Map Position Research Articles

Development of DNA Markers From Physically Mapped Loci in Aegilops comosa and Aegilops umbellulata Using Single-Gene FISH and Chromosome Sequences.

Breeding of agricultural crops adapted to climate change and resistant to diseases and pests is hindered by a limited gene pool because of domestication and thousands of years of human selection. One way to increase genetic variation is chromosome-mediated gene transfer from wild relatives by cross hybridization. In the case of wheat (Triticum aestivum), the species of genus Aegilops are a particularly attractive source of new genes and alleles. However, during the evolution of the Aegilops and Triticum genera, diversification of the D-genome lineage resulted in the formation of diploid C, M, and U genomes of Aegilops. The extent of structural genome alterations, which accompanied their evolution and speciation, and the shortage of molecular tools to detect Aegilops chromatin hamper gene transfer into wheat. To investigate the chromosome structure and help develop molecular markers with a known physical position that could improve the efficiency of the selection of desired introgressions, we developed single-gene fluorescence in situ hybridization (FISH) maps for M- and U-genome progenitors, Aegilops comosa and Aegilops umbellulata, respectively. Forty-three ortholog genes were located on 47 loci in Ae. comosa and on 52 loci in Ae. umbellulata using wheat cDNA probes. The results obtained showed that M-genome chromosomes preserved collinearity with those of wheat, excluding 2 and 6M containing an intrachromosomal rearrangement and paracentric inversion of 6ML, respectively. While Ae. umbellulata chromosomes 1, 3, and 5U maintained collinearity with wheat, structural reorganizations in 2, 4, 6, and 7U suggested a similarity with the C genome of Aegilops markgrafii. To develop molecular markers with exact physical positions on chromosomes of Aegilops, the single-gene FISH data were validated in silico using DNA sequence assemblies from flow-sorted M- and U-genome chromosomes. The sequence similarity search of cDNA sequences confirmed 44 out of the 47 single-gene loci in Ae. comosa and 40 of the 52 map positions in Ae. umbellulata. Polymorphic regions, thus, identified enabled the development of molecular markers, which were PCR validated using wheat-Aegilops disomic chromosome addition lines. The single-gene FISH-based approach allowed the development of PCR markers specific for cytogenetically mapped positions on Aegilops chromosomes, substituting as yet unavailable segregating map. The new knowledge and resources will support the efforts for the introgression of Aegilops genes into wheat and their cloning.

Newly Identified Hemodynamic Parameter to Predict Thin-Walled Regions of Unruptured Cerebral Aneurysms Using Computational Fluid Dynamics Analysis

The thin-walled regions (TIWRs) of intracranial aneurysms have a high risk of rupture during surgical manipulation. They have been reported to be predicted by wall shear stress and pressure (PS) based on computational fluid dynamics analysis, although this remains controversial. In this study, we investigated whether the oscillatory shear index (OSI) can predict TIWRs. Twenty-five unruptured aneurysms were retrospectively analyzed; the position and orientation of the computational fluid dynamics color maps were adjusted to match the intraoperative micrographs. The red area on the aneurysm wall was defined as TIWR, and if most of the regions on the color map corresponding to TIWR were OSI low (lower quartile range), time-averaged wall shear stress (TAWSS) high, or PS high (upper quartile range), each region was defined as a matched region and divided by the total number of TIWRs to calculate the match rate. In addition, the mean values of OSI, TAWSS, and PS corresponding to TIWRs were quantitatively compared with those in adjacent thick-walled regions. Among 27 TIWRs of 25 aneurysms, 23, 10, and 14 regions had low OSI, high TAWSS, and high PS regions (match rate: 85.2%, 37.0%, and 51.9%), respectively. Receiver operating characteristic curve analysis demonstrated that OSI was the most effective hemodynamic parameter (area under the curve, 0.881), followed by TAWSS (0.798). Multivariate analysis showed that OSI was a significant independent predictor of TIWRs (odds ratio, 18.30 [95% CI, 3.2800-102.00], P < 0.001). OSI may be a unique predictor for TIWRs. Low OSI strongly corresponds with TIWRs of intracranial aneurysms.

