Physical Map Research Articles

Two functional CC-NBS-LRR proteins from rye chromosome 6RS confer differential age-related powdery mildew resistance to wheat.

Rye (Secale cereale), a valuable relative of wheat, contains abundant powdery mildew resistance (Pm) genes. Using physical mapping, transcriptome sequencing, barley stripe mosaic virus-induced gene silencing, ethyl methane sulfonate mutagenesis, and stable transformation, we isolated and validated two coiled-coil, nucleotide-binding site and leucine-rich repeat (CC-NBS-LRR) alleles, PmTR1 and PmTR3, located on rye chromosome 6RS from different triticale lines. PmTR1 confers age-related resistance starting from the three-leaf stage, whereas its allele, PmTR3, confers typical all-stage resistance, which may be associated with their differential gene expression patterns. Overexpression in Nicotiana benthamiana showed that the CC, CC-NBS, and CC-LRR fragments of PMTR1 induce cell death, whereas in PMTR3 the CC and full-length fragments perform this function. Luciferase complementation imaging and pull-down assays revealed distinct interaction activities between the CC and NBS fragments. Our study elucidates two novel rye-derived Pm genes and their derivative germplasm resources and provides novel insights into the mechanism of age-related resistance, which can aid the improvement of resistance against wheat powdery mildew.

Identification of Fusarium head blight sources of resistance and associated QTLs in historical and modern Canadian spring wheat.

Fusarium head blight (FHB) is one the most globally destructive fungal diseases in wheat and other small grains, causing a reduction in grain yield by 10-70%. The present study was conducted in a panel of historical and modern Canadian spring wheat (Triticum aestivum L.) varieties and lines to identify new sources of FHB resistance and map associated quantitative trait loci (QTLs). We evaluated 249 varieties and lines for reaction to disease incidence, severity, and visual rating index (VRI) in seven environments by artificially spraying a mixture of four Fusarium graminearum isolates. A subset of 198 them were genotyped with the Wheat 90K iSelect single nucleotide polymorphisms (SNPs) array. Genome-wide association mapping performed on the overall best linear unbiased estimators (BLUE) computed from all seven environments and the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v2.0 physical map of 26,449 polymorphic SNPs out of the 90K identified sixteen FHB resistance QTLs that individually accounted for 5.7-10.2% of the phenotypic variance. The positions of two of the FHB resistance QTLs overlapped with plant height and flowering time QTLs. Four of the QTLs (QFhb.dms-3B.1, QFhb.dms-5A.5, QFhb.dms-5A.7, and QFhb.dms-6A.4) were simultaneously associated with disease incidence, severity, and VRI, which accounted for 27.0-33.2% of the total phenotypic variance in the combined environments. Three of the QTLs (QFhb.dms-2A.2, QFhb.dms-2D.2, and QFhb.dms-5B.8) were associated with both incidence and VRI and accounted for 20.5-22.1% of the total phenotypic variance. In comparison with the VRI of the checks, we identified four highly resistant and thirty-three moderately resistant lines and varieties. The new FHB sources of resistance and the physical map of the associated QTLs would provide wheat breeders valuable information towards their efforts in developing improved varieties in western Canada.

Efficient hydrogenation of aliphatic acyclic amides to amines by bimetallic NiMo nitrides via heterogeneous catalysis

Primary amines are vital building blocks in pharmaceutical and polymer industry. The heterogeneous catalytic hydrogenation of aliphatic acyclic amides to amines is rather attractive but challenging due to low reactivity of aliphatic acyclic amides, and then rarely be reported. Herein, cheap bimetallic NiMo nitride catalysts were synthesized by hydrothermal method and firstly utilized to the efficient conversion of a wide range of aliphatic acyclic amides to amines, achieving 93.9 % conversion of hexanamide and 75.1 % yield to hexylamine. Characterizations such XRD, N2 Physical adsorption, TGA, Raman, XPS, SEM-EDX Mapping and (HR)TEM revealed that Ni2Mo3N is crucially important for the activation of hexanamide while the synergetic effect between Ni2Mo3N and Ni6Mo6C1.06 would further promote the conversion of hexanamide, and higher TOFs (145.9 h−1) and lower Ea (29.5 kJ mol−1) are achieved. The CO bond of the amide can be activated by the surface Lewis acid site of bimetallic NiMo nitrides, while the simultaneous dissociation of H2 to form H atoms is beneficial for hydrogenation. This catalyst is also found to be recyclable with stable catalytic performance upon consecutive runs. The present work provides a novel and unique option for the efficient conversion of aliphatic acyclic amides to amines, being a strong supplementary to those reported for the hydrogenation of cyclic-amides, secondary amides, and tertiary amides.

