Natural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies.

The inter-subspecific indica-japonica hybrid rice confer potential higher yield than the widely used indica-indica intra-subspecific hybrid rice. Nevertheless, the utilization of this strong heterosis is currently hindered by asynchronous diurnal floret opening time (DFOT) of indica and japonica parental lines. Here, we identify OsMYB8 as a key regulator of rice DFOT. OsMYB8 induces the transcription of JA-Ile synthetase OsJAR1, thereby regulating the expression of genes related to cell osmolality and cell wall remodeling in lodicules to promote floret opening. Natural variations of OsMYB8 promoter contribute to its differential expression, thus differential transcription of OsJAR1 and accumulation of JA-Ile in lodicules of indica and japonica subspecies. Furthermore, introgression of the indica haplotype of OsMYB8 into japonica effectively promotes DFOT in japonica. Our findings reveal an OsMYB8-OsJAR1 module that regulates differential DFOT in indica and japonica, and provide a strategy for breeding early DFOT japonica to facilitate breeding of indica-japonica hybrids.

PRMD: an integrated database for plant RNA modifications.

The scope and function of RNA modifications in model plant systems have been extensively studied, resulting in the identification of an increasing number of novel RNA modifications in recent years. Researchers have gradually revealed that RNA modifications, especially N6-methyladenosine (m6A), which is one of the most abundant and commonly studied RNA modifications in plants, have important roles in physiological and pathological processes. These modifications alter the structure of RNA, which affects its molecular complementarity and binding to specific proteins, thereby resulting in various of physiological effects. The increasing interest in plant RNA modifications has necessitated research into RNA modifications and associated datasets. However, there is a lack of a convenient and integrated database with comprehensive annotations and intuitive visualization of plant RNA modifications. Here, we developed the Plant RNA Modification Database (PRMD; http://bioinformatics.sc.cn/PRMD and http://rnainformatics.org.cn/PRMD) to facilitate RNA modification research. This database contains information regarding 20 plant species and provides an intuitive interface for displaying information. Moreover, PRMD offers multiple tools, including RMlevelDiff, RMplantVar, RNAmodNet and Blast (for functional analyses), and mRNAbrowse, RNAlollipop, JBrowse and Integrative Genomics Viewer (for displaying data). Furthermore, PRMD is freely available, making it useful for the rapid development and promotion of research on plant RNA modifications.

Targeted manipulation of grain shape genes effectively improves outcrossing rate and hybrid seed production in rice.

Stigma exsertion rate (SER) of the male sterile line is a key limiting factor for hybrid seed production in rice. Although a large number of quantitative trait loci associated with SER have been reported, few genes have been molecularly cloned and functionally characterized, severely hindering the genetic improvement of SER of the male sterile line and the breeding efficiency of hybrid rice. In this study, we identified three grain shape regulatory genes, GS3, GW8 and GS9, as potential candidate genes for targeted manipulation of grain shape and SER. We show that simultaneously knocking out these three genes could effectively increase SER by increasing the ratio of spikelet length/spikelet width and length of stigma and style, without negative impacts on other agronomic traits. Cellular examination and transcriptomic analyses revealed a role of these genes in coordinated regulation of transverse and longitudinal cell division in the pistils. Moreover, we demonstrate that targeted manipulation of these grain shape genes could significantly improve the outcrossing rate in both the ZH11 (a japonica variety) and Zhu6S (an indica male sterile line) backgrounds. Our results provide new insights into the mechanisms of rice SER regulation and develop an effective strategy to improve SER and out-crossing rate in rice, thus facilitating hybrid rice production.

Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase.