An effective method to resolve ambiguous bisulfite-treated reads

BackgroundThe combination of the bisulfite treatment and the next-generation sequencing is an important method for methylation analysis, and aligning the bisulfite-treated reads (BS-reads) is the critical step for the downstream applications. As bisulfite treatment reduces the complexity of the sequences, a large portion of BS-reads might be aligned to multiple locations of the reference genome ambiguously, called multireads. These multireads cannot be employed in the downstream applications since they are likely to introduce artifacts. To identify the best mapping location of each multiread, existing Bayesian-based methods calculate the probability of the read at each position by considering how does it overlap with unique mapped reads. However, sim 25% of multireads are not overlapped with any unique reads, which are unresolvable for existing method.ResultsHere we propose a novel method (EM-MUL) that not only rescues multireads overlapped with unique reads, but also uses the overall coverage and accurate base-level alignment to resolve multireads that cannot be handled by current methods. We benchmark our method on both simulated datasets and real datasets. Experimental results show that it is able to align more than 80% of multireads to the best mapping position with very high accuracy.ConclusionsEM-MUL is an effective method designed to accurately determine the best mapping position of multireads in BS-reads. For the downstream applications, it is useful to improve the methylation resolution on the repetitive regions of genome. EM-MUL is free available at https://github.com/lmylynn/EM-MUL.

Single nucleotide polymorphisms reveal genetic diversity in New Mexican chile peppers (Capsicum spp.)

BackgroundChile peppers (Capsicum spp.) are among the most important horticultural crops in the world due to their number of uses. They are considered a major cultural and economic crop in the state of New Mexico in the United States. Evaluating genetic diversity in current New Mexican germplasm would facilitate genetic improvement for different traits. This study assessed genetic diversity, population structure, and linkage disequilibrium (LD) among 165 chile pepper genotypes using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS).ResultsA GBS approach identified 66,750 high-quality SNP markers with known map positions distributed across the 12 chromosomes of Capsicum. Principal components analysis revealed four distinct clusters based on species. Neighbor-joining phylogenetic analysis among New Mexico State University (NMSU) chile pepper cultivars showed two main clusters, where the C. annuum genotypes grouped together based on fruit or pod type. A Bayesian clustering approach for the Capsicum population inferred K = 2 as the optimal number of clusters, where the C. chinense and C. frutescens grouped in a single cluster. Analysis of molecular variance revealed majority of variation to be between the Capsicum species (76.08 %). Extensive LD decay (~ 5.59 Mb) across the whole Capsicum population was observed, demonstrating that a lower number of markers would be required for implementing genome wide association studies for different traits in New Mexican type chile peppers. Tajima’s D values demonstrated positive selection, population bottleneck, and balancing selection for the New Mexico Capsicum population. Genetic diversity for the New Mexican chile peppers was relatively low, indicating the need to introduce new alleles in the breeding program to broaden the genetic base of current germplasm.ConclusionsGenetic diversity among New Mexican chile peppers was evaluated using GBS-derived SNP markers and genetic relatedness on the species level was observed. Introducing novel alleles from other breeding programs or from wild species could help increase diversity in current germplasm. We present valuable information for future association mapping and genomic selection for different traits for New Mexican chile peppers for genetic improvement through marker-assisted breeding.

Converting single nucleotide variants between genome builds: from cautionary tale to solution.

Next-generation sequencing studies are dependent on a high-quality reference genome for single nucleotide variant (SNV) calling. Although the two most recent builds of the human genome are widely used, position information is typically not directly comparable between them. Re-alignment gives the most accurate position information, but this procedure is often computationally expensive, and therefore, tools such as liftOver and CrossMap are used to convert data from one build to another. However, the positions of converted SNVs do not always match SNVs derived from aligned data, and in some instances, SNVs are known to change chromosome when converted. This is a significant problem when compiling sequencing resources or comparing results across studies. Here, we describe a novel algorithm to identify positions that are unstable when converting between human genome reference builds. These positions are detected independent of the conversion tools and are determined by the chain files, which provide a mapping of contiguous positions from one build to another. We also provide the list of unstable positions for converting between the two most commonly used builds GRCh37 and GRCh38. Pre-excluding SNVs at these positions, prior to conversion, results in SNVs that are stable to conversion. This simple procedure gives the same final list of stable SNVs as applying the algorithm and subsequently removing variants at unstable positions. This work highlights the care that must be taken when converting SNVs between genome builds and provides a simple method for ensuring higher confidence converted data. Unstable positions and algorithm code, available at https://github.com/cathaloruaidh/genomeBuildConversion

Stellar map centroid positioning based on dark channel denoising and feasibility of jitter detection on ZiYuan3 satellite platform

