The soybean Rpp3 gene encodes a TIR-NBS-LRR protein that confers resistance to Phakopsora pachyrhizi.

Soybean rust is an economically significant disease caused by the fungus Phakopsora pachyrhizi that negatively impacts soybean (Glycine max (L.) Merr.) production throughout the world. Susceptible plants infected by P. pachyrhizi develop tan-colored lesions on the leaf surface that give rise to funnel-shaped uredinia as the disease progresses. While most soybean germplasm is susceptible, seven genetic loci (Rpp1 to Rpp7) that provide race-specific resistance to P. pachyrhizi (Rpp) have been identified. Rpp3 was first discovered and characterized in the soybean accession PI 462312 (Ankur), and it was also determined to be one of two Rpp genes present in PI 506764 (Hyuuga). Genetic crosses with PI 506764 were later used to fine-map the Rpp3 locus to a 371 kb region on chromosome 6. The corresponding region in the susceptible Williams 82 (Wm82) reference genome contains several homologous nucleotide binding site-leucine rich repeat (NBS-LRR) genes. To identify Rpp3, we designed oligonucleotide primers to amplify Rpp3 candidate (Rpp3C) NBS-LRR genes at this locus from PI 462312, PI 506764, and Wm82 using polymerase chain reaction (PCR). Five Rpp3C genes were identified in both Rpp3-resistant soybean lines, and co-silencing these genes compromised resistance to P. pachyrhizi. Gene expression analysis and sequence comparisons of the Rpp3C genes in PI 462312 and PI 506764 suggest that a single candidate gene, Rpp3C3, is responsible for Rpp3-mediated resistance.

Response shift in coronary artery disease.

PURPOSE: Patients with coronary artery disease (CAD) experience significant angina symptoms and lifestyle changes. Revascularization procedures can result in better patient-reported outcomes (PROs) than optimal medical therapy (OMT) alone. This study evaluates the impact of response shift (RS) on changes in PROs of patients with CAD across treatment strategies. METHODS: Data were from patients with CAD in the Alberta Provincial Project on Outcome Assessment in Coronary Heart Disease (APPROACH) registry who completed the 16-item Canadian version of the Seattle Angina Questionnaire at 2 weeks and 1 year following a coronary angiogram. Multi-group confirmatory factor analysis (MG-CFA) was used to assess measurement invariance across treatment groups at week 2. Longitudinal MG-CFA was used to test for RS according to receipt of coronary artery bypass grafting (CABG), percutaneous coronary intervention (PCI), or optimal medical therapy (OMT) alone. RESULTS: Of the 3116 patients included in the analysis, 443 (14.2%) received CABG, 2049(65.8%) PCI, and the remainder OMT alone. The MG-CFA revealed a partial-strong invariance across the treatment groups at 2 weeks (CFI = 0.98, RMSEA [90% CI] = 0.05 [0.03, 0.06]). Recalibration RS was detected on the Angina Symptoms and Burden subscale and its magnitude in the OMT, PCI, and CABG groups were 0.32, 0.28, and 0.53, respectively. After adjusting for RS effects, the estimated target changes were largest in the CABG group and negligible in the OMT group. CONCLUSION: Adjusting for RS is recommended in studies that use SAQ-CAN to assess changes in patients with CAD who have received revascularization versus OMT alone.

Myocardial Injury After Noncardiac Surgery in Major General Surgical Patients a Prospective Observational Cohort Study.