Development of novel wheat-rye 6RS small fragment translocation lines with powdery mildew resistance and physical mapping of the resistance gene PmW6RS.

Novel wheat-rye 6RS small fragment translocation lines with powdery mildew resistance were developed, and the resistance gene PmW6RS was physically mapped onto 6RS-0.58-0.66-bin corresponding to 18.38Mb in Weining rye. Rye (Secale cereale L., RR) contains valuable genes for wheat improvement. However, most of the rye resistance genes have not been successfully used in wheat cultivars. Identification of new rye resistance genes and transfer of these genes to wheat by developing small fragment translocation lines will make these genes more usable for wheat breeding. In this study, a broad-spectrum powdery mildew resistance gene PmW6RS was localized on rye chromosome arm 6RS using a new set of wheat-rye disomic and telosomic addition lines. To further study and use PmW6RS, 164 wheat-rye 6RS translocation lines were developed by 60Coγ-ray irradiation. Seedling and adult stage powdery mildew resistance analysis showed that 106 of the translocation lines were resistant. A physical map of 6RS was constructed using the 6RS translocation and deletion lines, and PmW6RS was localized in the 6RS-0.58-0.66-bin, flanked by markers X6RS-3 and X6RS-10 corresponding to the physical interval of 50.23-68.61Mb in Weining rye genome. A total of 23 resistance-related genes were annotated. Nine markers co-segregate with the 6RS-0.58-0.66-bin, which can be used to rapidly trace the 6RS fragment carrying PmW6RS. Small fragment translocation lines with powdery mildew resistance were backcrossed with wheat cultivars, and 39 agronomically acceptable homozygous 6RS small fragment translocation lines were obtained. In conclusion, this study not only provides novel gene source and germplasms for wheat resistance breeding, but also laid a solid foundation for cloning of PmW6RS.

A Cyber–Physical Systems-Based Double-Layer Mapping Petri Net Model for Factory Process Flow Control

This study is concerned with the imperfect virtual-reality mapping relationship in cyber–physical systems (CPSs) and the challenge faced in knowledge-based decisions. Regarding those problems, a double-layer mapping Petri net (DMPN) model is proposed. By deploying the programmable automation gateway PAG200, combining the CPS technology with the principle of Petri net and establishing the monitoring Petri net in the cyber space, this model realizes mapping between the physical entity and the digital object. Meanwhile, the knowledge-based decision problem in CPS is defined as a Petri net conflict. In accordance with this, a control network for resolving the conflict is established. Finally, through a practical case, the workflow of DMPN is illustrated and a task allocation algorithm and a quality decision algorithm are proposed to resolve Petri net conflicts. Consequently, it is proven that DMPN is feasible in solving actual production process flow control. At the same time, it also provides a solution for enterprise workflow analysis.

A physical map of traits of agronomic importance based on potato and tomato genome sequences.

Potato, tomato, pepper, and eggplant are worldwide important crop and vegetable species of the Solanaceae family. Molecular linkage maps of these plants have been constructed and used to map qualitative and quantitative traits of agronomic importance. This research has been undertaken with the vision to identify the molecular basis of agronomic characters on the one hand, and on the other hand, to assist the selection of improved varieties in breeding programs by providing DNA-based markers that are diagnostic for specific agronomic characters. Since 2011, whole genome sequences of tomato and potato became available in public databases. They were used to combine the results of several hundred mapping and map-based cloning studies of phenotypic characters between 1988 and 2022 in physical maps of the twelve tomato and potato chromosomes. The traits evaluated were qualitative and quantitative resistance to pathogenic oomycetes, fungi, bacteria, viruses, nematodes, and insects. Furthermore, quantitative trait loci for yield and sugar content of tomato fruits and potato tubers and maturity or earliness were physically mapped. Cloned genes for pathogen resistance, a few genes underlying quantitative trait loci for yield, sugar content, and maturity, and several hundred candidate genes for these traits were included in the physical maps. The comparison between the physical chromosome maps revealed, in addition to known intrachromosomal inversions, several additional inversions and translocations between the otherwise highly collinear tomato and potato genomes. The integration of the positional information from independent mapping studies revealed the colocalization of qualitative and quantitative loci for resistance to different types of pathogens, called resistance hotspots, suggesting a similar molecular basis. Synteny between potato and tomato with respect to genomic positions of quantitative trait loci was frequently observed, indicating eventual similarity between the underlying genes.

