A maize semidwarf mutant reveals a GRAS transcription factor involved in brassinosteroid signaling.

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR.

MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles.

Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.

Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize and Setaria viridis.

The Heat Shock Factor (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess and compare the composition, heat responsiveness, and chromatin profiles of the HSF families in maize and Setaria viridis (Setaria), two model C4 panicoid grasses. Both species encode a similar number of HSFs, and examples of both conserved and variable expression responses to a heat stress event were observed between the two species. Chromatin accessibility and genome-wide DNA-binding profiles were generated to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both chromatin accessibility and promoter occupancy within similarly regulated sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. Additionally, we observed the widespread presence of TF binding at HSF promoters in control conditions, even at HSFs that are only expressed in response to heat stress. TF-binding peaks were typically near putative HSF-binding sites in HSFs upregulated in response to heat stress, but not in stable or not expressed HSFs. These observations collectively support a complex scenario of expansion and subfunctionalization within this transcription factor family and suggest that within-family HSF transcriptional regulation is a conserved, defining feature of the family.

Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize.

BACKGROUND: Genetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches. RESULTS: Here, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits. CONCLUSION: Our study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.

Mapping responsive genomic elements to heat stress in a maize diversity panel.

BACKGROUND: Many plant species exhibit genetic variation for coping with environmental stress. However, there are still limited approaches to effectively uncover the genomic region that regulates distinct responsive patterns of the gene across multiple varieties within the same species under abiotic stress. RESULTS: By analyzing the transcriptomes of more than 100 maize inbreds, we reveal many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTLs in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress-responsive expression likely result from distinct promoter activities, and the differential heat responses of the alleles are confirmed for selected genes using transient expression assays. Global footprinting of transcription factor binding is performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. CONCLUSIONS: Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

Structural variants in the barley gene pool: precision and sensitivity to detect them using short-read sequencing and their association with gene expression and phenotypic variation.

KEY MESSAGE: Structural variants (SV) of 23 barley inbreds, detected by the best combination of SV callers based on short-read sequencing, were associated with genome-wide and gene-specific gene expression and, thus, were evaluated to predict agronomic traits. In human genetics, several studies have shown that phenotypic variation is more likely to be caused by structural variants (SV) than by single nucleotide variants. However, accurate while cost-efficient discovery of SV in complex genomes remains challenging. The objectives of our study were to (i) facilitate SV discovery studies by benchmarking SV callers and their combinations with respect to their sensitivity and precision to detect SV in the barley genome, (ii) characterize the occurrence and distribution of SV clusters in the genomes of 23 barley inbreds that are the parents of a unique resource for mapping quantitative traits, the double round robin population, (iii) quantify the association of SV clusters with transcript abundance, and (iv) evaluate the use of SV clusters for the prediction of phenotypic traits. In our computer simulations based on a sequencing coverage of 25x, a sensitivity > 70% and precision > 95% was observed for all combinations of SV types and SV length categories if the best combination of SV callers was used. We observed a significant (P < 0.05) association of gene-associated SV clusters with global gene-specific gene expression. Furthermore, about 9% of all SV clusters that were within 5 kb of a gene were significantly (P < 0.05) associated with the gene expression of the corresponding gene. The prediction ability of SV clusters was higher compared to that of single-nucleotide polymorphisms from an array across the seven studied phenotypic traits. These findings suggest the usefulness of exploiting SV information when fine mapping and cloning the causal genes underlying quantitative traits as well as the high potential of using SV clusters for the prediction of phenotypes in diverse germplasm sets.

Interdependence of a mechanosensitive anion channel and glutamate receptors in distal wound signaling.