OBJECTIVE: The objective of this study was to determine the prognostic relevance, clinical characteristics, and 30-day outcomes associated with myocardial injury after noncardiac surgery (MINS) in major general surgery patients. BACKGROUND: MINS has been independently associated with 30-day mortality after noncardiac surgery. The characteristics and prognostic importance of MINS in major general surgical patients have not been described. METHODS: This was an international prospective cohort study of a representative sample of 22,552 noncardiac surgery patients 45 years or older, of whom 4490 underwent major general surgery in 24 centers in 13 countries. All patients had fifth-generation plasma high-sensitivity troponin T (hsTnT) concentrations measured during the first 3 postoperative days. MINS was defined as a hsTnT of 20-65 ng/L and absolute change >5 ng/L or hsTnT ≥65 ng/L secondary to ischemia. The objectives of the present study were to determine (1) whether MINS is prognostically important in major general surgical patients, (2) the clinical characteristics of major general surgical patients with and without MINS, (3) the 30-day outcomes for major general surgical patients with and without MINS, and (4) the proportion of MINS that would have gone undetected without routine postoperative monitoring. RESULTS: The incidence of MINS in the major general surgical patients was 16.3% (95% CI, 15.3-17.4%). Thirty-day all-cause mortality in the major general surgical cohort was 6.8% (95% CI, 5.1%-8.9%) in patients with MINS compared with 1.2% (95% CI, 0.9%-1.6%) in patients without MINS ( P <0.01). MINS was independently associated with 30-day mortality in major general surgical patients (adjusted odds ratio 4.7, 95% CI, 3.0-7.4). The 30-day mortality was higher both among MINS patients with no ischemic features (ie, no ischemic symptoms or electrocardiogram findings) (5.4%, 95% CI, 3.7%-7.7%) and among patients with 1 or more clinical ischemic features (10.6%, 95% CI, 6.7%-15.8%). The proportion of major general surgical patients who had MINS without ischemic symptoms was 89.9% (95% CI, 87.5-92.0). CONCLUSIONS: Approximately 1 in 6 patients experienced MINS after major general surgery. MINS was independently associated with a nearly 5-fold increase in 30-day mortality. The vast majority of patients with MINS were asymptomatic and would have gone undetected without routine postoperative troponin measurement.

A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database.

SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variant data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.

P2Y12 inhibitor adherence trajectories in patients with acute coronary syndrome undergoing percutaneous coronary intervention: prognostic implications.

AIMS: Post-acute coronary syndrome (ACS) P2Y12 inhibitor non-adherence is common and associated with greater risk of major adverse cardiovascular events (MACEs). Non-adherence can follow different trajectories from an inability to initiate, implement, or continue therapy for the intended duration. We aimed to evaluate P2Y12 inhibitor adherence trajectories among ACS patients treated with percutaneous coronary intervention (PCI), their frequency, and association with MACE. METHODS AND RESULTS: We conducted a cohort study of adults discharged alive after PCI for ACS (2012-16) using the Alberta Provincial Project for Outcome Assessment in Coronary Heart Disease registry linked with administrative data. The primary outcome was P2Y12 inhibitor adherence trajectory in the year after PCI assessed using group-based trajectory modelling. We used logistic regression and Cox proportional-hazards regression to assess associations of trajectories with risk factors and MACE, respectively. We included 12 844 patients (mean age 62.4 years, 23.6% female). Five trajectories were identified: early consistent non-adherence (11.0%), rapid decline (7.7%), delayed initiation (6.0%), gradual decline (20.5%), and persistent adherence (54.8%). Compared with persistent adherence, rapid decline [hazard ratio (HR) 1.23, 95% confidence interval (CI) 1.01-1.49] and delayed initiation (HR 1.41, 95% CI 1.12-1.78) were associated with higher MACE in the overall cohort, whereas early consistent non-adherence was associated with higher MACE only in the subgroup receiving a drug-eluting stent (HR 2.44, 95% CI 1.60-3.71). CONCLUSION: After PCI for ACS, patients followed one of five distinct P2Y12 inhibitor adherence trajectories. Rapid decline and delayed initiation were associated with a higher risk of MACE, whereas early consistent non-adherence was only associated with higher MACE risk in patients with a drug-eluting stent.

Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing.

BACKGROUND: Leaf angle is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. The "smart canopy" model proposes more vertical leaves in the top plant layers and more horizontal leaves in the lower canopy, maximizing conversion efficiency and photosynthesis. Sorghum leaf arrangement is opposite to that proposed in the "smart canopy" model, indicating the need for improvement. Although leaf angle quantitative trait loci (QTL) have been previously reported, only the Dwarf3 (Dw3) auxin transporter gene, colocalizing with a major-effect QTL on chromosome 7, has been validated. Additionally, the genetic architecture of leaf angle across canopy layers remains to be elucidated. RESULTS: This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. A set of 284 differentially expressed genes for at least one layer comparison (FDR < 0.05) co-localized with 69 leaf angle QTL and were consistently identified across genotypes. These genes are involved in transmembrane transport, hormone regulation, oxidation-reduction process, response to stimuli, lipid metabolism, and photosynthesis. The most relevant eleven candidate genes for layer-specific angle modification include those homologous to genes controlling leaf angle in rice and maize or genes associated with cell size/expansion, shape, and cell number. CONCLUSIONS: Considering the predicted functions of candidate genes, their potential undesirable pleiotropic effects should be further investigated across tissues and developmental stages. Future validation of proposed candidates and exploitation through genetic engineering or gene editing strategies targeted to collar cells will bring researchers closer to the realization of a "smart canopy" sorghum.