Stellar map denoising and centroid positioning, which directly determine the postpositioning accuracy of star trackers, are key technologies in stellar map processing. Due to the influence of a complex starry sky background, there is often a large amount of noise in stellar maps, which makes it difficult to accurately locate the stellar centroid. A stellar map processing method based on dark channel denoising and continuous multiframe stellar map centroid positioning combined with centroid trajectory constraints is proposed. First, a dark channel noise template is used for denoising, and the single-point and multipoint noises in the denoising result are filtered. Second, in the process of stellar map positioning, if the maximum gray value of the stellar is not unique, it is constrained by the previous stellar positioning result, an adaptive window is established, and the gray-scale centroid weighting method is used to locate the centroid. Then, the star angular distance is used to analyze the precision of the centroid positioning. Finally, the jitter frequency of the satellite platform based on the continuous multiframe centroid positioning result is used to detect satellite attitude. The experimental results show that the performance of dark channel denoising, which can solve many strip noise and background noise problems in stellar maps, is better than that of the existing stellar map denoising method. The centroid positioning results improves the star angular distance by 18.85 arc sec compared with the Gaussian filter and by 8.03 arc sec compared with the global threshold segmentation method, significantly improving the accuracy of stellar map centroid positioning and laying a foundation for improving the star tracker positioning accuracy. A jitter frequency of 0.67 Hz was detected on the ZiYuan3 satellite platform based on the centroid positioning results. It enriches the jitter detection methods and provides a theoretical and technical basis for the design of future high-resolution ground observation remote sensing satellite platforms and geometric accuracy compensation.

Statistical mechanics of dislocation pileups in two dimensions.

Dislocation pileups directly impact the material properties of crystalline solids through the arrangement and collective motion of interacting dislocations. We study the statistical mechanics of these ordered defect structures embedded in two-dimensional crystals, where the dislocations themselves form one-dimensional lattices. In particular, pileups exemplify a new class of inhomogeneous crystals characterized by spatially varying lattice spacings. By analytically formulating key statistical quantities and comparing our theory to numerical experiments using an intriguing mapping of dislocation positions onto the eigenvalues of recently studied random matrix ensembles, we uncover two types of one-dimensional phase transitions in dislocation pileups: A thermal depinning transition out of long-range translational order from the pinned-defect phase, due to a periodic Peierls potential, to a floating-defect state, and finally the melting out of a quasi-long-range ordered floating-defect solid phase to a defect liquid. We also find the set of transition temperatures at which these transitions can be directly observed through the one-dimensional structure factor, where the delta function Bragg peaks, at the pinned-defect to floating-defect transition, broaden into algebraically diverging Bragg peaks, which then sequentially disappear as one approaches the two-dimensional melting transition of the host crystal. We calculate a set of temperature-dependent critical exponents for the structure factor and radial distribution function, and obtain their exact forms for both uniform and inhomogeneous pileups using random matrix theory.

Mapping Positions on Forgiving an Aggressor in Sport.

The objective of the present study was to map amateur athletes’ positions on forgiving an aggressor in sport under various circumstances. One hundred and twenty-eight participants judged forgiveness in 32 scenarios built from combinations of five factors (moral disengagement, intention, consequence, apology, and incentive). Following a cluster analysis, ANOVAs, and chi-squared tests, a three-cluster solution was found: “Mainly Forgive, with Non-Additive Integration,” “Seldom Forgive, with Additive Integration,” and “Moderately Forgive, with Additive Integration.” The clusters’ composition was related to the members’ sex and type of sport. Cluster 1 contained 19% of the women and 32% of the athletes from collision sports. Cluster 2 contained 72% of the men, 53% of the athletes from non-contact sports, and 43% of the athletes from contact sports. Cluster 3 contained 54% of the women, and 58% of the athletes from collision sports.

Vectorial Holograms with Spatially Continuous Polarization Distributions.

Metasurface-based holography presents opportunities for applications that include optical displays, data storage, and optical encryption. Holograms that control polarization are sometimes referred to as vectorial holograms. Most studies on this topic have concerned devices that display different images when illuminated with different polarization states. Fewer studies have demonstrated holographic images whose polarization varies spatially, i.e., as a function of the position within the image. Here, we experimentally demonstrate a vectorial hologram that produces an image with a spatially continuous distribution of polarization states, for the first time to our knowledge. An unlimited number of polarization states can be achieved within the image. Furthermore, the holographic image and its polarization map (polarization vs position in image) are independent. The same image can be thus encoded with different polarization maps. As far as we know, our approach is conceptually new. We anticipate that it could broaden the application scope of metasurface holography.

