively, with ABCB5 and ABCG family members being the most effective. Furthermore, the suppression of ABCB5, ABCG4, ABCG7, ABCG16, ABCG17, ABCG26 and MRP12 significantly increased the sensitivity of the CyR strain to cyantraniliprole. These results indicate that ABCs may play crucial roles in cyantraniliprole resistance and may provide information for shaping resistance management strategies.

Antagonistic effect of selenium on mercuric chloride in the central immune organs of chickens: The role of microRNA-183/135b-FOXO1/TXNIP/NLRP3 inflammasome axis.

Mercury (Hg) is a persistent environmental and industrial pollutant that accumulated in the body and induces oxidative stress and inflammation damage. Selenium (Se) has been reported to antagonize immune organs damage caused by heavy metals. Here, we aimed to investigate the prevent effect of Se on mercuric chloride (HgCl2 )-induced thymus and bursa of Fabricius (BF) damage in chickens. The results showed that HgCl2 caused immunosuppression by reducing the relative weight, cortical area of the thymus and BF, and the number of peripheral blood lymphocytes. Meanwhile, HgCl2 induced oxidative stress and imbalance in cytokines expression in the thymus and BF. Further, we found that thioredoxin-interacting protein (TXNIP) and the NOD-like receptor pyrin domain containing 3 (NLRP3) inflammasome mediated HgCl2 -induced oxidative stress and inflammation. Mechanically, the targeting and inhibitory effect of microRNA (miR)-135b/183 on forkhead box O1 (FOXO1) were an upstream event for HgCl2 -activated TXNIP/NLRP3 inflammasome pathway. Most importantly, Se effectively attenuated the aforementioned damage in the thymus and BF caused by HgCl2 and inhibited the TXNIP/NLRP3 inflammasome pathway by reversing the expression of FOXO1 through inhibiting miR-135b/183. In conclusion, the miR-135b/183-FOXO1/TXNIP/NLRP3 inflammasome axis might be a novel mechanism for Se to antagonize HgCl2 -induced oxidative stress and inflammation in the central immune organs of chickens.

Identifying circRNA- and lncRNA-associated-ceRNA networks in the hippocampi of rats exposed to PM2.5 using RNA-seq analysis.

Non-coding RNAs appear to be involved in the regulation of the nervous system. However, no competing endogenous RNA (ceRNA) network related to PM2.5 damage in the hippocampal function has yet been constructed. Herein, we used whole-transcriptome sequencing technology to systematically study the ceRNA network in rat hippocampi after PM2.5 exposure. We identified 100 circRNAs, 67 lncRNAs, 28 miRNAs, and 539 mRNAs and constructed the most comprehensive ceRNA network to date, to our knowledge. Gene Ontology and KEGG analyses showed that the network molecules are involved in synapses, neural projections, and neural development and involve signal pathways such as the synaptic vesicle cycle. Finally, the expression of the differentially expressed RNAs confirmed by quantitative real-time PCR was consistent with the sequencing data. This study systematically dissected the ceRNA atlas related to cognitive memory function in the hippocampal tissue of PM2.5-exposed rats for the first time, to our knowledge, and promotes the development of potential new treatments for cognitive impairment.

Chemosensory Proteins Are Associated with Thiamethoxam and Spirotetramat Tolerance in Aphis gossypii Glover.

Chemosensory proteins (CSPs) are a class of transporters in arthropods. Deeper research on CSPs showed that CSPs may be involved in some physiological processes beyond chemoreception, such as insect resistance to pesticides. We identified two upregulated CSPs in two resistant strains of Aphis gossypii Glover. To understand their role in the resistance of aphids to pesticides, we performed the functional verification of CSP1 and CSP4 in vivo and in vitro. Results showed that the sensitivity of the thiamethoxam-resistant strain to thiamethoxam increased significantly with the silencing of CSP1 and CSP4 by RNAi (RNA interference), and the sensitivity of the spirotetramat-resistant strain to spirotetramat increased significantly with the silencing of CSP4. Transgenic Drosophila melanogaster expressing CSPs exhibited stronger resistance to thiamethoxam, spirotetramat, and alpha-cypermethrin than the control did. In the bioassay of transgenic Drosophila, CSPs showed different tolerance mechanisms for different pesticides, and the overexpressed CSPs may play a role in processes other than resistance to pesticides. In brief, the present results prove that CSPs are related to the resistance of cotton aphids to insecticides.

A Yeast-Based Drug Discovery Platform To Identify Plasmodium falciparum Type II NADH Dehydrogenase Inhibitors.

Conventional methods utilizing in vitro protein activity assay or in vivo parasite survival to screen for malaria inhibitors suffer from high experimental background and/or inconvenience. Here, we introduce a yeast-based system to facilitate chemical screening for specific protein or pathway inhibitors. The platform comprises several isogeneic Pichia strains that differ only in the target of interest, so that a compound which inhibits one strain but not the other is implicated in working specifically against the target. We used Plasmodium falciparum NDH2 (PfNDH2), a type II NADH dehydrogenase, as a proof of principle to show how well this works. Three isogenic Pichia strains harboring, respectively, exogeneously introduced PfNDH2, its own complex I (a type I NADH dehydrogenase), and PfNDH2 with its own complex I, were constructed. In a pilot screen of more than 2,000 compounds, we identified a highly specific inhibitor that acts on PfNDH2. This compound poorly inhibits the parasites at the asexual blood stage; however, is highly effective in repressing oocyst maturation in the mosquito stage. Our results demonstrate that the yeast cell-based screen platform is feasible, efficient, economical, and has very low background noise. Similar strategies could be extended to the functional screen for interacting molecules of other targets.

Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance.

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.

Selenium alleviates mercury chloride-induced liver injury by regulating mitochondrial dynamics to inhibit the crosstalk between energy metabolism disorder and NF-κB/NLRP3 inflammasome-mediated inflammation.

Mercury (Hg) is a persistent heavy metal contaminant with definite hepatotoxicity. Selenium (Se) has been shown to alleviate liver damage induced by heavy metals. Therefore, the present study aimed to explore the mechanism of the antagonistic effect of Se on mercury chloride (HgCl2)-induced hepatotoxicity in chickens. Firstly, we confirmed that Se alleviated HgCl2-induced liver injury through histopathological observation and liver function analyzation. The results also showed that Se prevented HgCl2-induced liver lipid accumulation and dyslipidemia by regulating the gene expression related to lipid as well as glucose metabolism. Moreover, Se blocked the nuclear factor kappa B (NF-κB)/NLR family pyrin domain containing 3 (NLRP3) inflammasome signaling pathway, which was the key to alleviate the inflammation caused by HgCl2. Mechanically, Se inhibited immoderate mitochondrial division, fusion, and biogenesis caused by HgCl2, and also improved mitochondrial respiration, which were essential for preventing energy metabolism disorder and inflammation. In conclusion, our results suggested that Se inhibited energy metabolism disorder and inflammation by regulating mitochondrial dynamics, thereby alleviating HgCl2-induced liver injury in chickens. These results are expected to provide potential intervention and therapeutic targets for diseases caused by inorganic mercury poisoning.