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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Colistin resistance plasmids dually enhance bacterial virulence and antibiotic resistance via surface polysaccharide biosynthesis

Plasmids carrying the mobilized colistin-resistance gene mcr-1 are prevalent among multidrug-resistant Gram-negative pathogens, yet their broad impact on bacterial physiology and virulence remains unclear. Here, we demonstrate that acquisition of an mcr-1 plasmid concurrently increases antimicrobial resistance and pathogenicity in Escherichia coli. On the same plasmid, the XRE-family transcriptional regulator EcaR cooperates with MCR-1 to activate the wec operon, driving biosynthesis of two surface polysaccharides: enterobacterial common antigen (ECA) and a high-molecular-weight O-chain. Expression of these surface polysaccharides increases bile resistance and virulence in a murine model and further elevates colistin resistance. MCR-1 enhances transcription of upstream genes in the wec operon, whereas EcaR directly activates an internal promoter (PwecE) to induce downstream gene expression. Thus, both components are required for surface polysaccharide expression, and deletion of either abolishes the phenotype. Genomic analysis of publicly available mcr plasmids reveals widespread co-occurrence of mcr-1 and ecaR on IncI2 and IncX4 plasmids, indicating their functional complementarity. These findings uncover a mechanism by which resistance plasmids remodel the bacterial surface, linking horizontal gene transfer to coordinated regulation of antimicrobial resistance and virulence.

Antimicrobial resistance↗
DOE OSTI2025

Draft genome sequence of Gleimia europaea DSM 26657

Here, we report the draft genome sequence of Gleimia europaea DSM 26657, a pathogenic gram-positive bacillus, isolated from a patient with a subcutaneous fistula in 2007 in Germany. The genome is 2.0 Mb in size with 1,813 predicted genes, having only one putative antibiotic resistance gene.

antibiotic resistance↗
DOE OSTI2023

Targeted metagenomic assessment reflects critical colonization in battlefield injuries

Current diagnostics and clinical management strategies for combat wounds are based on decisions made by expert clinicians. However, even in the hands of experienced surgeons, wounds from combat injuries can exhibit failed healing and complications related to limitations in the rapid and comprehensive generation of diagnostic information. Previous studies have demonstrated the possible use of genomic sequencing approaches to detect microbial signatures involved in combat casualty care. While effective, whole metagenome sequencing is limited by the depth required to confidently detect all relevant signatures. To address this, we developed a targeted capture sequencing panel to detect microbial signatures relevant to wound healing. These targets include known microbial nosocomial pathogens, wound colonizers, and genes involved in virulence and antimicrobial resistance. A bioinformatics pipeline was built to identify genomic regions of interest and over 8,000 oligonucleotide probes were designed for capture. The panel was synthesized and validated using control reference genomes in human background and on wound-effluent samples from a cohort of combat-injured U.S. service members. Our panel was sensitive against wound-colonizing species, Acinetobacter baumannii and Pseudomonas aeruginosa, and was specific in detecting corresponding virulence and antimicrobial-resistance genes as well as other pathogenic species present in microflora mixtures. Random forest feature permutation confirmed the prevalence of Acinetobacter and Pseudomonas in critically colonized wounds and wounds that failed to heal, respectively. Our results demonstrate the capability of targeted sequencing tools and analysis platforms to profile and deliver information on pathogenic factors influencing wound progression, thereby guiding therapeutic intervention.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Inhibition of ethylene involved in resistance to E. turcicum in an exotic-derived double haploid maize population