Expression of Mst89B and CG31287 is Needed for Effective Sperm Storage and Egg Fertilization in Drosophila

In Drosophila, male reproductive fitness can be affected by any number of processes, ranging from development of gametes, transfer to and storage of mature sperm within the female sperm storage organs, and utilization of sperm for fertilization. We have previously identified the 89B cytogenetic map position of D. melanogaster as a hub for genes that effect male paternity success when disturbed. Here, we used RNA interference to test 11 genes that are highly expressed in the testes and located within the 89B region for their role in sperm competition and male fecundity when their expression is perturbed. Testes-specific knockdown (KD) of bor and CSN5 resulted in complete sterility, whereas KD of CG31287, Manf and Mst89B, showed a breakdown in sperm competitive success when second to mate (P2 < 0.5) and reduced fecundity in single matings. The low fecundity of Manf KD is explained by a significant reduction in the amount of mature sperm produced. KD of Mst89B and CG31287 does not affect sperm production, sperm transfer into the female bursa or storage within 30 min after mating. Instead, a significant reduction of sperm in female storage is observed 24 h after mating. Egg hatchability 24 h after mating is also drastically reduced for females mated to Mst89B or CG31287 KD males, and this reduction parallels the decrease in fecundity. We show that normal germ-line expression of Mst89B and CG31287 is needed for effective sperm usage and egg fertilization.

E-money Academic: Lesson from Literature Visualizing Scientometric Positioning (1968-2019)

There is no overview of literature in the area of e-money research which shows the big picture using data from all countries This paper aims to review the status and visual map position of research in the e-money literature indexed Scopus that used a scientometric positioning overview. The research was carried out using bibliometric techniques. Data analysis as well as visualization utilizing VOSViewer program and the Scopus function for analyse search results. In this review, the details collected applied to 3,011 documents issued from 1968 through 2019. The study reveal that Miller, A. and Chinese Academy of Sciences were the most active individual scientists and affiliated institutions in e-money literature. In emoney, computer science and Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics were the most areas of study and dissemination sources. There were nine worldwide group maps with collaborative researchers. In order to identify the body of knowledge created from fifty-one years of literature, this study constructed a convergence axis grouping comprising of e-money: Mobile telecommunication system, Electronic cash system, Finance, Profitability, Investments, Intelligent system, abbreviated as MEFPII themes.

Startup Test Plan and Predictions for Highly Enriched Uranium to Low-Enriched Uranium Fuel Conversion at the University of Missouri Research Reactor

Nonpower reactors licensed by the U.S. Nuclear Regulatory Commission require a startup test plan as part of any facility modification to verify operability prior to resumption of operations. In order to support conversion of the University of Missouri Research Reactor from the use of highly enriched uranium to low-enriched uranium (LEU) fuel, a startup test plan has been devised to measure certain reactor physics parameters for the initial all-fresh LEU core licensing documentation that will be submitted. These parameters include the approach to critical, primary coolant void coefficient of reactivity, flux trap void coefficient of reactivity, determination of flux trap sample reactivity worth, radial and axial thermal neutron flux mapping, control blade worth calibration, primary and pool coolant temperature coefficient of reactivity, and flux mapping of experimental positions. In this paper, predictions for these parameters made using the Monte Carlo N-Particle Version 5 (MCNP5) radiation transport code are reported. These predictions will support the startup tests by providing a baseline set of expectations and additional insight into the performance of the LEU core.

Human activity monitoring based on indoor map positioning

Human activity monitoring based on indoor map positioning

High-Resolution ChIP-MNase Mapping of Nucleosome Positions at Selected Genomic Loci and Alleles.

The positioning of nucleosomes regulates the accessibility of genomic DNA and can impact the activities of functional elements. Nucleosome positioning is highly consistent at each genomic location in any particular cell-type, but can vary in an orchestrated fashion between different cell-types and between genomic loci according to their activities. Here, we describe a technique-"ChIP-MNase" (chromatin immunoprecipitation linked to micrococcal nuclease mapping)-to determine nucleosome positions at chosen sets of genomic features that can be defined by their molecular composition and recovered by chromatin immunoprecipitation. ChIP-MNase enables high-resolution analysis of nucleosome positioning at genomic regions-of-interest and can allow differential analysis of alleles undergoing distinct molecular processes.