Karyotype and Phylogenetic Relationship Analysis of Five Varieties and Cultivars of Zanthoxylum armatum Based on Oligo-FISH.

Green prickly ash (Zanthoxylum armatum) has edible and medicinal value and is an economically significant plant in many countries. Z. armatum has many cultivars and varieties with similar phenotypes that are difficult to distinguish via traditional methods. In this study, we utilized oligo-FISH to distinguish five varieties and cultivars of Z. armatum on the basis of three oligonucleotide probes of 5S rDNA, (AG3T3)3, and (GAA)6. Karyotype analysis of the five varieties and cultivars of Z. armatum showed that the Z. armatum 'Tengjiao' karyotype formula was 2n = 2x = 98m with karyotype type 1C and an arm ratio of 4.3237, including two pairs of 5S rDNA signals and five pairs of (GAA)6 signals. The karyotype formula of Z. armatum 'Youkangtengjiao' was 2n = 2x = 128m + 8sm with karyotype type 2B and an arm ratio of 3.5336, including three pairs of 5S rDNA signals and 17 pairs of (GAA)6 signals. The karyotype formula of Z. armatum var. novemfolius was 2n = 2x = 134m + 2sm with karyotype type 1C and an arm ratio of 5.5224, including two pairs of 5S rDNA signals and eight pairs of (GAA)6 signals. The karyotype formula of Z. armatum 'YT-03' was 2n = 2x = 2M + 128m + 4sm + 2st with karyotype type 2C and an arm ratio of 4.1829, including three pairs of 5S rDNA signals and nine pairs of (GAA)6 signals. The karyotype formula of Z. armatum 'YT-06' was 2n = 2x = 126m + 10sm with cytotype 2B and an arm ratio of 3.3011, including three pairs of 5S rDNA signals and two pairs of (GAA)6 signals. The five varieties and cultivars of Z. armatum had (AG3T3)3 signals on all chromosomes. The chromosomal symmetry of Z. armatum 'Tengjiao' was high, whereas the chromosomal symmetry of Z. armatum 'YT-03' was low, with the karyotypes of the five materials showing a trend toward polyploid evolution. The phylogenetic relationship between Z. armatum 'Tengjiao' and Z. armatum var. novemfolius was the closest, while that between Z. armatum 'YT-03' and Z. armatum 'YT-06' was closer than with Z. armatum 'Youkangtengjiao' according to oligo-FISH. The results provided a karyotype profile and a physical map that contributes to the distinction of varieties and cultivars of Z. armatum and provides strategies for distinguishing other cultivated species.

The Fluorescence in situ hybridization (FISH): types and application: a review

The macromolecule identification method known as fluorescence in situ hybridization (FISH) is regarded as a recent development in the study of cytology. It was first created as a physical mapping method to identify genes inside chromosomes. Later, biological and medical studies benefited from the precision and adaptability of FISH. This attractive method offers a level of resolution in between chromosomal studies and DNA analysis. A hybridizing DNA probe used in FISH can either be directly or indirectly labeled. Fluorescent nucleotides are employed in direct labeling, whereas reporter molecules used in indirect labeling are afterwards recognized through affinity molecules, fluorescent antibodies, or other means. An excessively high number of chromosomes in a cell, unique gene fusions, or the loss of a chromosomal segment or an entire chromosome are examples of genetic disorders that can be detected with FISH. It is also used in a variety of scientific projects, including gene mapping and the discovery of fresh oncogenes. This article examines the FISH idea, its use, and its benefits in medical research.

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene (R-gene) Pm69 derived from tetraploid wild emmer wheat. A conventional positional cloning approach was not effective owing to suppressed recombination. Chromosome sorting was compromised by insufficient purity. A Pm69 physical map, constructed by assembling Oxford Nanopore Technology (ONT) long-read genome sequences, revealed a rapidly evolving nucleotide-binding leucine-rich repeat (NLR) R-gene cluster with structural variations. A single candidate NLR was identified by anchoring RNA sequencing reads from susceptible mutants to ONT contigs and was validated by virus-induced gene silencing. Pm69 is likely a newly evolved NLR and was discovered in only one location across the wild emmer wheat distribution range in Israel. Pm69 was successfully introgressed into cultivated wheat, and a diagnostic molecular marker was used to accelerate its deployment and pyramiding with other R-genes.

Extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass.

An Italian ryegrass population from Arkansas, USA developed glyphosate resistance due to 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene amplification. The plants in this population with approximately 70 EPSPS copies were used in the present study for the physical mapping of amplified copies of EPSPS gene to determine the possible mechanism of EPSPS gene amplification conferring glyphosate resistance in Italian ryegrass. Fluorescence in situ hybridization (FISH) analysis of glyphosate resistant (GR) Italian ryegrass plants with approximately 70 EPSPS copies displayed EPSPS hybridization signals randomly on most of the metaphase chromosomes. Glyphosate susceptible (GS) Italian ryegrass plants with one EPSPS copy displayed single prominent EPSPS hybridization signal, which was co-localized with 5S rDNA locus along with few additional signals on the outside of chromosomes. Pulsed-field gel electrophoresis (PFGE) followed by DNA blot using EPSPS gene as a probe identified a prominent EPSPS hybridization around the 400 kb region in GR DNA samples, but not in GS DNA samples. We report the extrachromosomal DNA-mediated glyphosate resistance in Italian ryegrass. Physical mapping of amplified copies of EPSPS gene in Italian ryegrass by FISH gives us a clue that the amplified copies of EPSPS gene may be present in the extrachromosomal DNA elements. Further analysis by PFGE followed by DNA blotting revealed that the extrachromosomal DNA containing EPSPS is approximately 400 kb similar in size with that of eccDNA replicon in Amaranthus palmeri. © 2023 Society of Chemical Industry.

Genetic analysis and physical mapping of oat adult plant resistance loci against Puccinia coronata f. sp. avenae.

Six quantitative trait loci (QTL) for adult plant resistance (APR) against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations (RILs). Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTL were mapped on six different chromosomes, namely: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTL for coefficient of infection range from 12.2 to 46.9%, while heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking SNP markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTL in each population were determined using SNP haplotype data, which showed significantly lower coefficient of infection (CI) in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, Polymerase Chain Reaction Allelic Competitive Extension (PACE) markers for the APR loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.

Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants.

Modern plant pathology relies on bioinformatics approaches to create novel plant disease diagnostic tools. In recent years, a significant amount of biological data has been generated due to rapid developments in genomics and molecular biology techniques. The progress in the sequencing of agriculturally important crops has made it possible to develop a better understanding of plant-pathogen interactions and plant resistance. The availability of host-pathogen genome data offers effective assistance in retrieving, annotating, analyzing, and identifying the functional aspects for characterization at the gene and genome levels. Physical mapping facilitates the identification and isolation of several candidate resistance (R) genes from diverse plant species. A large number of genetic variations, such as disease-causing mutations in the genome, have been identified and characterized using bioinformatics tools, and these desirable mutations were exploited to develop disease resistance. Moreover, crop genome editing tools, namely the CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer novel and efficient strategies for developing durable resistance. This review paper describes some aspects concerning the databases, tools, and techniques used to characterize resistance (R) genes for plant disease management.

Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L.

We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.

Physical Mapping of QTLs for Root Traits in a Population of Recombinant Inbred Lines of Hexaploid Wheat

Root architecture is key in determining how effective plants are at intercepting and absorbing nutrients and water. Previously, the wheat (Triticum aestivum) cultivars Spica and Maringa were shown to have contrasting root morphologies. These cultivars were crossed to generate an F6:1 population of recombinant inbred lines (RILs) which was genotyped using a 90 K single nucleotide polymorphisms (SNP) chip. A total of 227 recombinant inbred lines (RILs) were grown in soil for 21 days in replicated trials under controlled conditions. At harvest, the plants were scored for seven root traits and two shoot traits. An average of 7.5 quantitative trait loci (QTL) were associated with each trait and, for each of these, physical locations of the flanking markers were identified using the Chinese Spring reference genome. We also compiled a list of genes from wheat and other monocotyledons that have previously been associated with root growth and morphology to determine their physical locations on the Chinese Spring reference genome. This allowed us to determine whether the QTL discovered in our study encompassed genes previously associated with root morphology in wheat or other monocotyledons. Furthermore, it allowed us to establish if the QTL were co-located with the QTL identified from previously published studies. The parental lines together with the genetic markers generated here will enable specific root traits to be introgressed into elite wheat lines. Moreover, the comprehensive list of genes associated with root development, and their physical locations, will be a useful resource for researchers investigating the genetics of root morphology in cereals.