Glutamate has dual roles in metabolism and signaling; thus, signaling functions must be isolatable and distinct from metabolic fluctuations, as seen in low-glutamate domains at synapses. In plants, wounding triggers electrical and calcium (Ca2+) signaling, which involve homologs of mammalian glutamate receptors. The hydraulic dispersal and squeeze-cell hypotheses implicate pressure as a key component of systemic signaling. Here, we identify the stretch-activated anion channel MSL10 as necessary for proper wound-induced electrical and Ca2+ signaling. Wound gene induction, genetics, and Ca2+ imaging indicate that MSL10 acts in the same pathway as the glutamate receptor­like proteins (GLRs). Analogous to mammalian NMDA glutamate receptors, GLRs may serve as coincidence detectors gated by the combined requirement for ligand binding and membrane depolarization, here mediated by stretch activation of MSL10. This study provides a molecular genetic basis for a role of mechanical signal perception and the transmission of long-distance electrical and Ca2+ signals in plants.

The native cistrome and sequence motif families of the maize ear.

Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas.

Admission Blood Glucose in the Emergency Department is Associated with Increased In-Hospital Mortality in Nontraumatic Critically Ill Patients.

BACKGROUND: Abnormal admission blood glucose was reported as a useful predictor of outcome in critically ill patients. OBJECTIVES: To identify patients at higher risk, this study aimed to evaluate the relationship between admission blood glucose levels and patient mortality during the management of nontraumatic critically ill patients in the emergency department (ED). METHODS: In this prospective, single-center observational study in a German university ED, all adult patients admitted to the resuscitation room of the ED were included between September 1, 2014 and August 31, 2015. Directly after resuscitation room admission, blood samples for admission blood glucose were taken, and adult patients were divided into groups according to predefined cut-offs between the admission blood glucose. Study endpoint was in-hospital mortality. RESULTS: During the study period, 532 patients were admitted to the resuscitation room. The data of 523 patients (98.3%) were available for analysis. The overall in-hospital mortality was 34.2%. In comparison with an in-hospital mortality of 25.2% at an admission blood glucose of 101-136 mg/dL (n = 107), admission blood glucose of ≤ 100 mg/dL (n = 25, odds ratio [OR] 6.30, 95% confidence interval [CI] 2.44-16.23, p < 0.001), 272-361 mg/dL (n = 63, OR 2.53, 95% CI 1.31-4.90, p = 0.007), and ≥ 362 mg/dL (n = 44, OR 2.96, 95% CI 1.42-6.18, p = 0.004) were associated with a higher mortality. CONCLUSIONS: Abnormal admission blood glucose is associated with a high in-hospital mortality. Admission blood glucose is an inexpensive and rapidly available laboratory parameter that may predict mortality and help to identify critically ill patients at risk in a general nontraumatic critically ill ED patient cohort. The breakpoint for in-hospital mortality may be an admission blood glucose ≤ 100 and ≥ 272 mg/dL.

Distinct identities of leaf phloem cells revealed by single cell transcriptomics.

The leaf vasculature plays a key role in solute translocation. Veins consist of at least seven distinct cell types, with specific roles in transport, metabolism, and signaling. Little is known about leaf vascular cells, in particular the phloem parenchyma (PP). PP effluxes sucrose into the apoplasm as a basis for phloem loading, yet PP has been characterized only microscopically. Here, we enriched vascular cells from Arabidopsis leaves to generate a single-cell transcriptome atlas of leaf vasculature. We identified at least 19 cell clusters, encompassing epidermis, guard cells, hydathodes, mesophyll, and all vascular cell types, and used metabolic pathway analysis to define their roles. Clusters comprising PP cells were enriched for transporters, including SWEET11 and SWEET12 sucrose and UmamiT amino acid efflux carriers. We provide evidence that PP development occurs independently from ALTERED PHLOEM DEVELOPMENT, a transcription factor required for phloem differentiation. PP cells have a unique pattern of amino acid metabolism activity distinct from companion cells (CCs), explaining differential distribution/metabolism of amino acids in veins. The kinship relation of the vascular clusters is strikingly similar to the vein morphology, except for a clear separation of CC from the other vascular cells including PP. In summary, our single-cell RNA-sequencing analysis provides a wide range of information into the leaf vasculature and the role and relationship of the leaf cell types.

Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves.