Real-Time Eye Tracking for Bare and Sunglasses-Wearing Faces for Augmented Reality 3D Head-Up Displays

Eye pupil tracking is important for augmented reality (AR) three-dimensional (3D) head-up displays (HUDs). Accurate and fast eye tracking is still challenging due to multiple driving conditions with eye occlusions, such as wearing sunglasses. In this paper, we propose a system for commercial use that can handle practical driving conditions. Our system classifies human faces into bare faces and sunglasses faces, which are treated differently. For bare faces, our eye tracker regresses the pupil area in a coarse-to-fine manner based on a revised Supervised Descent Method based eye-nose alignment. For sunglasses faces, because the eyes are occluded, our eye tracker uses whole face alignment with a revised Practical Facial Landmark Detector for pupil center tracking. Furthermore, we propose a structural inference-based re-weight network to predict eye position from non-occluded areas, such as the nose and mouth. The proposed re-weight sub-network revises the importance of different feature map positions and predicts the occluded eye positions by non-occluded parts. The proposed eye tracker is robust via a tracker-checker and a small model size. Experiments show that our method achieves high accuracy and speed, approximately 1.5 and 6.5 mm error for bare and sunglasses faces, respectively, at less than 10 ms on a 2.0GHz CPU. The evaluation dataset was captured indoors and outdoors to reflect multiple sunlight conditions. Our proposed method, combined with AR 3D HUDs, shows promising results for commercialization with low crosstalk 3D images.

Total Placenta Previa with High-risk MAP and Transverse Lie Fetal Position

Placenta accreta is one of the emergency conditions and has resulted in increased mortality and morbidity of pregnant women due to the massive obstetric hemorrhage. Placenta accreta can lead to secondary complications including coagulopathy, multisystem organ failure, acute respiratory distress syndrome, need for repeat surgery, and death. Assessment by anesthesia should be carried out as early as possible before surgery to reduce or even eliminate morbidity and mortality. In this report, we present the case of a patient with total placenta previa and high-risk MAP score with a transverse lie fetal position. The various anesthetic treatments and transfusion strategies are discussed with a multidisciplinary approach to delivery.

Deciphering the Oxygen Absorption Pre‐edge: A Caveat on its Application for Probing Oxygen Redox Reactions in Batteries

The pre‐edges of oxygen‐K X‐ray absorption spectra have been ubiquitous in transition metal (TM) oxide studies in various fields, especially on the fervent topic of oxygen redox states in battery electrodes. However, critical debates remain on the use of the O‐K pre‐edge variations upon electrochemical cycling as evidences of oxygen redox reactions, which has been a popular practice in the battery field. This study presents an investigation of the O‐K pre‐edge of 55 oxides covering all 3d TMs with different elements, structures, and electrochemical states through combined experimental and theoretical analyses. It is shown unambiguously that the O‐K pre‐edge variation in battery cathodes is dominated by changing TM‐d states. Furthermore, the pre‐edge enables a unique opportunity to project the lowest unoccupied TM‐d states onto one common energy window, leading to a summary map of the relative energy positions of the low‐lying TM states, with higher TM oxidation states at lower energies, corresponding to higher electrochemical potentials. The results naturally clarify some unusual redox reactions, such as Cr3+/6+. This work provides a critical clarification on O‐K pre‐edge interpretation and more importantly a benchmark database of O‐K pre‐edge for characterizing redox reactions in batteries and other energy materials.

Vascular cognitive impairment due to dilated perivascular spaces in putamen: Connections with the ventrolateral prefrontal cortex and neurological deficits

AbstractBackgroundAnatomical studies in animals have described multiple striatal circuits and suggested that sub‐components of the striatum project to distinct cortical areas. Researchers that reconstructed tracts of the left and right putamen have shown ipsilateral projections to the primary motor area, primary somatosensory area, supplementary motor area, premotor area, cerebellum, thalamus and prefrontal cortex (specifically to the ventrolateral prefrontal cortex). The ventrolateral prefrontal cortex appears to have a specific role in spatial processing and memory retrieval.MethodCase report and analyses of MR Images (T1, T2 and Flair) of a patient presenting with vascular cognitive impairment due to dilated perivascular spaces in putamen bilaterally.ResultMale patient, 81 years‐old, right‐handed, with four years of formal education and high cerebrovascular risk. His cognitive complaints began twelve years ago, and worsened in the last two years (losing personal belongings inside his own house, sometimes forgetting names of well‐known persons, with word finding difficulties). He denied impairment in activities of daily living, was able to organize his home budget, take his medications and go to the market alone. Now, he is physically and intellectually active (walking, reading newspapers, and talking about Philosophy), and still drives cars. His CDR score is 0.5, and his MMSE score is 29 (with 3 points in evoked memory). Word List Memory Task (Immediate Recall):4/5/8 (intrusion of "vessel" in the first two lists); Evocation:6 (intrusion of "vessel"); Recognition:10; Verbal Fluency (Animals):20; Verbal Fluency (Fruits):9. MR (10/15/2018): mild supratentorial microangiopathy; encephalomalacia/gliosis in the vermis and the left cerebellar hemisphere; Fasekas = 1 / Scheltens = 1 (bilaterally); bilateral supratentorial dilated perivascular spaces, particularly in the putamen.ConclusionOur patient does not have dementia, regardless of more than ten years of cognitive impairment. Bilateral dilated perivascular spaces in the putamen may cause deficits in memory retrieval and spatial processing. Neuropsychological evaluations must consider specific areas of brain injury. Our patient has impaired memory retrieval (with false memories verified by constant intrusions in the Word List Memory Task), and the high occurrence of losing personal belongings inside his house can be due to difficulties in spatial processing (mental map of positions of items in space).