Physical mapping of the wheat genes in low-recombination regions: radiation hybrid mapping of the C-locus.

This work reports the physical mapping of an important gene affecting spike compactness located in a low-recombination region of hexaploid wheat. This work paves the way for the eventual isolation and characterization of the factor involved but also opens up possibilities to use this approach to precisely map other wheat genes located on proximal parts of wheat chromosomes that show highly reduced recombination. Mapping wheat genes, in the centromeric and pericentromeric regions (~ 2/3rd of a given chromosome), poses a formidable challenge due to highly suppressed recombination. Using an example of compact spike locus (C-locus), this study provides an approach to precisely map wheat genes in the pericentromeric and centromeric regions that house ~ 30% of wheat genes. In club-wheat, spike compactness is controlled by the dominant C-locus, but previous efforts have failed to localize it, on a particular arm of chromosome 2D. We integrated radiation hybrid (RH) and high-resolution genetic mapping to locate C-locus on the short arm of chromosome 2D. Flanking markers of the C-locus span a physical distance of 11.0Mb (231.0-242Mb interval) and contain only 11 high-confidence annotated genes. This work demonstrates the value of this integrated strategy in mapping dominant genes in the low-recombination regions of the wheat genome. A comparison of the mapping resolutions of the RH and genetic maps using common anchored markers indicated that the RH map provides ~ 9 times better resolution that the genetic map even with much smaller population size. This study provides a broadly applicable approach to fine map wheat genes in regions of suppressed recombination.

Fixed Allele Differences Associated With the Centromere Reveal Chromosome Morphology and Rearrangements in a Reptile (Varanus acanthurus BOULENGER).

Chromosome rearrangements are often implicated with genomic divergence and are proposed to be associated with species evolution. Rearrangements alter the genomic structure and interfere with homologous recombination by isolating a portion of the genome. Integration of multiplatform next-generation DNA sequencing technologies has enabled putative identification of chromosome rearrangements in many taxa; however, integrating these data sets with cytogenetics is still uncommon beyond model genetic organisms. Therefore, to achieve the ultimate goal for the genomic classification of eukaryotic organisms, physical chromosome mapping remains critical. The ridge-tailed goannas (Varanus acanthurus BOULENGER) are a group of dwarf monitor lizards comprised of several species found throughout northern Australia. These lizards exhibit extreme divergence at both the genic and chromosomal levels. The chromosome polymorphisms are widespread extending across much of their distribution, raising the question if these polymorphisms are homologous within the V. acanthurus complex. We used a combined genomic and cytogenetic approach to test for homology across divergent populations with morphologically similar chromosome rearrangements. We showed that more than one chromosome pair was involved with the widespread rearrangements. This finding provides evidence to support de novo chromosome rearrangements have occurred within populations. These chromosome rearrangements are characterized by fixed allele differences originating in the vicinity of the centromeric region. We then compared this region with several other assembled genomes of reptiles, chicken, and the platypus. We demonstrated that the synteny of genes in Reptilia remains conserved despite centromere repositioning across these taxa.

CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map.

The arrangement of markers on the genome can be defined in either physical or linkage terms. While a physical map represents the inter-marker distances in base pairs, a genetic (or linkage) map pictures the recombination rate between pairs of markers. High-resolution genetic maps are key elements for genomic research, such as fine-mapping of quantitative trait loci, but they are also needed for creating and updating chromosome-level assemblies of whole-genome sequences. Based on published results on a large pedigree of German Holstein cattle and newly obtained results with German/Austrian Fleckvieh cattle, we aim at providing a platform that allows users to interactively explore the bovine genetic and physical map. We developed the R Shiny app CLARITY available online at https://nmelzer.shinyapps.io/clarity and as R package at https://github.com/nmelzer/CLARITY that provides access to the genetic maps built on the Illumina Bovine SNP50 genotyping array with markers ordered according to the physical coordinates of the most recent bovine genome assembly ARS-UCD1.2. The user is able to interconnect the physical and genetic map for a whole chromosome or a specific chromosomal region and can inspect a landscape of recombination hotspots. Moreover, the user can investigate which of the frequently used genetic-map functions locally fits best. We further provide auxiliary information about markers being putatively misplaced in the ARS-UCD1.2 release. The corresponding output tables and figures can be downloaded in various formats. By ongoing data integration from different breeds, the app also facilitates comparison of different genome features, providing a valuable tool for education and research purposes.