CRISPR-Cas base editing (BE) system is a powerful tool to expand the scope and efficiency of genome editing with single-nucleotide resolution. The editing efficiency, product purity, and off-target effect differ among various BE systems. Herein, we developed CRISPRbase (http://crisprbase.maolab.org), by integrating 1 252 935 records of base editing outcomes in more than 50 cell types from 17 species. CRISPRbase helps to evaluate the putative editing precision of different BE systems by integrating multiple annotations, functional predictions and a blasting system for single-guide RNA sequences. We systematically assessed the editing window, editing efficiency and product purity of various BE systems. Intensive efforts were focused on increasing the editing efficiency and product purity of base editors since the byproduct could be detrimental in certain applications. Remarkably, more than half of cancer-related off-target mutations were non-synonymous and extremely damaging to protein functions in most common tumor types. Luckily, most of these cancer-related mutations were passenger mutations (4840/5703, 84.87%) rather than cancer driver mutations (863/5703, 15.13%), indicating a weak effect of off-target mutations on carcinogenesis. In summary, CRISPRbase is a powerful and convenient tool to study the outcomes of different base editors and help researchers choose appropriate BE designs for functional studies.

OsLTP47 may function in a lipid transfer relay essential for pollen wall development in rice.

In plants, lipid transfer proteins (LTPs) transport pollen wall constituents from the tapetum to the exine, a process essential for pollen wall development. However, the functional cooperation of different LTPs in pollen wall development is not well understood. In this study, we have identified and characterized a grass-specific LTP gene, OsLTP47, an important regulator of pollen wall formation in rice (Oryza sativa). OsLTP47 encodes a membrane-localized LTP and in vitro lipid-binding assays confirms that OsLTP47 has lipid-binding activity. Dysfunction of OsLTP47 causes disordered lipid metabolism and defective pollen walls, leading to male sterility. Yeast two-hybrid and pull-down assays reveal that OsLTP47 physically interacts with another LTP, OsC6. These findings suggest that the plasma membrane-localized OsLTP47 may function as a mediator in a lipid transfer relay through association with cytosolic and/or locular OsC6 for pollen wall development and that various LTPs may function in a coordinated manner to transport lipid molecules during pollen wall development.

A NAC transcription factor OsNAC3 positively regulates ABA response and salt tolerance in rice.

BACKGROUND: NAC (NAM, ATAF and CUC) transcription factors (TFs) play vital roles in plant development and abiotic stress tolerance. Salt stress is one of the most limiting factors for rice growth and production. However, the mechanism underlying salt tolerance in rice is still poorly understood. RESULTS: In this study, we functionally characterized a rice NAC TF OsNAC3 for its involvement in ABA response and salt tolerance. ABA and NaCl treatment induced OsNAC3 expression in roots. Immunostaining showed that OsNAC3 was localized in all root cells. OsNAC3 knockout decreased rice plants' sensitivity to ABA but increased salt stress sensitivity, while OsNAC3 overexpression showed an opposite effect. Loss of OsNAC3 also induced Na+ accumulation in the shoots. Furthermore, qRT-PCR and transcriptomic analysis were performed to identify the key OsNAC3 regulated genes related to ABA response and salt tolerance, such as OsHKT1;4, OsHKT1;5, OsLEA3-1, OsPM-1, OsPP2C68, and OsRAB-21. CONCLUSIONS: This study shows that rice OsNAC3 is an important regulatory factor in ABA signal response and salt tolerance.

Association between anemia and outcome in patients hospitalized for acute heart failure syndromes: findings from Beijing Acute Heart Failure Registry (Beijing AHF Registry).

