Identification of novel soybean oil content-related genes using QTL-based collinearity analysis from the collective soybean genome

Soybean is a global principal source of edible plant oil. As more soybean oil-related quantitative trait loci(QTLs) have been located in the collective genome, it is urgent to establish a classification system for these distributed QTLs. A collinear platform may be useful to characterize and identify relationships among QTLs as well as aid in novel gene discovery. In this study, the collinearity MCScan X algorithm and collective soybean genomic information were used to construct collinearity blocks, to which soybean oil-related QTLs were mapped. The results demonstrated that 666 collinearity blocks were detected in the soybean genome across 20 chromosomes, and 521 collinearity relationships existed in 231 of the 242 effective soybean oil-related QTLs. This included 214 inclusion relationships and 307 intersecting relationships. Among them, the collinearity among QTLs that are related to soybean oil content was shown on a maximum of seven chromosomes and minimum of one chromosome, with the majority of QTLs having collinearity on two chromosomes. Using overlapping hotspot regions in the soybean oil QTLs with collinearity, we mined for novel oil content-related genes. Overall, we identified 23 putatively functional genes associated with oil content in soybean and annotated them using a number of annotation databases. Our findings provide a valuable framework for elucidating evolutionary relationships between soybean oil-related QTLs and lay a foundation for functional marker-assisted breeding relating to soybean oil content.

On the Performances of Classical VAR and Sims-Zha Bayesian VAR Models in the Presence of Collinearity and Autocorrelated Error Terms

In time series literature, many authors have found out that multicollinearity and autocorrelation usually afflict time series data. In this paper, we compare the performances of classical VAR and Sims-Zha Bayesian VAR models with quadratic decay on bivariate time series data jointly influenced by collinearity and autocorrelation. We simulate bivariate time series data for different collinearity levels (﹣0.99, ﹣0.95, ﹣0.9, ﹣0.85, ﹣0.8, 0.8, 0.85, 0.9, 0.95, 0.99) and autocorrelation levels (﹣0.99, ﹣0.95, ﹣0.9, ﹣0.85, ﹣0.8, 0.8, 0.85, 0.9, 0.95, 0.99) for time series length of 8, 16, 32, 64, 128, 256 respectively. The results from 10,000 simulations reveal that the models performance varies with the collinearity and autocorrelation levels, and with the time series lengths. In addition, the results reveal that the BVAR4 model is a viable model for forecasting. Therefore, we recommend that the levels of collinearity and autocorrelation, and the time series length should be considered in using an appropriate model for forecasting.

Toward Circumventing Collinearity Effect in Nonlinear Spectral Mixture Analysis by Using a Spectral Shape Measure

Nonlinear spectral mixture analysis (NSMA) is a widely used unmixing algorithm. It can fit the mixed spectra adequately, but collinearity effect among true and virtual endmembers will decrease the retrieval accuracies of endmember fractions. Use of linear spectral mixture analysis (LSMA) can effectively reduce the degree of collinearity in the NSMA. However, the inadequate modeling of mixed spectra in the LSMA will also yield retrieval errors, especially for the cases where the multiple scattering is not ignorable. In this study, a generalized spectral unmixing scheme based on a spectral shape measure, i.e. spectral information divergence (SID), was applied to overcome the limitations of the conventional NSMA and LSMA. Two simulation experiments were undertaken to test the performances of the SID, LSMA and NSMA in the mixture cases of treesoil, tree-concrete and tree-grass. Results demonstrated that the SID yielded higher accuracies than the LSMA for almost all the mixture cases in this study. On the other hand, performances of the SID method were comparable with the NSMA for the tree-soil and tree-grass mixture cases, but significantly better than the NSMA for the tree-concrete mixture case. All the results indicate that the SID method is fairly effective to circumvent collinearity effect within the NSMA, and compensate the inadequate modeling of mixed spectra within the LSMA.

A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference versions.Demands for clade-specific homology inference and analysis have increased in the pangenomic era.Here we present a novel method,GeneTribe(https://chenym1.github.io/genetribe/),for homology inference among genetically similar genomes that incorporates gene collinearity and shows bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and scalability.The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and rye.We built Triticeae-GeneTribe(http://wheat.cau.edu.cn/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions.With macrocollinearity analysis,we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events.With collinearity analysis at both the macro-and microscale,we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vm2,which evolved as a combined result of genome translocation,duplication,and polyploidization and gene loss events.Our work provides a useful practice for connecting emerging genome assemblies,with awareness of the extensive polyploidy in plants,and will help researchers efficiently exploit genome sequence re-sources.