Northern corn leaf blight (NCLB) is an economically important disease of maize. While the genetic architecture of NCLB has been well characterized, the pathogen is known to overcome currently deployed resistance genes, and the role of hormones in resistance to NCLB is an area of active research. The objectives of the study were (i) to identify significant markers associated with resistance to NCLB, (ii) to identify metabolic pathways associated with NCLB resistance, and (iii) to examine role of ethylene in resistance to NCLB. We screened 252 lines from the exotic-derived double haploid BGEM maize population for resistance to NCLB in both field and greenhouse environments. We used a genome wide association study (GWAS) and stepwise regression to identify four markers associated with resistance, followed by a pathway association study tool (PAST) to identify important metabolic pathways associated with disease severity and incubation period. The ethylene synthesis pathway was significant for disease severity and incubation period. We conducted a greenhouse assay in which we inhibited ethylene to examine the role of ethylene in resistance to NCLB. We observed a significant increase in incubation period and a significant decrease in disease severity between plants treated with the ethylene inhibitor and mock-treated plants. Our study confirms the potential of the BGEM population as a source of novel alleles for resistance. We also confirm the role of ethylene in resistance to NCLB and contribute to the growing body of literature on ethylene and disease resistance in monocots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genomic dissection of anthracnose resistance response in sorghum [Sorghum bicolor (L.) Moench]

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important grain crop behind maize, wheat, rice, and barley. Today, it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals, and as a source of biomass for co-firing. The productivity and profitability of sorghum are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum. The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Over the last three years, our research efforts have been directed to identify new sources of resistance in temperate adapted and tropical germplasm, and to delimited genomic regions associated with the observe anthracnose resistant response. Three biparental mapping populations derived from the resistant lines SC112-14, QL3 and IS18760 were evaluated for anthracnose resistance response in Texas, Georgia, Florida and Puerto Rico. In parallel, three high density recombination maps were constructed and used to identify resistant loci. Anthracnose resistant response in line SC112-14 is controlled by a major locus on chromosome 5. Segregation analysis of 1,500 progenies delimited the resistance locus on chromosome 5 to a 23-kb region harboring three candidate genes, including Sobic.005G17230 identified by GWAS of the sorghum association panel (SAP). The latter gene belongs to a family of genes encoding F-box proteins indicating that this resistance response involved in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. In contrast, anthracnose resistant response in lines QL3 and IS18760 is controlled by multiple small-effect genes. Greenhouse evaluation of a representative subset of the three mapping populations against nine pathotypes found that lines susceptible in the field could be resistant to a single pathotype in the greenhouse. Thus, the activation of a resistance response system by a single pathotype could not provide a broader resistance response against multiple pathotypes. The screening of 1,801 sweet sorghum accessions from the National Plant Germplasm System identified 654 accessions with Brix value larger than 10, which in turn was used to select a subset of 233 accessions for evaluation of anthracnose resistant response. Even though most of the accessions were not completely infected by anthracnose, 28 accessions were completely resistant against pathotypes from Texas, Georgia, Florida and Puerto Rico. Genotyping-by-sequencing analysis of this subset identified 157,843 single nucleotide polymorphisms. Population structure analysis of the subset based on a subset of 2,345 unlinked SNPs found that the genetic diversity could be divided into four populations. The genetic relatedness among accessions within populations suggests most of the resistant germplasm may contain few different resistance sources. These resistance sources present in sweet sorghum germplasm could expedite the development of new resistant sweet sorghum cultivars and hybrids by avoiding time-consuming introgression breeding approaches with non-sweet sorghums serving as donor of the resistance alleles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Sorghum F-Box Protein Induces an Oxidative Burst in the Defense Against Colletotrichum sublineola