Whether the anemia increases the risk of mortality in patients with acute heart failure (AHF) remains unclear. This study aims to explore the relationship between anemia and outcomes in patients with AHF including subgroup analysis. This study included 3279 patients with hemoglobin available from the Beijing Acute Heart Failure Registry (Beijing AHF Registry) study. The primary endpoint was all-cause mortality in 1 year, and the secondary endpoint was 1-year all-cause events including all-cause death and readmission. Logistic regression models were applied to describe related variables of anemia in patients with AHF. Multivariate Cox proportional hazards models described associations of anemia with clinical outcomes in the overall cohort and subgroups. 45.4% of the patients were found anemic. They were older and had more comorbidities than non-anemic patients. Variables including older age, female, chronic kidney dysfunction (CKD), lower hematocrit, lower albumin, with loop diuretics applied, without beta-blockers, angiotensin-converting enzyme inhibitors /angiotensin receptor blockers (ACEIs/ARBs) and spironolactone applied in the emergency department (ED) were associated with anemia in AHF patients. Anemic patients had higher 1-year mortality (38.4% vs. 27.2%, p < 0.0001) and 1-year events rates (63.2% vs. 56.7%, p < 0.0001). After adjusted for covariates, anemia was associated with the increase of 1-year mortality (hazard ratio [HR] 1.278; 95% confidence interval [CI] 1.114-1.465; p = 0.0005) and 1-year events (HR 1.136; 95% CI 1.025-1.259; p = 0.0154). The severer anemia patients had higher risks both of 1-year mortality and events. In the subgroup analysis, the independent associations of anemia with 1-year mortality were shown in the subgroups including age < 75 years, male, body mass index < 25 kg/m2 and BMI ≥ 25 kg/m2, New York Heart Association (NYHA) functional class I-II and NYHA functional class III-IV, with and without cardiovascular ischemia, heart rate (HR) < 100 bpm and HR ≥ 100 bpm, systolic blood pressure (SBP) < 120 mmHg and SBP ≥ 120 mmHg, left ventricular ejection fraction (LVEF) < 40% and LVEF ≥ 40%, serum creatinine (Scr) < 133 umol/l, and with diuretics use, with and without beta-blockers use, without ACEIs/ARBs use in the ED. Anemia is associated with older age, female, CKD, volume overload, malnutrition, with loop diuretics, without beta-blockers, ACEIs/ARBs and spironolactone administration, and higher mortality and readmission in AHF. The risk associations are particular significantly obvious in younger, male, overweight, preserved LVEF, lower Scr, with diuretics and beta-blockers, without ACEIs/ARBs administration subgroups.Clinical trial No. ChiCTR-RIC-17014222.

Characteristics, Management, and Outcomes of Acute Heart Failure in the Emergency Department: A Multicenter Registry Study with 1-year Follow-up in a Chinese Cohort in Beijing.

BACKGROUND: The emergency department (ED) has a pivotal influence on the management of acute heart failure (AHF), but data concerning current ED management are scarce. This Beijing AHF Registry Study investigated the characteristics, ED management, and short- and long-term clinical outcomes of AHF. METHODS: This prospective, multicenter, observational study consecutively enrolled 3335 AHF patients who visited 14 EDs in Beijing from January 1, 2011, to September 23, 2012. Baseline data on characteristics and management were collected in the EDs. Follow-up data on death and readmissions were collected until November 31, 2013, with a response rate of 92.80%. The data were reported as median (interquartile range) for the continuous variables, or as number (percentage) for the categorical variables. RESULTS: The median age of the enrolled patients was 71 (58-79) years, and 46.84% were women. In patients with AHF, coronary heart disease (43.27%) was the most common etiology, and myocardium ischemia (30.22%) was the main precipitant. Most of the patients in the ED received intravenous treatments, including diuretics (79.28%) and vasodilators (74.90%). Fewer patients in the ED received neurohormonal antagonists, and 25.94%, 31.12%, and 33.73% of patients received angiotensin converting enzyme inhibitors/angiotensin receptor blockers, beta-blockers, and spironolactone, respectively. The proportions of patients who were admitted, discharged, left against medical advice, and died were 55.53%, 33.58%, 7.08%, and 3.81%, respectively. All-cause mortalities at 30 days and 1 year were 15.30% and 32.27%, respectively. CONCLUSIONS: Substantial details on characteristics and ED management of AHF were investigated. The clinical outcomes of AHF patients were dismal. Thus, further investigations of ED-based therapeutic approaches for AHF are needed.

Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement.

Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived. We identified 1,313 selective sweeps (SSWs) revealing four stage-specific selection patterns corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan traceable blocks (cHTBs) introduced from different donors and conserved in >3 breeding generations were the core genomic regions for superior performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs) identified for 13 improved traits in the pedigree, we reproduced their improvement process in silico, highlighting improving breeding works well for traits controlled by major/major + minor effect QTLs, but was inefficient for traits controlled by QTLs with complex interactions or explaining low levels of phenotypic variation. These results indicate long-term breeding improvement is efficient to construct superior genetic architecture for elite performance, yet molecular breeding with designed genotype of QTLs can facilitate complex traits improvement.

Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.

Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6× depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design.