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At least 235 records · Page 13

Evaluating genetic and environmental controls on silicon accumulation in Populus trichocarpa leaves

Background and aims: Silicon (Si) accumulation and formation of non-crystalline silica particles (phytoliths) inside plant cells contribute to plant function, soil carbon storage, and Si reservoirs in soils. A better understanding of how genetic and environmental factors control Si accumulation may improve understanding of Si cycling between plants and soil and its impacts on other ecosystem processes. Methods: This study examined how genetic potential for Si uptake and silicification translated to Si concentrations and phytolith formation in Populus trichocarpa leaves. Leaves were collected from four different genotypes of cultivated poplar trees that were grown in a common garden and possess established differences in leaf-level gene expression related to Si transport and silicification. Scanning electron microscopy and subsequent image analysis were used to quantify Si concentrations and phytolith abundance and features. Results: Phytoliths were identified in nearly all leaves but were often absent at very low (< 0.5 wt.%) Si concentrations at the leaf surface. The proportion of leaf area occupied by phytoliths increased as Si content increased. Silicon content and phytolith abundance at the leaf surface did not vary across genotypes, but surface Si was weakly correlated with plant available Si in soil. Conclusion: Phytoliths were prevalent in P. trichocarpa leaves; however, the genetic potential for Si uptake and silicification at the leaf-level poorly predicted foliar Si and phytolith abundance. Uniformly low expression of Si uptake genes in the roots may have reduced differences across genotypes. Consequently, Si accumulation in leaves was likely more strongly influenced by soil Si bioavailability, phenology, or additional environmental factors.

Image analysis↗

Recent advancements in the genetic engineering of microalgae

The development of more sustainable food, feed, and bio-products is critical to mitigating the environmental stresses facing our world today. Algae, which includes seaweeds, eukaryotic microalgae, and cyanobacteria, are a promising platform to achieving this, as they have low energy and space requirements, are safe for human and animal consumption, and can be manipulated to produce a diversity of valuable bioproducts. This review focuses on microalgae, both eukaryotic and cyanobacteria. In the past, addressing the major challenges of bringing microalgal production systems to an economically viable scale only had a relatively small genetic toolset to work with, in comparison to other microbial systems such as bacteria and yeast. Expanding the molecular tools available for genetic engineering of microalgae will lead to higher product yields, and accelerate the development of new microalgal bioproducts for commercial applications, thereby supporting the shift towards more environmentally friendly products. In this review, we highlight significant advances from recent years on the design of microalgal expression vectors, discovery of genetic regulatory elements (promoters and transcription factors), optimization of transformation methods, and development of new strain improvement techniques, all aimed at advancing microalgae to become a more efficient biomanufacturing platform. We then discuss how these tools have been applied to improving recombinant protein production, and to enhance metabolic pathway engineering.

09 BIOMASS FUELS↗

Genetics of osteoporosis

Highlights: • Single-nucleotide polymorphisms (SNPs) associated with osteoporosis were identified. • SNPs mapped close to or within VDR and ESR1 are associated with bone mineral density. • WNT signaling pathway plays a pivotal role in regulating bone mineral density. • Genetic studies will be useful for identification of new therapeutic targets. - Abstract: Osteoporosis is a skeletal disease characterized by low bone mineral density (BMD) and microarchitectural deterioration of bone tissue, which increases susceptibility to fractures. BMD is a complex quantitative trait with normal distribution and seems to be genetically controlled (in 50–90% of the cases), according to studies on twins and families. Over the last 20 years, candidate gene approach and genome-wide association studies (GWAS) have identified single-nucleotide polymorphisms (SNPs) that are associated with low BMD, osteoporosis, and osteoporotic fractures. These SNPs have been mapped close to or within genes including those encoding nuclear receptors and WNT-β-catenin signaling proteins. Understanding the genetics of osteoporosis will help identify novel candidates for diagnostic and therapeutic targets.

60 APPLIED LIFE SCIENCES↗

Genetic variations and their interaction with thirdhand smoke exposure on anxiety and memory in Collaborative Cross mice