Excess years of life lost to COVID-19 and other causes of death by sex, neighbourhood deprivation, and region in England and Wales during 2020: A registry-based study.

BACKGROUND: Deaths in the first year of the Coronavirus Disease 2019 (COVID-19) pandemic in England and Wales were unevenly distributed socioeconomically and geographically. However, the full scale of inequalities may have been underestimated to date, as most measures of excess mortality do not adequately account for varying age profiles of deaths between social groups. We measured years of life lost (YLL) attributable to the pandemic, directly or indirectly, comparing mortality across geographic and socioeconomic groups. METHODS AND FINDINGS: We used national mortality registers in England and Wales, from 27 December 2014 until 25 December 2020, covering 3,265,937 deaths. YLLs (main outcome) were calculated using 2019 single year sex-specific life tables for England and Wales. Interrupted time-series analyses, with panel time-series models, were used to estimate expected YLL by sex, geographical region, and deprivation quintile between 7 March 2020 and 25 December 2020 by cause: direct deaths (COVID-19 and other respiratory diseases), cardiovascular disease and diabetes, cancer, and other indirect deaths (all other causes). Excess YLL during the pandemic period were calculated by subtracting observed from expected values. Additional analyses focused on excess deaths for region and deprivation strata, by age-group. Between 7 March 2020 and 25 December 2020, there were an estimated 763,550 (95% CI: 696,826 to 830,273) excess YLL in England and Wales, equivalent to a 15% (95% CI: 14 to 16) increase in YLL compared to the equivalent time period in 2019. There was a strong deprivation gradient in all-cause excess YLL, with rates per 100,000 population ranging from 916 (95% CI: 820 to 1,012) for the least deprived quintile to 1,645 (95% CI: 1,472 to 1,819) for the most deprived. The differences in excess YLL between deprivation quintiles were greatest in younger age groups; for all-cause deaths, a mean of 9.1 years per death (95% CI: 8.2 to 10.0) were lost in the least deprived quintile, compared to 10.8 (95% CI: 10.0 to 11.6) in the most deprived; for COVID-19 and other respiratory deaths, a mean of 8.9 years per death (95% CI: 8.7 to 9.1) were lost in the least deprived quintile, compared to 11.2 (95% CI: 11.0 to 11.5) in the most deprived. For all-cause mortality, estimated deaths in the most deprived compared to the most affluent areas were much higher in younger age groups, but similar for those aged 85 or over. There was marked variability in both all-cause and direct excess YLL by region, with the highest rates in the North West. Limitations include the quasi-experimental nature of the research design and the requirement for accurate and timely recording. CONCLUSIONS: In this study, we observed strong socioeconomic and geographical health inequalities in YLL, during the first calendar year of the COVID-19 pandemic. These were in line with long-standing existing inequalities in England and Wales, with the most deprived areas reporting the largest numbers in potential YLL.

Physical Activity in Renal Disease and the Effect on Hypertension: A Randomized Controlled Trial.

INTRODUCTION: Exercise is an effective strategy for blood pressure (BP) reduction in the general population, but its efficacy for the management of hypertension in chronic kidney disease (CKD) is not known. We evaluated the difference in 24-h ambulatory systolic BP (SBP) with exercise training in people with moderate to severe CKD. METHODS: Participants with an estimated glomerular filtration rate (eGFR) of 15-44 mL/min per 1.73 m2 and SBP >120 mm Hg were randomized to receive thrice-weekly moderate-intensity aerobic-based exercise over 24 weeks, or usual care. Phase 1 included supervised in-center and home-based sessions for 8 weeks. Phase 2 was 16 weeks of home-based sessions. BP, arterial stiffness, cardiorespiratory fitness, and markers of cardiovascular (CV) risk were analyzed using mixed linear regression. RESULTS: We randomized 44 people; 36% were female, the median age was 69 years, 55% had diabetes, and the median eGFR was 28 mL/min per 1.73 m2. Compared with usual care, there was no significant change in 24-ambulatory SBP at 8 weeks (2.96 mm Hg; 95% confidence interval (CI): -2.56, 8.49) or 24 weeks. Peak oxygen uptake improved by 1.9 mL/kg/min in the exercise group (95% CI: 0.03, 3.79) at 8 weeks with a trend toward higher body mass index 1.84 kg/m2 (95% CI: -0.10, 3.78) and fat free mass, but this was not sustained at 24 weeks. Markers of CV risk were unchanged. CONCLUSIONS: Despite an improvement in peak aerobic capacity and body composition, we did not detect a change in 24-h ambulatory SBP in people with moderate-to-severe CKD.