Leaves are asymmetric, with different functions for adaxial and abaxial tissue. The bundle sheath (BS) of C3 barley (Hordeum vulgare) is dorsoventrally differentiated into three types of cells: adaxial structural, lateral S-type, and abaxial L-type BS cells. Based on plasmodesmatal connections between S-type cells and mestome sheath (parenchymatous cell layer below bundle sheath), S-type cells likely transfer assimilates toward the phloem. Here, we used single-cell RNA sequencing to investigate BS differentiation in C4 maize (Zea mays L.) plants. Abaxial BS (abBS) cells of rank-2 intermediate veins specifically expressed three SWEET sucrose uniporters (SWEET13a, b, and c) and UmamiT amino acid efflux transporters. SWEET13a, b, c mRNAs were also detected in the phloem parenchyma (PP). We show that maize has acquired a mechanism for phloem loading in which abBS cells provide the main route for apoplasmic sucrose transfer toward the phloem. This putative route predominates in veins responsible for phloem loading (rank-2 intermediate), whereas rank-1 intermediate and major veins export sucrose from the PP adjacent to the sieve element companion cell complex, as in Arabidopsis thaliana. We surmise that abBS identity is subject to dorsoventral patterning and has components of PP identity. These observations provide insights into the unique transport-specific properties of abBS cells and support a modification to the canonical phloem loading pathway in maize.

Arabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions.

O-GlcNAc modification plays important roles in metabolic regulation of cellular status. Two homologs of O-GlcNAc transferase, SECRET AGENT (SEC) and SPINDLY (SPY), which have O-GlcNAc and O-fucosyl transferase activities, respectively, are essential in Arabidopsis but have largely unknown cellular targets. Here we show that AtACINUS is O-GlcNAcylated and O-fucosylated and mediates regulation of transcription, alternative splicing (AS), and developmental transitions. Knocking-out both AtACINUS and its distant paralog AtPININ causes severe growth defects including dwarfism, delayed seed germination and flowering, and abscisic acid (ABA) hypersensitivity. Transcriptomic and protein-DNA/RNA interaction analyses demonstrate that AtACINUS represses transcription of the flowering repressor FLC and mediates AS of ABH1 and HAB1, two negative regulators of ABA signaling. Proteomic analyses show AtACINUS's O-GlcNAcylation, O-fucosylation, and association with splicing factors, chromatin remodelers, and transcriptional regulators. Some AtACINUS/AtPININ-dependent AS events are altered in the sec and spy mutants, demonstrating a function of O-glycosylation in regulating alternative RNA splicing.

Elevated admission lactate levels in the emergency department are associated with increased 30-day mortality in non-trauma critically ill patients.

BACKGROUND: Elevated blood lactate levels were reported as useful predictors of clinical outcome and mortality in critically ill patients. To identify higher-risk patients, this investigation evaluated the relationship between patient mortality and admission lactate levels during the management of non-trauma critically ill patients in the emergency department (ED). METHODS: In this prospective, single centre observational study in a German university ED, all adult patients who were admitted to the ED resuscitation room were evaluated between September 1, 2014 and August 31, 2015. Blood samples for blood gas analysis, including lactate levels, were obtained immediately at admission. Study endpoint was 30-day mortality. RESULTS: During the study period, 532 patients were admitted to the resuscitation room of the ED. The data of 523 patients (98.3%) were available. The overall 30-day mortality was 34.2%. Patients presenting to the resuscitation room with admission lactate levels < 2.0 mmol/l had a 30-day mortality of 22.7%, while admission lactate levels above 8.0 mmol/l were associated with higher mortality (8.0-9.9 mmol/l: OR: 2.83, 95%CI: 1.13-7.11, p = 0.03, and ≥ 10 mmol/l: OR: 7.56, 95%CI: 4.18-13.77, p < 0.001). CONCLUSION: High lactate levels at admission are associated with an increased 24-h and 30-day mortality. These measurements may be used not only to predict mortality, but to help identify patients at risk for becoming critically ill. The breakpoint for mortality may be an ALL ≥8.0 mmol/l.

Association between rapid weather changes and incidence of chiefly cardiovascular complaints in the emergency department.