Ultrafast dynamics of femtosecond laser-induced high spatial frequency periodic structures on silicon surfaces

Femtosecond laser-induced periodic surface structures(LIPSS)have been extensively studied over the past few decades.In particular,the period and groove width of high-spatial-frequency LIPSS(HSFL)is much smaller than the diffraction limit,making it a useful method for efficient nanomanufacturing.However,compared with the low-spatial-frequency LIPSS(LSFL),the structure size of the HSFL is smaller,and it is more easily submerged.Therefore,the formation mechanism of HSFL is complex and has always been a research hotspot in this field.In this study,regular LSFL with a period of 760 nm was fabricated in advance on a silicon surface with two-beam interference using an 800 nm,50 fs femtosecond laser.The ultrafast dynamics of HSFL formation on the silicon surface of prefabricated LSFL under single femtosecond laser pulse irradiation were observed and analyzed for the first time using collinear pump-probe imaging method.In general,the evolution of the surface structure undergoes five sequential stages:the LSFL begins to split,becomes uniform HSFL,degenerates into an irregular LSFL,undergoes secondary splitting into a weakly uniform HSFL,and evolves into an irregular LSFL or is submerged.The results indicate that the local enhancement of the submerged nanocavity,or the nanoplasma,in the prefabricated LSFL ridge led to the splitting of the LSFL,and the thermodynamic effect drove the homogenization of the splitting LSFL,which evolved into HSFL.

Application of Nonlinear Lamb Wave Mixing Method for Residual Stress Measurement in Metal Plate

Harmonic nonlinear ultrasound can offer high sensitivity for residual stress measurements;however,it cannot be used for local stress measurements at a point in space and exhibits nonlinear distortions in the experimental system.This paper presents a feasibility study on the measurement of residual stress in a metal plate using a nonlinear Lamb wave-mixing technique.The resonant conditions for two Lamb waves to generate a mixing frequency wave are obtained via theoretical analysis.Finite element simulations are performed to investigate the nonlinear interactions between the two Lamb waves.Results show that two incident A0 waves interact in regions of material nonlinearity and generate a rightward S0 wave at the sum frequency.Residual stress measurement experiments are conducted on steel plate specimens using the collinear Lamb wave-mixing technique.By setting different delays for two transmitters,the generated sum-frequency component at different spatial locations is measured.Experimental results show that the spatial distribution of the amplitude of the sum-frequency component agrees well with the spatial distribution of the residual stress measured using X-rays.The proposed collinear Lamb wave-mixing method is effective for measuring the distribution of residual stress in metal plates.

Control and data acquisition system for collinear laser spectroscopy experiments

A control and data acquisition system was implemented for the recently developed collinear laser spectroscopy setup.This system is dedicated to data recording,storage,processing,monitoring of the beam intensity and energy,and visualization of various spectra.In comparison to the conventional resonance nuclear reaction system,the key technique is the precise synchronization of the detected counts with the actual scanning voltage(or probing laser frequency).The functions of the system were tested by measuring the hyperfine structure spectra of stable calcium(e.g.,^(40)Ca^(+))and radioactive potassium(e.g.,^(38)K)in the bunched and continuous modes,respectively.This system will be routinely applied and further improved in subsequent laser spectroscopy experiments on unstable isotopes at the Beijing Radioactive Ion-beam Facility(BRIF).

Genome-wide analysis of expansins and their role in fruit spine development in cucumber(Cucumis sativus L.)

Cucumber is one of the most widely consumed vegetables worldwide,and the fruit spine is an important fruit quality trait.Expansins play critical roles in fruit development;however,the regulation of expansins in cucumber fruit spine development has not been reported.In this study,33 expansin genes were identified in the cucumber genome V3;additionally,expansin genes in Citrullus lanatus,Cucumis melo,Cucurbita maxima,Lagenaria siceraria,and Benincasa hispida were also identified.Phylogenetic analysis of expansin proteins in Cucurbitaceae and Arabidopsis showed that they evolved separately in each plant species.Phylogenetic analysis showed that C.maxima was derived earlier than the other five Cucurbitaceae species.The expression of CsEXPA2,CsEXPA14,and CsEXLA3 varied in cucumber lines with different fruit spine densities.A yeast two-hybrid assay showed that a putative auxin transporter encoded by numerous spine gene(ns)interacts with CsEXLA2,which may be involved in the development of the numerous spines in cucumber.These results provide novel insights into the expansins related to plant development and fruit spine development in cucumber.