Thirdhand smoke (THS) is linked to adverse health effects, but the effect of genetic variations on behavioral outcomes is poorly understood. To investigate this, we assessed anxiety- and memory-related behaviors in 820 mice from 21 strains of the genetically diverse Collaborative Cross (CC) mouse that were exposed to THS from 4 through 10 weeks of age. Anxiety was evaluated with a light/dark box assay with a previously established risk score system. Females were generally more sensitive: THS reduced anxiety risk in strains CC013, CC019, and CC051, but increased risk in CC036 and CC061, while males showed no significant effects. Memory was tested using passive avoidance: impairments were observed in both sexes in CC016 and CC019, with sex-dependent effects in CC002 and CC051. A genome-wide association study identified 2,347 SNPs associated with anxiety and 1,568 SNPs with memory, with 32 and 85 SNPs, respectively, interacting with THS exposure. Enrichment analyses revealed distinct biological processes underlying susceptibility, including axonogenesis, synapse organization, cognition, and learning and memory. KEGG pathway analysis identified distinct genetic pathways, including GTPase binding and GTPase regulatory activity, that act as critical molecular switches in the brain that regulate synaptic plasticity, dendritic spine structure, and neuronal signaling, directly influencing anxiety-like behaviors and memory formation. These findings show that THS exposure affects neurobehavioral outcomes in a sex- and genotype-dependent manner, highlighting critical gene-environment interactions and providing a foundation for mechanistic insights into THS neurotoxicity

Anxiety↗

Genetic algorithm optimization of tin–copper graded shielding for improved plutonium safeguards measurements

Plutonium nuclear material safeguards is essential to ensure that states do not divert plutonium to clandestine nuclear weapons programs. Traditional safeguards methods rely on correlated neutron measurements. Detection systems based on organic scintillators, which are sensitive to fast neutrons and photons, are gaining support for use in safeguards applications due to increased capabilities and shorter measurement times compared to the current state-of-the-art. A drawback of organic scintillators in plutonium measurements is data throughput limitations; 241 Am builds up in plutonium samples and emits 60-keV gamma rays with a high specific activity. In this work, a genetic algorithm is used to design graded shielding made of tin and copper to attenuate the 60-keV gamma rays. The shield is designed to limit the attenuation of the higher-energy, fission photons, because fission photons can be used as a signature. The genetic algorithm optimization takes days to run, while a complete search space exploration would take years. The genetic algorithm was run for different levels of 60-keV gamma-ray attenuation, and the thickness of the required shielding layers was determined at each level. Tin–copper shielding was placed in front of an array of organic scintillation detectors for a measurement of approximately 4.5 kg of alpha-phase, weapons-grade plutonium, an AmLi source, and a 252 Cf source. We show that the shield successfully attenuated low-energy, non-fission gamma rays, which significantly improved the organic scintillator performance.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Biocontainment of genetically modified organisms by synthetic protein design

Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. In this paper, we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. Finally, this work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

Abstract Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked tocis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, includingvgt1,ZmTRE1and the MITE transposon nearZmNAC111under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functionalcis-variation accessible at scale for genetic studies and targeted engineering of complex traits.

Genetics & Heredity↗

Reconstruction of larval origins based on genetic relatedness and biophysical modeling

The assessment of the mechanisms and patterns of larval connectivity between geographically separated populations leads to a better understanding of benthic marine population dynamics, especially in commercially valuable species. This study investigated for the first time the fine-scale temporal genetic variability of new settlers and their origins in a benthic marine organism with one of the longest pelagic larval phases, the Caribbean spiny lobster (Panulirus argus). We genotyped newly settled postlarvae in the Florida Keys and adults of spiny lobster from the Florida Keys and throughout the Caribbean Sea. We identified strong larval connectivity between Dominican Republic, Belize, Nicaragua, the Florida Keys, and West-Florida. the larval dispersal modeling suggests that Florida’s lobster population could receive recruits from within and from other areas outside its state and national maritime boundaries. The genetic analyses refine the oceanographic model indicating that the connectivity patterns described could also result from unknown parental populations sourcing adults and postlarvae in different spawning seasons to the Florida Keys. We discuss the importance of small temporal scales to identify patterns in larval export. Our findings are significant on two levels. From the larval dispersal perspective, genetic results and biophysical modeling identify patterns of gene flow enhancing persistence of local populations. From an economic and fishery perspective, P. argus is the most important commercial species in the Caribbean and our results inform how considering larval source and sink dynamics across international boundaries could improve management plans at local, national, and regional levels.

59 BASIC BIOLOGICAL SCIENCES↗

Gut microbiome partially mediates and coordinates the effects of genetics on anxiety-like behavior in Collaborative Cross mice

Abstract Growing evidence suggests that the gut microbiome (GM) plays a critical role in health and disease. However, the contribution of GM to psychiatric disorders, especially anxiety, remains unclear. We used the Collaborative Cross (CC) mouse population-based model to identify anxiety associated host genetic and GM factors. Anxiety-like behavior of 445 mice across 30 CC strains was measured using the light/dark box assay and documented by video. A custom tracking system was developed to quantify seven anxiety-related phenotypes based on video. Mice were assigned to a low or high anxiety group by consensus clustering using seven anxiety-related phenotypes. Genome-wide association analysis (GWAS) identified 141 genes (264 SNPs) significantly enriched for anxiety and depression related functions. In the same CC cohort, we measured GM composition and identified five families that differ between high and low anxiety mice. Anxiety level was predicted with 79% accuracy and an AUC of 0.81. Mediation analyses revealed that the genetic contribution to anxiety was partially mediated by the GM. Our findings indicate that GM partially mediates and coordinates the effects of genetics on anxiety.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment

The interplay between host genetics, tumor microenvironment and environmental exposure in cancer susceptibility remains poorly understood. Here we assessed the genetic control of stromal mediation of mammary tumor susceptibility to low dose ionizing radiation (LDIR) using backcrossed F1 into BALB/c (F1Bx) between cancer susceptible (BALB/c) and resistant (SPRET/EiJ) mouse strains. Tumor formation was evaluated after transplantation of non-irradiated Trp53-/- BALB/c mammary gland fragments into cleared fat pads of F1Bx hosts. Genome-wide linkage analysis revealed 2 genetic loci that constitute the baseline susceptibility via host microenvironment. However, once challenged with LDIR, we discovered 13 additional loci that were enriched for genes involved in cytokines, including TGFβ1 signaling. Surprisingly, LDIR-treated F1Bx cohort significantly reduced incidence of mammary tumors from Trp53-/- fragments as well as prolonged tumor latency, compared to sham-treated controls. We demonstrated further that plasma levels of specific cytokines were significantly correlated with tumor latency. Using an ex vivo 3-D assay, we confirmed TGFβ1 as a strong candidate for reduced mammary invasion in SPRET/EiJ, which could explain resistance of this strain to mammary cancer risk following LDIR. Our results open possible new avenues to understand mechanisms of genes operating via the stroma that affect cancer risk from external environmental exposures.

59 BASIC BIOLOGICAL SCIENCES↗

A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)

Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.

59 BASIC BIOLOGICAL SCIENCES↗

Barcoded reciprocal hemizygosity analysis via sequencing illuminates the complex genetic basis of yeast thermotolerance

Decades of successes in statistical genetics have revealed the molecular underpinnings of traits as they vary across individuals of a given species. But standard methods in the field cannot be applied to divergences between reproductively isolated taxa. Genome-wide reciprocal hemizygosity mapping (RH-seq), a mutagenesis screen in an interspecies hybrid background, holds promise as a method to accelerate the progress of interspecies genetics research. Here, we describe an improvement to RH-seq in which mutants harbor barcodes for cheap and straightforward sequencing after selection in a condition of interest. As a proof of concept for the new tool, we carried out genetic dissection of the difference in thermotolerance between two reproductively isolated budding yeast species. Experimental screening identified dozens of candidate loci at which variation between the species contributed to the thermotolerance trait. Hits were enriched for mitosis genes and other housekeeping factors, and among them were multiple loci with robust sequence signatures of positive selection. Together, these results shed new light on the mechanisms by which evolution solved the problems of cell survival and division at high temperature in the yeast clade, and they illustrate the power of the barcoded RH-seq approach.

59 BASIC BIOLOGICAL SCIENCES↗

Climate-driven reduction of genetic variation in plant phenology alters soil communities and nutrient pools

Here, we examined the hypothesis that climate–driven evolution of plant traits will influence associated soil microbiomes and ecosystem function across the landscape. Using a foundation tree species, Populus angustifolia , observational and common garden approaches, and a base population genetic collection that spans 17 river systems in the western United States, from AZ to MT, we show that (a) as mean annual temperature (MAT) increases, genetic and phenotypic variation for bud break phenology decline; (b) soil microbiomes, soil nitrogen (N), and soil carbon (C) vary in response to MAT and conditioning by trees; and (c) with losses of genetic variation due to warming, population–level regulation of community and ecosystem functions strengthen. These results demonstrate a relationship between the potential evolutionary response of populations and subsequent shifts in ecosystem function along a large temperature gradient.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic Basis of Non–Photochemical Quenching and Photosystem II Efficiency Responses to Chilling in the Biomass Crop Miscanthus