INTRODUCTION: Studies suggest that there is an association between weather and cardiovascular disease (CVD) related visits in emergency departments (ED). METHODS: We used a case-crossover study design to investigate the association between ED visits for CVD and changes in temperature, atmospheric pressure, and relative humidity. Patient and weather data from the years 2014 and 2015 were used to investigate relevance of changes associated with weather in the frequency of CVD-related ED visits. They were correlated to overall variability of the visits adjusted to day of the week. RESULTS: In the study period 20,558 ED visits were related to CVD (mean per day: 28.3). Significant associations were identified for all three variables (temperature, atmospheric pressure, and relative humidity). Significant odds ratio (OR) was found for a large decrease in temperature 1.29 (95%-CI, 1.1-1.52). However, the related effects, although significant, were small compared to overall variability of visits. CONCLUSION: We found an association between rapid weather changes on the day before ED admission and ED visits due to CVD. In conclusion, a drop in temperature and an increase or decrease in atmospheric pressure and relative humidity are associated with a slight increase in CVD admissions. However, the observed significant effects seem to be too small to draw any conclusions in terms of ED capacity due to weather changes.

A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays.

A central problem in speciation is the origin and mechanisms of reproductive barriers that block gene flow between sympatric populations. Wind-pollinated plant species that flower in synchrony with one another rely on post-pollination interactions to maintain reproductive isolation. In some locations in Mexico, sympatric populations of domesticated maize and annual teosinte grow in intimate associate and flower synchronously, but rarely produce hybrids. This trait is typically conferred by a single haplotype, Teosinte crossing barrier1-s. Here, we show that the Teosinte crossing barrier1-s haplotype contains a pistil-expressed, potential speciation gene, encoding a pectin methylesterase homolog. The modification of the pollen tube cell wall by the pistil, then, is likely a key mechanism for pollen rejection in Zea and may represent a general mechanism for reproductive isolation in grasses.

Airway Management in the Emergency Department (The OcEAN-Study) - a prospective single centre observational cohort study.

BACKGROUND: Emergency airway management (AM) is a major key for successful resuscitation of critically ill non-traumatic (CINT) patients. Details of the AM of these patients in German emergency departments (ED) are unknown. This observational study describes epidemiology, airway techniques, success rates and complications of AM in CINT ED patients in the resuscitation room (RR). METHODS: Data was collected prospectively on adult CINT patients admitted to the RR of a single German university ED September 2014 to August 2015. Patient characteristics, out-of-hospital and in-hospital RR AM, complications and success rates were recorded using a self-developed airway registry form. RESULTS: During the study period 34,303 patients were admitted to the ED, out of those 21,074 patients for non-trauma emergencies. Suffering from severe acute life-threatening problems, 532 CINT patients were admitted to the RR. 150 (28.2%) CINT patients had received out-of-hospital AM. In 16 of these cases (10.7%) the inserted airway needed to be changed after RR admission (unrecognized oesophageal intubation: n = 2, laryngeal tube exchange: n = 14). 136 (25.6%) CINT patients without out-of-hospital AM received RR AM immediately after admission. The first-pass and overall success rate in the RR were 71 and 100%, respectively, and multiple intubation attempts were necessary in 29%. A lower Cormack/Lehane (C/L) grade was associated with less intubation attempts (C/L1/2 vs. 3/4: 1.2 ± 0.5 vs. 1.8 ± 1.2, p = 0.0002). Complication rate was 43%. CONCLUSIONS: OcEAN demonstrates the challenges of AM in CINT patients in a German ED RR. We propose a nation-wide ED airway registry to better track outcomes in the future.

Early Lactate Dynamics in Critically Ill Non-Traumatic Patients in a Resuscitation Room of a German Emergency Department (OBSERvE-Lactate-Study).