BUNDLE ADJUSTMENTS CCD CAMERA CALIBRATION BASED ON COLLI NEARITY EQUATION

The solid template CCD camera calibration method of bundle adjustments basedon collinearity equation is presented considering the characteristics of space large-dimensionon-line measurement. In the method, a more comprehensive camera model is adopted which is based onthe pinhole model extended with distortions corrections. In the process of calibration, calibrationprecision is improved by imaging at different locations in the whole measurement space,multi-imaging at the same location and bundle adjustments optimization. The calibration experimentproves that the calibration method is able to fulfill calibration requirement of CCD camera appliedto vision measurement.

Genome-wide identification of Gossypium INDETERMINATE DOMAIN genes and their expression profiles in ovule development and abiotic stress responses

Background:INDETERMINATE DOMAIN(IDD)transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development,such as flower induction in term of flowering control.Till date,systematic and functional analysis of IDD genes remained infancy in cotton.Results:In this study,we identified total of 162 IDD genes from eight different plant species including 65 IDD genes in Gossypium hirsutum.Phylogenetic analysis divided IDDs genes into seven well distinct groups.The gene structures and conserved motifs of GhIDD genes depicted highly conserved exon-intron and protein motif distribution patterns.Gene duplication analysis revealed that among 142 orthologous gene pairs,54 pairs have been derived by segmental duplication events and four pairs by tandem duplication events.Further,Ka/Ks values of most of orthologous/paralogous gene pairs were less than one suggested the purifying selection pressure during evolution.Spatiotemporal expression pattern by qRT-PCR revealed that most of the investigated GhIDD genes showed higher transcript levels in ovule of seven days post anthesis,and upregulated response under the treatments of multiple abiotic stresses.Conclusions:Evolutionary analysis revealed that IDD gene family was highly conserved in plant during the rapid phase of evolution.Whole genome duplication,segmental as well as tandem duplication significantly contributed to the expansion of IDD gene family in upland cotton.Some distinct genes evolved into special subfamily and indicated potential role in the allotetraploidy Gossypium hisutum evolution and development High transcript levels of GhIDD genes in ovules illustrated their potential roles in seed and fiber development Further,upregulated responses of GhIDD genes under the treatments of various abiotic stresses suggested them as important genetic regulators to improve stress resistance in cotton breeding.

Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

ZAT(Zinc Finger of Arabidopsis thaliana)proteins are composed of a plant-specific transcription factor family,which play an important role in plant growth,development,and stress resista nee.To study the potential function of ZAT family in cotton,the whole genome identification,expression,and structure analysis of ZAT gene family were carried out.In this study,our analysis revealed the presenee of 115Z 56,59,and 115 ZAT genes in Gossypium hirsutum,G raimondii,G.arboreum and G barbadense,respectively.According to the number of domains and phylogenetic characteristics,we divided ZAT genes of four Gossypium species into 4 different clades,and further divided them into 11 subfamilies.The results of collinearity an alysis showed that segmental duplicati on was the main method to amplify the cotton ZAT genes family.Analysis of c/s-elements of promoters indicated that most GhZAT genes contained c/5-elements related to plant hormones and abiotic stress.According to heatmap analysis,the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold,heat,salt,and PEG stress,possibly through different mechanisms.Among the highly expressed genes,we cloned a G hirsutum gene GhZAT67.Through virus-induced gene silencing(VIGS),we found that its expression level decreased significantly after being sileneed.Under alkaline treatment,the wilting degree of silenced plants was even greater than the wild type,which proved that GhZAT67 gene was involved in the response to alkaline stress.

Vehicle Positioning Based on Optical Camera Communication in V2I Environments

Demand for precise vehicle positioning(VP)increases as autonomous vehicles have recently been drawing attention.This paper proposes a scheme for positioning vehicles on the move based on optical camera communication(OCC)technology in the vehicle-to-infrastructure(V2I)environment.Light-emitting diode(LED)streetlights and vehicle cameras are used as transmitters and receivers respectively.Regions of streetlights are detected and traced by examining images that are obtained from cameras of vehicles.Then,a scheme for analyzing visible light data extracted from the images is proposed.The proposed vehicle positioning scheme uses information on angles between vectors that are formed under the collinearity conditions between the absolute coordinates of at least three received streetlights,and the coordinates of an image sensor.The experiments are performed under stationary state and moving state at a speed of 5 and 20 km/h.To verify the reliability of the proposed scheme,a comparison is made between the actual and estimated location of the camera in the stationary state.In addition,the path of a moving vehicle and the estimated path of the vehicle are compared to check the performance of the scheme.The performance of the proposed technique is analyzed and experimental demonstration confirms that the proposed OCC-based VP scheme achieves positioning accuracy of under 1 m.