Approaching the mapping limit with closed-loop mapping strategy for deploying neural networks on neuromorphic hardware.

The decentralized manycore architecture is broadly adopted by neuromorphic chips for its high computing parallelism and memory locality. However, the fragmented memories and decentralized execution make it hard to deploy neural network models onto neuromorphic hardware with high resource utilization and processing efficiency. There are usually two stages during the model deployment: one is the logical mapping that partitions parameters and computations into small slices and allocate each slice into a single core with limited resources; the other is the physical mapping that places each logical core to a physical location in the chip. In this work, we propose the mapping limit concept for the first time that points out the resource saving upper limit in logical and physical mapping. Furthermore, we propose a closed-loop mapping strategy with an asynchronous 4D model partition for logical mapping and a Hamilton loop algorithm (HLA) for physical mapping. We implement the mapping methods on our state-of-the-art neuromorphic chip, TianjicX. Extensive experiments demonstrate the superior performance of our mapping methods, which can not only outperform existing methods but also approach the mapping limit. We believe the mapping limit concept and the closed-loop mapping strategy can help build a general and efficient mapping framework for neuromorphic hardware.

Filter functions for the Glauber-Sudarshan P -function regularization

The phase-space quasiprobability distribution formalism for representing quantum states provides practical tools for various applications in quantum optics such as identifying the nonclassicality of quantum states. We study filter functions that are introduced to regularize the Glauber-Sudarshan $P$ function. We show that the quantum map associated with a filter function is completely positive and trace preserving and hence physically realizable if and only if the Fourier transform of this function is a probability density distribution. We also derive a lower bound on the fidelity between the input and output states of a physical quantum filtering map. Therefore, based on these results, we show that any quantum state can be approximated, to arbitrary accuracy, by a quantum state with a regular Glauber-Sudarshan $P$ function. We propose applications of our results for estimating the output state of an unknown quantum process and estimating the outcome probabilities of quantum measurements.

Neighborhood deprivation, built environment, and overweight in adolescents in the city of Oslo

BackgroundEven though the social and built environment characteristics of neighborhoods have been studied as potential determinants of social inequalities in obesity among adults, fewer studies have focused on children. Our first aim was to investigate whether there were differences in the food and physical activity environments between different neighborhood deprivation levels in the city of Oslo. We also explored whether there was an association between the prevalence of overweight (including obesity) among adolescents and (i) neighborhood deprivation levels and (ii) food and physical activity environments of the neighborhoods they live in.MethodsWe conducted a food and physical activity environment mapping (using ArcGIS Pro) in all neighborhoods of Oslo, which were defined by administrative boundaries (sub-districts). The neighborhood deprivation score was calculated based on the percentage of households living in poverty, unemployment in the neighborhood, and residents with low education. A cross-sectional study including 802 seventh graders from 28 primary schools in Oslo residing in 75 out of 97 sub-districts in Oslo was also performed. MANCOVA and partial correlations were ran to compare the built environment distribution between different neighborhood deprivation levels, and multilevel logistic regression analyses were used to explore the effect of neighborhood deprivation and the food and physical activity environments on childhood overweight.ResultsWe found that deprived neighborhoods had greater availability of fast food restaurants and fewer indoor recreational facilities compared to low-deprived neighborhoods. Additionally, we observed that the residential neighborhoods of the adolescents with overweight had greater availability of grocery and convenience stores when compared to the residential neighborhoods of the adolescents without overweight. Adolescents living in neighborhoods with high deprivation had a two-fold higher odds (95% CI = 1.1–3.8) to have overweight compared to adolescents living in neighborhoods with low deprivation, regardless of participants’ ethnicity and parental education. However, the built environment did not determine the relationship between neighborhood deprivation and overweight in adolescents.ConclusionThe neighborhoods in Oslo with higher deprivation levels had more obesogenic characteristics than the low-deprived neighborhoods. Adolescents living in high-deprived neighborhoods were more likely to have overweight than their counterparts from low-deprived neighborhoods. Thus, preventive measures targeting adolescents from high-deprived neighborhoods should be put in place in order to reduce incidence of overweight.