BACKGROUND: Management of critically ill non-trauma patients in the resuscitation room of an emergency department (ED) is very challenging, and it is difficult to identify patients with a higher risk of death. Previous studies have shown that lactate indices can predict survival for selected diseases and syndromes. OBJECTIVE: As reported for other patient populations, we set out to determine whether admission lactate or lactate dynamics (LD) within 24 h can predict 30-day mortality in unselected critically ill non-traumatic patients. METHODS: In this retrospective study over a 1-year period, admission lactate, time weighted average lactate (LacTW) and LD of all critically ill adult patients admitted from ED to intensive care unit were analyzed. A linear regression model was implemented to estimate lactate data 1 h after admission. RESULTS: The admission lactate, LacTW, and LD within 24 h were analyzed from 392 critically ill patients. The overall 30-day mortality rate was around 29%. Admission lactate (4.1 ± 4.0 mmol/L vs. 6.6 ± 6.1 mmol/L; p < 0.01) and LacTW (1.8 ± 1.7 mmol/L vs. 4.1 ± 4.8 mmol/L; p < 0.01) were different between survivors and non-survivors. LD between survivors and non-survivors did not differ at 1 h, 6 h, 12 h, or 24 h. After excluding patients with out-of-hospital or in-hospital cardiac arrest during resuscitation room management, admission lactate and LD between survivors and non-survivors did not differ at 1 h, 12 h, and 24 h. LD at 6 h (44% ± 42% vs. 33% ± 58%; p = 0.042) and LacTW (1.7 ± 1.6 mmol/L vs. 2.6 ± 3.0 mmol/L; p < 0.01) did differ. CONCLUSIONS: In critically ill ED patients initially requiring treatment in a resuscitation room setting, LD at 6 h and LacTW may predict their survival beyond 30 days. These findings need to be confirmed in a prospective study design.

Impaired phloem loading in zmsweet13a,b,c sucrose transporter triple knock-out mutants in Zea mays.

Crop yield depends on efficient allocation of sucrose from leaves to seeds. In Arabidopsis, phloem loading is mediated by a combination of SWEET sucrose effluxers and subsequent uptake by SUT1/SUC2 sucrose/H+ symporters. ZmSUT1 is essential for carbon allocation in maize, but the relative contribution to apoplasmic phloem loading and retrieval of sucrose leaking from the translocation path is not known. Here we analysed the contribution of SWEETs to phloem loading in maize. We identified three leaf-expressed SWEET sucrose transporters as key components of apoplasmic phloem loading in Zea mays L. ZmSWEET13 paralogues (a, b, c) are among the most highly expressed genes in the leaf vasculature. Genome-edited triple knock-out mutants were severely stunted. Photosynthesis of mutants was impaired and leaves accumulated high levels of soluble sugars and starch. RNA-seq revealed profound transcriptional deregulation of genes associated with photosynthesis and carbohydrate metabolism. Genome-wide association study (GWAS) analyses may indicate that variability in ZmSWEET13s correlates with agronomical traits, especifically flowering time and leaf angle. This work provides support for cooperation of three ZmSWEET13s with ZmSUT1 in phloem loading in Z. mays.

Genomic diversity of a nectar yeast clusters into metabolically, but not geographically, distinct lineages.

Both dispersal limitation and environmental sorting can affect genetic variation in populations, but their contribution remains unclear, particularly in microbes. We sought to determine the contribution of geographic distance (as a proxy for dispersal limitation) and phenotypic traits (as a proxy for environmental sorting), including morphology, metabolic ability and interspecific competitiveness, to the genotypic diversity in a nectar yeast species, Metschnikowia reukaufii. To measure genotypic diversity, we sequenced the genomes of 102 strains of M. reukaufii isolated from the floral nectar of hummingbird-pollinated shrub, Mimulus aurantiacus, along a 200-km coastline in California. Intraspecific genetic variation showed no detectable relationship with geographic distance, but could be grouped into three distinct lineages that correlated with metabolic ability and interspecific competitiveness. Despite ample evidence for strong competitive interactions within and among nectar yeasts, a full spectrum of the genotypic and phenotypic diversity observed across the 200-km coastline was represented even at a scale as small as 200 m. Further, more competitive strains were not necessarily more abundant. These results suggest that dispersal limitation and environmental sorting might not fully explain intraspecific diversity in this microbe and highlight the need to also consider other ecological factors such as trade-offs, source-sink dynamics and niche modification.