Functional structure analysis and genome‑wide identification of CNX gene family in cotton

Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stressrelated candidate genes.Results:A total of 60 CNX family members have been identified in Gossypium hirsutum,G.barbadense,G.arboreum,and G.raimondii,and they were divided into two categories:CNX and CRT genes.Through the construction of a phylogenetic tree,they were subdivided into three classes.Further analysis of chromosome localization,conserved promoters,gene structure and selection under pressure showed that the family members were highly conserved in the evolution process.Analysis of cis-acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development,anaerobic,drought,defense and stress response,and plant hormones.Using RNA-seq data to study the expression pattern of GhCNX genes under cold,hot,salt stress and Polyethylene glycol,it was observed that the gene expression levels changed by different degrees under different stress conditions,indicating that GhCNX members were involved in the regulation of multiple biological stresses.Conclusion:This study provides an insight into the members of cotton CNX genes.The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.

Short Term Forecasting Performances of Classical VAR and Sims-Zha Bayesian VAR Models for Time Series with Collinear Variables and Correlated Error Terms

Forecasts can either be short term, medium term or long term. In this work we considered short term forecast because of the problem of limited data or time series data that is often encounter in time series analysis. This simulation study considered the performances of the classical VAR and Sims-Zha Bayesian VAR for short term series at different levels of collinearity and correlated error terms. The results from 10,000 iteration revealed that the BVAR models are excellent for time series length of T=8 for all levels of collinearity while the classical VAR is effective for time series length of T=16 for all collinearity levels except when ρ = -0.9 and ρ = -0.95. We therefore recommended that for effective short term forecasting, the time series length, forecasting horizon and the collinearity level should be considered.

Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly

Introduction:Genome sequence plays an important role in both basic and applied studies.Gossypium raimondii,the putative contributor of the D subgenome of upland cotton(G.hirsutum,highlights the need to improve the genome quality rapidly and efficiently.Methods:We performed Hi-C sequencing of G.raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds.We also compared the reassembled genome sequenee with the previously published G raimondii genomes for gene and genome sequence collinearity.Result:A total of 9842%of scaffold sequences were clustered successfully,among which 99.72%of the clustered sequences were ordered and 99.92%of the ordered sequences were oriented with high-quality.Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than the previous one(Nat Genet 44:98-1103,2012).Conclusion:This improvement in G raimondii genome not only provides a better reference to increase study efficiency but also offers a new way to assemble cotton genomes.Furthermore,Hi-C data of G.raimondii may be used for 3D structure research or regulating analysis.

Rank-Ordering of Topographic Variables Correlated with Temperature

Spatial variations in temperature may be ascribed to many variables. Among these, variables pertaining to topography are prominent. Thus various topographic variables were calculated from 50 m-resolution digital terrain models (DTMs) for three study areas in France and for Slovenia. The “classic” geomatic variables (altitude, aspect, gradient, etc.) are supplemented by the description of landforms (amplitude of humps and hollows). Special care is taken in managing collinearity among variables and building windows with different dimensions. Statistical processing involves linear regressions of daily temperatures taken as the response variables and six topographic variables (explanatory variables). Altitude accounts significantly for the spatial variation in temperatures in 90% of cases, except in the Gironde, a lowlying area (50%). The scale of landforms also appears to be highly correlated to the measured temperature. Variations in the frequency with which topographic descriptors account for temperatures are examined from several standpoints. Altitude is less frequently taken as an explanatory variable for spatial variation of temperatures in winter (75%) than in spring (80%) and late summer (85%). Minimum temperatures are influenced on average much more by the amplitude of humps and hollows (56%) than maximum temperatures (38%) are. The frequency with which these two landforms account for the spatial variation of temperature is reversed between the minima and maxima.

Exact analytic solutions for an elliptic hole with asymmetric collinear cracks in a one-dimensional hexagonal quasi-crystal

Using the complex variable function method and the technique of conformal mapping, the anti-plane shear problem of an elliptic hole with asymmetric colfinear cracks in a one-dimensional hexagonal quasi-crystal is solved, and the exact analytic solutions of the stress intensity factors （SIFs） for mode Ⅲ problem are obtained. Under the limiting conditions, the present results reduce to the Griffith crack and many new results obtained as well, such as the circular hole with asymmetric collinear cracks, the elliptic hole with a straight crack, the mode T crack, the cross crack and so on. As far as the phonon field is concerned, these results, which play an important role in many practical and theoretical applications, are shown to be in good agreement with the classical results.