A study protocol for improving the delivery of acute kidney replacement therapy (KRT) to critically ill patients in Alberta - DIALYZING WISELY.

BACKGROUND: Acute kidney replacement therapy (KRT) is delivered to acutely ill patients to support organ function and life in the Intensive Care Unit (ICU). Implementing standardized acute KRT pathways can ensure its safe and effective management. At present, there is no standardized approach to the management of acute KRT in Alberta ICUs. METHODS: Dialyzing Wisely is a registry embedded, stepped-wedge, interrupted time-series evaluation of the implementation of a standardized, stakeholder-informed, and evidence-based acute KRT pathway into Alberta ICUs. The acute KRT pathway will consist of two distinct phases. First, we will implement routine monitoring of evidence-informed key performance indicators (KPIs) of acute KRT. Second, we will provide prescriber and program reports for acute KRT initiation patterns. After the implementation of both phases of the pathway, we will evaluate acute KRT performance quarterly and implement a customized suite of interventions aimed at improving performance. We will compare this with baseline and evaluate iterative post implementation effects of the care pathway. DISCUSSION: Dialyzing Wisely will implement, monitor, and report a suite of KPIs of acute KRT, coupled with a care pathway that will transform the quality of acute KRT across ICUs in Alberta. This program will provide a framework for scaling evidence-informed approaches to monitoring and management of acute KRT in other jurisdictions. We anticipate improvements in acute KRT performance, decreased healthcare system costs and improved patient quality of life by decreasing patient dependence on maintenance dialysis. TRIAL REGISTRATION: Clinicaltrials.gov , NCT05186636. Registered 11, January, 2022.

Effect of Clinical Decision Support With Audit and Feedback on Prevention of Acute Kidney Injury in Patients Undergoing Coronary Angiography: A Randomized Clinical Trial.

Importance: Contrast-associated acute kidney injury (AKI) is a common complication of coronary angiography and percutaneous coronary intervention (PCI) that has been associated with high costs and adverse long-term outcomes. Objective: To determine whether a multifaceted intervention is effective for the prevention of AKI after coronary angiography or PCI. Design, Setting, and Participants: A stepped-wedge, cluster randomized clinical trial was conducted in Alberta, Canada, that included all invasive cardiologists at 3 cardiac catheterization laboratories who were randomized to various start dates for the intervention between January 2018 and September 2019. Eligible patients were aged 18 years or older who underwent nonemergency coronary angiography, PCI, or both; who were not undergoing dialysis; and who had a predicted AKI risk of greater than 5%. Thirty-four physicians performed 7820 procedures among 7106 patients who met the inclusion criteria. Participant follow-up ended in November 2020. Interventions: During the intervention period, cardiologists received educational outreach, computerized clinical decision support on contrast volume and hemodynamic-guided intravenous fluid targets, and audit and feedback. During the control (preintervention) period, cardiologists provided usual care and did not receive the intervention. Main Outcomes and Measures: The primary outcome was AKI. There were 12 secondary outcomes, including contrast volume, intravenous fluid administration, and major adverse cardiovascular and kidney events. The analyses were conducted using time-adjusted models. Results: Of the 34 participating cardiologists who were divided into 8 clusters by practice group and center, the intervention group included 31 who performed 4327 procedures among 4032 patients (mean age, 70.3 [SD, 10.7] years; 1384 were women [32.0%]) and the control group included 34 who performed 3493 procedures among 3251 patients (mean age, 70.2 [SD, 10.8] years; 1151 were women [33.0%]). The incidence of AKI was 7.2% (310 events after 4327 procedures) during the intervention period and 8.6% (299 events after 3493 procedures) during the control period (between-group difference, -2.3% [95% CI, -0.6% to -4.1%]; odds ratio [OR], 0.72 [95% CI, 0.56 to 0.93]; P = .01). Of 12 prespecified secondary outcomes, 8 showed no significant difference. The proportion of procedures in which excessive contrast volumes were used was reduced to 38.1% during the intervention period from 51.7% during the control period (between-group difference, -12.0% [95% CI, -14.4% to -9.4%]; OR, 0.77 [95% CI, 0.65 to 0.90]; P = .002). The proportion of procedures in eligible patients in whom insufficient intravenous fluid was given was reduced to 60.8% during the intervention period from 75.1% during the control period (between-group difference, -15.8% [95% CI, -19.7% to -12.0%]; OR, 0.68 [95% CI, 0.53 to 0.87]; P = .002). There were no significant between-group differences in major adverse cardiovascular events or major adverse kidney events. Conclusions and Relevance: Among cardiologists randomized to an intervention including clinical decision support with audit and feedback, patients undergoing coronary procedures during the intervention period were less likely to develop AKI compared with those treated during the control period, with a time-adjusted absolute risk reduction of 2.3%. Whether this intervention would show efficacy outside this study setting requires further investigation. Trial Registration: ClinicalTrials.gov Identifier: NCT03453996.