The hemibiotrophic fungal pathogen Colletotrichum sublineola is the causal agent of anthracnose in sorghum ( Sorghum bicolor), resulting in leaf blight, stalk rot, and head blight in susceptible genotypes, with yield losses of up to 50%. The development of anthracnose-resistant cultivars can reduce reliance on fungicides and provide a more sustainable and economical means for disease management. A previous genome-wide association study of the sorghum association panel identified the candidate resistance gene Sobic.005G172300 encoding an F-box protein. To better understand the role of this gene in the defense against C. sublineola, gene expression following infection with C. sublineola was monitored by RNA sequencing in seedlings of sorghum accession SC110, which harbored the resistance allele, and three accessions that harbored a susceptible allele. Only in SC110 did the expression of Sobic.005G172300 increase during the biotrophic phase of infection. Subsequent transcriptome analysis, gene co-expression networks, and gene regulatory networks of inoculated and mock-inoculated seedlings of resistant and susceptible accessions suggest that the increase in expression of Sobic.005G172300 induces an oxidative burst by lowering the concentration of ascorbic acid during the biotrophic phase of infection. Based on gene regulatory network analysis, the protein encoded by Sobic.005G172300 is proposed to target proteins involved in the biosynthesis of ascorbic acid for polyubiquitination through the SCF E3 ubiquitin ligase, causing their degradation via the proteasome.

Plant Sciences↗
DOE OSTI2022

Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans

Rhodanobacter has been found as the dominant genus in aquifers contaminated with high concentrations of nitrate and uranium in Oak Ridge, TN, USA. The in situ stimulation of denitrification has been proposed as a potential method to remediate nitrate and uranium contamination. Among the Rhodanobacter species, Rhodanobacter denitrificans strains have been reported to be capable of denitrification and contain abundant metal resistance genes. However, due to the lack of a mutagenesis system in these strains, our understanding of the mechanisms underlying low-pH resistance and the ability to dominate in the contaminated environment remains limited. Here, we developed an in-frame markerless deletion system in two R. denitrificans strains. First, we optimized the growth conditions, tested antibiotic resistance, and determined appropriate transformation parameters in 10 Rhodanobacter strains. We then deleted the upp gene, which encodes uracil phosphoribosyltransferase, in R. denitrificans strains FW104-R3 and FW104-R5. The resulting strains were designated R3_Δupp and R5_Δupp and used as host strains for mutagenesis with 5-fluorouracil (5-FU) resistance as the counterselection marker to generate markerless deletion mutants. Further, to test the developed protocol, the narG gene encoding nitrate reductase was knocked out in the R3_Δupp and R5_Δupp host strains. As expected, the narG mutants could not grow in anoxic medium with nitrate as the electron acceptor. Overall, these results show that the in-frame markerless deletion system is effective in two R. denitrificans strains, which will allow for future functional genomic studies in these strains furthering our understanding of the metabolic and resistance mechanisms present in Rhodanobacter species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum

Abstract Plants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22—an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cyanobacterial photosystem II reaction center design in tobacco chloroplasts increases biomass in low light

Abstract The D1 polypeptide of the photosystem II (PSII) reaction center complex contains domains that regulate primary photochemical yield and charge recombination rate. Many prokaryotic oxygenic phototrophs express two or more D1 isoforms differentially in response to environmental light needs, a capability absent in flowering plants and algae. We report that tobacco (Nicotiana tabacum) plants carrying the Synechococcus (Synechococcus elongatus PCC 7942) low-light mutation (LL-E130Q) in the D1 polypeptide (NtLL) acquire the cyanobacterial photochemical phenotype: faster photodamage in high light and significantly more charge separations in productive linear electron flow in low light. This flux increase produces 16.5% more (dry) biomass under continuous low-light illumination (100 μE m−2 s−1, 24 h). This gain is offset by the predicted lower photoprotection at high light. By contrast, the introduction of the Synechococcus high-light mutation (HL-A152S) into tobacco D1 (NtHL) has slightly increased photoprotection, achieved by photochemical quenching, but no apparent impact on biomass yield compared to wild type under the tested conditions. The universal design principle of all PSII reaction centers trades off energy conversion for photoprotection in different proportions across all phototrophs and provides a useful guidance for testing in crop plants. The observed biomass advantage under continuous low light can be transferred between evolutionarily isolated lineages to benefit growth under artificial lighting conditions. However, removal of the selective marker gene was essential to observe the growth phenotype, indicating growth penalty imposed by use of the particular spectinomycin-resistance gene.