Miscanthus holds a promise as a biocrop due to its high yield, perenniality and ability to grow on infertile soils. However, the current commercial biomass production of Miscanthus is mostly limited to a single sterile triploid clone of M. × giganteus. Nevertheless, parental species of M. × giganteus, Miscanthus sacchariflorus and Miscanthus sinensis contain vast genetic diversity for crop improvement. With M. sacchariflorus having a natural geographic distribution in cold-temperate northeast China and eastern Russia, we hypothesised that it has substantial variation in physiological response to chilling. Using a semi-high-throughput method, we phenotyped 209 M. sacchariflorus genotypes belonging to six genetic groups for non-photochemical quenching (NPQ) and photosystem II efficiency (ΦPSII) kinetics under warm and chilling treatments in three growing seasons. In response to the chilling treatment, all genetic groups exhibited an increase in NPQ induction rate indicating faster activation of NPQ in light. Notably, under chilling, the Korea/NE China/Russia 2x and N China 2x groups stood out for the highest NPQ rate in light and the highest steady-state NPQ in light. This NPQ phenotype may contribute adaptation to chilling during bright, cold mornings of spring and early autumn in temperate climates, when faster NPQ would better protect from oxidative stress. Such enhanced adaptation could expand the growing season and thus productivity at a given location or expand the range of economically viable growing locations to higher latitudes and altitudes. A genome-wide association study identified 126 unique SNPs associated with NPQ and ΦPSII traits. Among the identified candidate genes were enzymes involved in the ascorbate recycle and shikimate pathway, gamma-aminobutyric acid and cation efflux transporters. Identifying natural variation and genes involved in NPQ and ΦPSII kinetics considerably enlarges the toolbox for breeding and/or engineering Miscanthus with optimised photosynthesis under warm and chilling conditions for sustainable feedstock production for bioenergy.

09 BIOMASS FUELS↗

Spatial Replication Is Important for Developing Landscape Genetic Inferences for a Wetland Salamander

Habitat fragmentation is a pressing threat to wildlife populations, and maintenance of gene flow between populations is an essential goal of conservation. Resistance surfaces have emerged as an important tool for modelling connectivity and developing management strategies to mitigate effects of habitat fragmentation. However, recent studies have noted inconsistencies in the factors most strongly associated with connectivity across different landscapes. Thus, replication of genetic-based resistance surface optimisation across landscapes may be necessary for making robust conclusions about the influence of environmental variables. Accordingly, replication represents a substantive challenge and opportunity in the field of landscape genetics. In this study, we conducted replicated landscape genetic analyses across five landscapes in Tennessee and Kentucky for a threatened wetland amphibian, the four-toed salamander (Hemidactylium scutatum). We tested multiple hypotheses of how different landscape features that could directly affect small, desiccation-intolerant amphibians (e.g., canopy cover) influenced gene flow and assessed the appropriate scale at which to model different features. We found some concordance in the landscape features that influenced gene flow (e.g., a common importance of forest cover and topography), but also some differences—potentially owing to the difference in variability of predictors across landscapes. We also found discordance in the scale of effect of different features across landscapes. In conclusion, our work emphasises that flat areas of moist forest not bisected by roads may be important for H. scutatum conservation, and our replicated design allows us to identify relationships that would have been missed if only using one study site.

59 BASIC BIOLOGICAL SCIENCES↗

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. Here, we surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

Community genetics↗

Synthetic genetic circuits as a means of reprogramming plant roots

We report the shape of a plant’s root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.

59 BASIC BIOLOGICAL SCIENCES↗

Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora

Abstract Background Over their evolutionary history, corals have adapted to sea level rise and increasing ocean temperatures, however, it is unclear how quickly they may respond to rapid change. Genome structure and genetic diversity contained within may highlight their adaptive potential. Results We present chromosome-scale genome assemblies and linkage maps of the critically endangered Atlantic acroporids,Acropora palmataandA. cervicornis. Both assemblies and linkage maps were resolved into 14 chromosomes with their gene content and colinearity. Repeats and chromosome arrangements were largely preserved between the species. The family Acroporidae and the genusAcroporaexhibited many phylogenetically significant gene family expansions. Macrosynteny decreased with phylogenetic distance. Nevertheless, scleractinians shared six of the 21 cnidarian ancestral linkage groups as well as numerous fission and fusion events compared to other distantly related cnidarians. Genetic linkage maps were constructed from oneA. palmatafamily and 16A. cervicornisfamilies using a genotyping array. The consensus maps span 1,013.42 cM and 927.36 cM forA. palmataandA. cervicornis, respectively. Both species exhibited high genome-wide recombination rates (3.04 to 3.53 cM/Mb) and pronounced sex-based differences, known as heterochiasmy, with 2 to 2.5X higher recombination rates estimated in the female maps. Conclusions Together, the chromosome-scale assemblies and genetic maps we present here are the first detailed look at the genomic landscapes of the critically endangered Atlantic acroporids. These data sets revealed that adaptive capacity of Atlantic acroporids is not limited by their recombination rates. The sister species maintain macrosynteny with few genes with high sequence divergence that may act as reproductive barriers between them. In the AtlanticAcropora, hybridization between the two sister species yields an F1 hybrid with limited fertility despite the high levels of macrosynteny and gene colinearity of their genomes. Together, these resources now enable genome-wide association studies and discovery of quantitative trait loci, two tools that can aid in the conservation of these species.

Biotechnology & Applied Microbiology↗