Commissioning of a high-resolution collinear laser spectroscopy apparatus with a laser ablation ion source

Collinear laser spectroscopy is a powerful tool for studying the nuclear spins,electromagnetic moments,and charge radii of exotic nuclei.To study the nuclear properties of unstable nuclei at the Beijing Radioactive Ion-beam Facility(BRIF)and the future High Intensity Heavy-ion Accelerator Facility(HIAF),we developed a collinear laser spectroscopy apparatus integrated with an offline laser ablation ion source and a laser system.The overall performance of this state-of-the-art technique was evaluated,and the system was commissioned using a bunched stable ion beam.The high-resolution optical spectra for the 4s ^(2)S_(1/2)→4p^(2)P_(3/2)(D2)ionic transition of ^(40;42;44;48)Ca isotopes were successfully measured.The extracted isotope shifts relative to ^(40)Ca showed excellent agreement with the literature values.This system is now ready for use at radioactive ion beam facilities such as the BRIF and paves the way for the further development of higher-sensitivity collinear resonance ionization spectroscopy techniques.

Physical analysis on improving the recovery accuracy of the Earth's gravity field by a combination of satellite observations in along-track and cross-track directions

The physical investigations on the accuracy improvement to the measurement of the Earth＇s gravity field recovery are carried out based on the next-generation Pendulum-A/B out-of-plane twin-satellite formation in this paper. Firstly, the Earth＇s gravity field complete up to degree and order 100 is, respectively, recovered by the collinear and pendulum satellite formations using the orbital parameters of the satellite and the matching accuracies of key payloads from the twin GRACE satellites. The research results show that the accuracy of the Earth＇s gravity field model from the Pendulum-A/B satellite formation is about two times higher than from the collinear satellite formation, and the further improvement of the determination accuracy of the Earth＇s gravity field model is feasible by the next-generation Pendulum-A/B out-of-plane twin-satellite formation. Secondly, the Earth＇s gravity field from Pendulum-A/B complete up to degree and order 100 is accurately recovered based on the orbital parameters of the satellite （e.g., an orbital altitude of 400 km, an intersatellite range of 100 km, an orbital inclination of 89° and an orbital eccentricity of 0.001）, the matching accuracies of space- borne instruments （e.g. 10-6 m in the intersatellite range, 10-3 m in the orbital position, 10-6 m/s in orbital velocity, and 10-11 m/s2 in non-conservative force）, an observation time of 30 days and a sampling interval of 10 s. The measurement accuracy of the Earth＇s gravity field from the next-generation Pendulum-A/B out-of-plane twin-satellite formation is full of promise for being improved by about l0 times compared with that from the current GRACE satellite formation. Finally, the physical requirements for the next-generation Pendulum-A/B out-of-plane twin-satellite formation are analyzed, and it is proposed that the satellite orbital altitude be preferably designed to be close to 400±50 km and the matching precision of key sensors from the Pendulum-A/B mission be about one order of magnitude higher than from the GRACE program.

The global mean sea surface model WHU2013

The mean sea surface （MSS） model is an important reference for the study of charting datum and sea level change. A global MSS model named WHU2013, with 2′ × 2′ spatial resolution between 80° S and 84°N, is established in this paper by combining nearly 20 years of multi-satellite altimetric data that include Topex/Poseidon （T/P）, Jason-1, Jason-2, ERS-2, ENVISAT and GFO Exact Repeat Mission （ERM） data, ERS-1/168, Jason-1/C geodetic mission data and Cryosat-2 low resolution mode （LRM） data. All the ERM data are adjusted by the collinear method to achieve the mean along-track sea surface height （SSH）, and the combined dataset of T/P, Jason-1 and Jason-2 from 1993 to 2012 after collinear adjustment is used as the reference data. The sea level variations in the non-ERM data （geodetic mission data and LRM data） are mainly investigated, and a combined method is proposed to correct the sea level variations between 66°S and 66°N by along-track sea level variation time series and beyond 66°S or 66°N by seasonal sea level variations. In the crossover adjustment between multi-altimetric data, a stepwise method is used to solve the problem of inconsistency in the reference data between the high and low latitude regions. The proposed model is compared with the CNES-CLS2011 and DTU13 MSS models, and the standard derivation （STD） of the differences between the models is about S cm between 80°S and 84°N, less than 3 cm between 66°S and 66°N, and less than 4 cm in the China Sea and its adjacent sea. Furthermore, the three models exhibit a good agreement in the SSH differences and the along-track gradient of SSH following comparisons with satellite altimetry data.