Coupling VIGS with Short- and Long-Term Stress Exposure to Understand the Fiskeby III Iron Deficiency Stress Response.

Yield loss due to abiotic stress is an increasing problem in agriculture. Soybean is a major crop for the upper Midwestern United States and calcareous soils exacerbate iron deficiency for growers, resulting in substantial yield losses. Fiskeby III is a soybean variety uniquely resistant to a variety of abiotic stresses, including iron deficiency. Previous studies identified a MATE transporter (Glyma.05G001700) associated with iron stress tolerance in Fiskeby III. To understand the function of this gene in the Fiskeby III response to iron deficiency, we coupled its silencing using virus-induced gene silencing with RNAseq analyses at two timepoints. Analyses of these data confirm a role for the MATE transporter in Fiskeby III iron stress responses. Further, they reveal that Fiskeby III induces transcriptional reprogramming within 24 h of iron deficiency stress, confirming that like other soybean varieties, Fiskeby III is able to quickly respond to stress. However, Fiskeby III utilizes novel genes and pathways in its iron deficiency response. Identifying and characterizing these genes and pathways in Fiskeby III provides novel targets for improving abiotic stress tolerance in elite soybean lines.

Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids.

BACKGROUND: Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation. RESULTS: A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene. CONCLUSIONS: The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.

Dynamic movements facilitate extreme gap crossing in flying snakes.

In arboreal habitats, direct routes between two locations can be impeded by gaps in the vegetation. Arboreal animals typically use dynamic movements, such as jumping, to navigate these gaps if the distance between supports exceeds their reaching ability. In contrast, most snakes only use the cantilever crawl to cross gaps. This behavior imposes large torques on the animal, inhibiting their gap-crossing capabilities. Flying snakes (Chrysopelea), however, are known to use dynamic behaviors in a different arboreal context: they use a high-acceleration jump to initiate glides. We hypothesized that flying snakes also use jumping take-off behaviors to cross gaps, allowing them to cross larger distances. To test this hypothesis, we used a six-camera motion-capture system to investigate the effect of gap size on crossing behavior in Chrysopelea paradisi, and analyzed the associated kinematics and torque requirements. We found that C. paradisi typically uses cantilevering for small gaps (<47.5% snout-vent length, SVL). Above this distance, C. paradisi were more likely to use dynamic movements than cantilevers, either arching upward or employing a below-branch loop of the body. These dynamic movements extended the range of horizontal crossing to ∼120% SVL. The behaviors used for the largest gaps were kinematically similar to the J-loop jumps used in gliding, and involved smaller torques than the cantilevers. These data suggest that the ability to jump allows flying snakes to access greater resources in the arboreal environment, and supports the broader hypothesis that arboreal animals jump across gaps only when reaching is not mechanically possible.

Trends in cardiovascular mortality of cancer patients in the US over two decades 1999-2019.