Zhang, Yuan (ORCID:0000000291785207)↗
DOE OSTI2025

A Chromosome-Scale Genome Assembly of the Flax Rust Fungus Reveals the Two Unusually Large Effector Proteins, AvrM3 and AvrN

Rust fungi comprise thousands of species, many of which cause disease on important crop plants. The flax rust fungus Melampsora lini has been a model species for the genetic dissection of plant immunity since the 1940s; however, the highly fragmented and incomplete reference genome has so far hindered progress in effector gene discovery. Here, we generated a fully phased, chromosome-scale assembly of the two nuclear genomes of M. lini strain CH5, resolving an additional 320 Mbp of the sequence. The 482-Mbp dikaryotic genome is at least 79% repetitive, with a large proportion (approximately 40%) of the genome comprising young, highly similar transposable elements. The assembly resolves the known effector gene loci, some of which carry complex duplications that were collapsed in the previous assembly. Using a genetic map followed by manual correction of gene models, we identified the AvrM3 and AvrN genes, which encode unusually large fungal effector proteins and trigger defense responses when co-expressed with the corresponding resistance genes. We located the genes linked to the tetrapolar mating system on chromosomes 4 and 9, but in contrast to the cereal rusts that have one pheromone receptor gene per haplotype, in flax rust, three pheromone receptor genes were found, with two of them closely linked on one haplotype. Taken together, we show that a high-quality assembly is crucial for resolving complex gene loci, and given the increasing number of fungal effectors of large size, the commonly applied criterion for effector candidates of being small proteins needs to be reconsidered.

Melampsora↗
DOE OSTI2022

Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults

Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24 ® ] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Analysis of Salmonella enterica Isolated from a Mixed-Use Watershed in Georgia, USA: Antimicrobial Resistance, Serotype Diversity, and Genetic Relatedness to Human Isolates

As the cases of Salmonella enterica infections associated with contaminated water are increasing, this study was conducted to address the role of surface water as a reservoir of S. enterica serotypes. We sampled rivers and streams (n = 688) over a 3-year period (2015 to 2017) in a mixed-use watershed in Georgia, USA, and 70.2% of the total stream samples tested positive for Salmonella. A total of 1,190 isolates were recovered and characterized by serotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis (PFGE). A wide range of serotypes was identified, including those commonly associated with humans and animals, with S. enterica serotype Muenchen being predominant (22.7%) and each serotype exhibiting a high degree of strain diversity by PFGE. About half (46.1%) of the isolates had PFGE patterns indistinguishable from those of human clinical isolates in the CDC PulseNet database. A total of 52 isolates (4.4%) were resistant to antimicrobials, out of which 43 isolates were multidrug resistant (MDR; resistance to two or more classes of antimicrobials). These 52 resistant Salmonella isolates were screened for the presence of antimicrobial resistance genes, plasmid replicons, and class 1 integrons, out of which four representative MDR isolates were selected for whole-genome sequencing analysis. The results showed that 28 MDR isolates resistant to 10 antimicrobials had blacmy-2 on an A/C plasmid. Persistent contamination of surface water with a high diversity of Salmonella strains, some of which are drug resistant and genetically indistinguishable from human isolates, supports a role of environmental surface water as a reservoir for and transmission route of this pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column

The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.

Pathak, Ashish↗
DOE OSTI2023

Structure of VanS from vancomycin-resistant enterococci: A sensor kinase with weak ATP binding

The VanRS two-component system regulates the resistance phenotype of vancomycin-resistant enterococci. VanS is a sensor histidine kinase that responds to the presence of vancomycin by autophosphorylating and subsequently transferring the phosphoryl group to the response regulator, VanR. The phosphotransfer activates VanR as a transcription factor, which initiates the expression of resistance genes. Structural information about VanS proteins has remained elusive, hindering the molecular-level understanding of their function. Here, we present X-ray crystal structures for the catalytic and ATP-binding (CA) domains of two VanS proteins, derived from vancomycin-resistant enterococci types A and C. Both proteins adopt the canonical Bergerat fold that has been observed for CA domains of other prokaryotic histidine kinases. We attempted to determine structures for the nucleotide-bound forms of both proteins; however, despite repeated efforts, these forms could not be crystallized, prompting us to measure the proteins' binding affinities for ATP. Unexpectedly, both CA domains displayed low affinities for the nucleotide, with K D values in the low millimolar range. Since these K D values are comparable to intracellular ATP concentrations, this weak substrate binding could reflect a way of regulating expression of the resistance phenotype.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds

Abstract Battlefield injury management requires specialized care, and wound infection is a frequent complication. Challenges related to characterizing relevant pathogens further complicates treatment. Applying metagenomics to wounds offers a comprehensive path toward assessing microbial genomic fingerprints and could indicate prognostic variables for future decision support tools. Wound specimens from combat-injured U.S. service members, obtained during surgical debridements before delayed wound closure, were subjected to whole metagenome analysis and targeted enrichment of antimicrobial resistance genes. Results did not indicate a singular, common microbial metagenomic profile for wound failure, instead reflecting a complex microenvironment with varying bioburden diversity across outcomes. Genus-level Pseudomonas detection was associated with wound failure at all surgeries. A logistic regression model was fit to the presence and absence of antimicrobial resistance classes to assess associations with nosocomial pathogens. A. baumannii detection was associated with detection of genomic signatures for resistance to trimethoprim, aminoglycosides, bacitracin, and polymyxin. Machine learning classifiers were applied to identify wound and microbial variables associated with outcome. Feature importance rankings averaged across models indicated the variables with the largest effects on predicting wound outcome, including an increase in P. putida sequence reads. These results describe the microbial genomic determinants in combat wound bioburden and demonstrate metagenomic investigation as a comprehensive tool for providing information toward aiding treatment of combat-related injuries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (> 20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of ‘Fiskeby III,’ a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genome‐wide association studies on resistance to powdery mildew in cultivated emmer wheat

Abstract Powdery mildew, caused by the fungal pathogenBlumeria graminis(DC.) E. O. Speer f. sp.triticiEm. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivumL.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimizeBgt’s fast evolving virulence. In tetraploid wheat (Triticum turgidumL.), wild emmer wheat [T. turgidumssp.dicoccoides(Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed manyPmresistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidumssp.dicoccum(Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction toBgtisolateOKS(14)‐B‐3‐1and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis ofBgtresistance in the panel, genome‐wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype‐by‐sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty‐five significant SNP markers were identified to be associated withBgtresistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derivedPm4a,Pm5a,PmG16, andPm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhanceBgtresistance in wheat.

Genetics & Heredity↗
DOE OSTI2024

Factors affecting the production of sugarcane yield and sucrose accumulation: suggested potential biological solutions

Environmental stresses are the main constraints on agricultural productivity and food security worldwide. This issue is worsened by abrupt and severe changes in global climate. The formation of sugarcane yield and the accumulation of sucrose are significantly influenced by biotic and abiotic stresses. Understanding the biochemical, physiological, and environmental phenomena associated with these stresses is essential to increase crop production. This review explores the effect of environmental factors on sucrose content and sugarcane yield and highlights the negative effects of insufficient water supply, temperature fluctuations, insect pests, and diseases. This article also explains the mechanism of reactive oxygen species (ROS), the role of different metabolites under environmental stresses, and highlights the function of environmental stress-related resistance genes in sugarcane. This review further discusses sugarcane crop improvement approaches, with a focus on endophytic mechanism and consortium endophyte application in sugarcane plants. Endophytes are vital in plant defense; they produce bioactive molecules that act as biocontrol agents to enhance plant immune systems and modify environmental responses through interaction with plants. This review provides an overview of internal mechanisms to enhance sugarcane plant growth and environmental resistance and offers new ideas for improving sugarcane plant fitness and crop productivity.

Mehdi, Faisal↗