Customer acceptance of ride-hailing in Indonesia

PurposeThe purpose of this paper is to investigate the enabling factors and the customers’ acceptance of ride-hailing in Indonesia.Design/methodology/approachThe authors adopt some constructs from the unified theory of acceptance and use of technology (UTAUT) 2 as the framework for the study to derive factors that influence the acceptance of ride-hailing in Indonesia. Samples through a convenience sampling method were collected from an online survey and were transformed into data through coding and subsequently processed using SPSS for descriptive analysis, reliability test, correlation and multiple regression analysis for hypothesis testing.FindingsRide-hailing started in 2015 in Indonesia. Five enabling factors make digital ride-hailing possible, the internet, smartphone, broadband wireless network, digital map and global positioning system. The authors found that performance expectancy, social influence and habit positively influence customers to accept ride-hailing in Indonesia.Research limitations/implicationsAlthough this research has a small sample, it is still relevant to understand people’s acceptance to the ride-hailing platform. As a ride-hailing platform is now transformed to a multisided markets platform, adoption studies or other studies on each market to cover the whole picture of the platform influence to the society, and its contribution to the national economy will be very interesting. The authors’ future research will cover various services covered by ride-hailing companies.Originality/valueThis study proposes and argues that four main enabling factors make digital ride-hailing a viable business. The study contributes to three significant factors that influence the acceptance of ride-hailing in Indonesia.

Investigating the accuracy of imputing autosomal variants in Nellore cattle using the ARS-UCD1.2 assembly of the bovine genome

BackgroundImputation accuracy among other things depends on the size of the reference panel, the marker’s minor allele frequency (MAF), and the correct placement of single nucleotide polymorphism (SNP) on the reference genome assembly. Using high-density genotypes of 3938 Nellore cattle from Brazil, we investigated the accuracy of imputation from 50 K to 777 K SNP density using Minimac3, when map positions were determined according to the bovine genome assemblies UMD3.1 and ARS-UCD1.2. We assessed the effect of reference and target panel sizes on the pre-phasing based imputation quality using ten-fold cross-validation. Further, we compared the reliability of the model-based imputation quality score (Rsq) from Minimac3 to the empirical imputation accuracy.ResultsThe overall accuracy of imputation measured as the squared correlation between true and imputed allele dosages (R2dose) was almost identical using either the UMD3.1 or ARS-UCD1.2 genome assembly. When the size of the reference panel increased from 250 to 2000, R2dose increased from 0.845 to 0.917, and the number of polymorphic markers in the imputed data set increased from 586,701 to 618,660. Advantages in both accuracy and marker density were also observed when larger target panels were imputed, likely resulting from more accurate haplotype inference. Imputation accuracy increased from 0.903 to 0.913, and the marker density in the imputed data increased from 593,239 to 595,570 when haplotypes were inferred in 500 and 2900 target animals. The model-based imputation quality scores from Minimac3 (Rsq) were systematically higher than empirically estimated accuracies. However, both metrics were positively correlated and the correlation increased with the size of the reference panel and MAF of imputed variants.ConclusionsAccurate imputation of BovineHD BeadChip markers is possible in Nellore cattle using the new bovine reference genome assembly ARS-UCD1.2. The use of large reference and target panels improves the accuracy of the imputed genotypes and provides genotypes for more markers segregating at low frequency for downstream genomic analyses. The model-based imputation quality score from Minimac3 (Rsq) can be used to detect poorly imputed variants but its reliability depends on the size of the reference panel and MAF of the imputed variants.