BACKGROUND: Cancer is the second most common cause of death globally after cardiovascular disease, and cancer patients are at an increased risk of CV death. This recognition has led to publication of cardio-oncological guidelines and to the widespread adoption of dedicated cardio-oncology services in many institutes. However, it is unclear whether there has been a change in the incidence of CV death in cancer patients. METHODS AND RESULTS: Using Centers for Disease Control and Prevention Wide-Ranging, Online Data for Epidemiologic Research (CDC WONDER) Multiple Cause of Death dataset, we determined national trends in age-standardised mortality rates attributed to cardiovascular diseases in patients with and without cancer, from 1999 to 2019, stratified by cancer type, age, gender, race, and place of residence (state and urbanisation status). Among more than 17.8 million cardiovascular deaths in the United States, 13.6% were patients with a concomitant cancer diagnosis. During the study period, among patients with cancer, the age-adjusted mortality rate dropped by 52% (vs 38% in patients with no cancer). In cancer patients, age-adjusted mortality rate dropped more significantly among patients with gastrointestinal, breast, and prostate malignancy than among patients with haematological malignancy (59%-63% vs. 41%). Similar reduction was observed in both genders (53%-54%), but more prominent reduction was observed in older patients and in those living in metro areas. CONCLUSIONS: Our findings emphasise the role of multidisciplinary management of cancer patients. Widespread adoption of cardio oncology services have the potential to impact the inherent risk of increased CV mortality in both cancer patients and survivors.

Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean.

Throughout the growing season, crops experience a multitude of short periods of various abiotic stresses. These stress events have long-term impacts on plant performance and yield. It is imperative to improve our understanding of the genes and biological processes underlying plant stress tolerance to mitigate end of season yield loss. The majority of studies examining transcriptional changes induced by stress focus on single stress events. Few studies have been performed in model or crop species to examine transcriptional responses of plants exposed to repeated or sequential stress exposure, which better reflect field conditions. In this study, we examine the transcriptional profile of soybean plants exposed to iron deficiency stress followed by phosphate deficiency stress (-Fe-Pi). Comparing this response to previous studies, we identified a core suite of genes conserved across all repeated stress exposures (-Fe-Pi, -Fe-Fe, -Pi-Pi). Additionally, we determined transcriptional response to sequential stress exposure (-Fe-Pi) involves genes usually associated with reproduction, not stress responses. These findings highlight the plasticity of the plant transcriptome and the complexity of unraveling stress response pathways.

Comparing Early Transcriptomic Responses of 18 Soybean (Glycine max) Genotypes to Iron Stress.

Iron deficiency chlorosis (IDC) is an abiotic stress that negatively affects soybean (Glycine max [L.] Merr.) production. Much of our knowledge of IDC stress responses is derived from model plant species. Gene expression, quantitative trait loci (QTL) mapping, and genome-wide association studies (GWAS) performed in soybean suggest that stress response differences exist between model and crop species. Our current understanding of the molecular response to IDC in soybeans is largely derived from gene expression studies using near-isogenic lines differing in iron efficiency. To improve iron efficiency in soybeans and other crops, we need to expand gene expression studies to include the diversity present in germplasm collections. Therefore, we collected 216 purified RNA samples (18 genotypes, two tissue types [leaves and roots], two iron treatments [sufficient and deficient], three replicates) and used RNA sequencing to examine the expression differences of 18 diverse soybean genotypes in response to iron deficiency. We found a rapid response to iron deficiency across genotypes, most responding within 60 min of stress. There was little evidence of an overlap of specific differentially expressed genes, and comparisons of gene ontology terms and transcription factor families suggest the utilization of different pathways in the stress response. These initial findings suggest an untapped genetic potential within the soybean germplasm collection that could be used for the continued improvement of iron efficiency in soybean.

Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean.

The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.

Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean.

Preserving crop yield is critical for US soybean production and the global economy. Crop species have been selected for increased yield for thousands of years with individual lines selected for improved performance in unique environments, constraints not experienced by model species such as Arabidopsis. This selection likely resulted in novel stress adaptations, unique to crop species. Given that iron deficiency is a perennial problem in the soybean growing regions of the USA and phosphate deficiency looms as a limitation to global agricultural production, nutrient stress studies in crop species are critically important. In this study, we directly compared whole-genome expression responses of leaves and roots to iron (Fe) and phosphate (Pi) deficiency, representing a micronutrient and macronutrient, respectively. Conducting experiments side by side, we observed soybean responds to both nutrient deficiencies within 24 h. While soybean responds largely to -Fe deficiency, it responds strongly to Pi resupply. Though the timing of the responses was different, both nutrient stress signals used the same molecular pathways. Our study is the first to demonstrate the speed and diversity of the soybean stress response to multiple nutrient deficiencies. We also designed the study to examine gene expression changes in response to multiple stress events. We identified 865 and 3375 genes that either altered their direction of expression after a second stress exposure or were only differentially expressed after a second stress event. Understanding the molecular underpinnings of these responses in crop species could have major implications for improving stress tolerance and preserving yield.

Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches.

BACKGROUND: Iron (Fe) is an essential micronutrient for plant growth and development. Iron deficiency chlorosis (IDC), caused by calcareous soils or high soil pH, can limit iron availability, negatively affecting soybean (Glycine max) yield. This study leverages genome-wide association study (GWAS) and a genome-wide epistatic study (GWES) with previous gene expression studies to identify regions of the soybean genome important in iron deficiency tolerance. RESULTS: A GWAS and a GWES were performed using 460 diverse soybean PI lines from 27 countries, in field and hydroponic iron stress conditions, using more than 36,000 single nucleotide polymorphism (SNP) markers. Combining this approach with available RNA-sequencing data identified significant markers, genomic regions, and novel genes associated with or responding to iron deficiency. Sixty-nine genomic regions associated with IDC tolerance were identified across 19 chromosomes via the GWAS, including the major-effect quantitative trait locus (QTL) on chromosome Gm03. Cluster analysis of significant SNPs in this region deconstructed this historically prominent QTL into four distinct linkage blocks, enabling the identification of multiple candidate genes for iron chlorosis tolerance. The complementary GWES identified SNPs in this region interacting with nine other genomic regions, providing the first evidence of epistatic interactions impacting iron deficiency tolerance. CONCLUSIONS: This study demonstrates that integrating cutting edge genome wide association (GWA), genome wide epistasis (GWE), and gene expression studies is a powerful strategy to identify novel iron tolerance QTL and candidate loci from diverse germplasm. Crops, unlike model species, have undergone selection for thousands of years, constraining and/or enhancing stress responses. Leveraging genomics-enabled approaches to study these adaptations is essential for future crop improvement.

Association of NT-proBNP and BNP With Future Clinical Outcomes in Patients With ESKD: A Systematic Review and Meta-analysis.

RATIONALE & OBJECTIVE: Use of brain natriuretic peptide (BNP) and N-terminal pro-BNP (NT-proBNP) for cardiovascular (CV) risk assessment in patients with end-stage kidney disease (ESKD) remains unclear. We examined the associations between different threshold elevations of these peptide levels and clinical outcomes in patients with ESKD. STUDY DESIGN: Systematic review and meta-analysis. SETTING & STUDY POPULATIONS: We searched MEDLINE and EMBASE (through September 2019) for observational studies of adults with ESKD (estimated glomerular filtration rate≤15mL/min/1.73m2 or receiving maintenance dialysis). SELECTION CRITERIA FOR STUDIES: Studies that reported NT-proBNP or BNP levels and future CV events, CV mortality, or all-cause mortality. DATA EXTRACTION: Cohort characteristics and measures of risk associated with study-specified peptide thresholds. ANALYTICAL APPROACH: Hazard ratios (HRs) for clinical outcomes associated with different NT-proBNP and BNP ranges were categorized into common thresholds and pooled using random-effects meta-analysis. RESULTS: We identified 61 studies for inclusion in our review (19,688 people). 49 provided sufficient detail for inclusion in meta-analysis. Pooled unadjusted HRs for CV mortality were progressively greater for greater thresholds of NT-proBNP, from 1.45 (95% CI, 0.91-2.32) for levels>2,000pg/mL to 5.95 (95% CI, 4.23-8.37) for levels>15,000pg/mL. Risk for all-cause mortality was significantly higher at all NT-proBNP thresholds ranging from> 1,000 to> 20,000pg/mL (HR range, 1.53-4.00). BNP levels>550pg/mL were associated with increased risk for CV mortality (HR, 2.54; 95% CI, 1.49-4.33), while the risks for all-cause mortality were 2.04 (95% CI, 0.82-5.12) at BNP levels>100pg/mL and 2.97 (95% CI, 2.21-3.98) at BNP levels>550pg/mL. Adjusted analyses demonstrated similarly greater risks for CV and all-cause mortality with greater NT-proBNP concentrations. LIMITATIONS: Incomplete outcome reporting and risk for outcome reporting bias. Estimation of risk for CV events for specific thresholds of both peptides were limited by poor precision. CONCLUSIONS: ESKD-specific NT-proBNP and BNP level thresholds of elevation are associated with increased risk for CV and all-cause mortality. This information may help guide interpretation of NT-proBNP and BNP levels in patients with ESKD.