Genome-wide prediction for hybrids between parents with distinguished difference on exotic introgressions in Brassica napus

Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis.The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions.We evaluated seed yield,seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments.The hybrids presented strong heterosis on seed yield,which was much higher than other investigated traits.Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive,dominance,and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids.The analysis showed that the trait complexity,exotic introgression,genetic relationship between the training set and testing set,training set size,and environments affected the prediction ability.The models with best prediction ability for different traits varied.However,relatively high prediction ability (e.g.,0.728 for seed yield) was also observed when the simplest models were used,excluding the effects of the special exotic introgression and epistasis effect by5-fold cross validation,which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression.The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.

Genome-wide prediction in a hybrid maize population adapted to Northwest China

Genome-wide prediction is a promising approach to boost selection gain in hybrid breeding.Our main objective was to evaluate the potential and limits of genome-wide prediction to identify superior hybrid combinations adapted to Northwest China.A total of 490 hybrids derived from crosses among 119 inbred lines from the Shaan A and Shaan B heterotic pattern were used for genome-wide prediction of ten agronomic traits.We tested eight different statistical prediction models considering additive(A)effects and in addition evaluated the impact of dominance(D)and epistasis(E)on the prediction ability.Employing five-fold cross validation,we show that the average prediction ability ranged from 0.386 to 0.794 across traits and models.Six parametric methods,i.e.ridge regression,LASSO,Elastic Net,Bayes B,Bayes C and reproducing kernel Hilbert space(RKHS)approach,displayed a very similar prediction ability for each trait and two non-parametric methods(random forest and support vector machine)had a higher prediction performance for the trait rind penetrometer resistance of the third internode above ground(RPR_TIAG).The models of A+D RKHS and A+D+E RKHS were slightly better for predicting traits with a relatively high non-additive variance.Integrating trait-specific markers into the A+D RKHS model improved the prediction ability of grain yield by 3%,from 0.528 to 0.558.Of all 6328 potential hybrids,selection of the top 44 hybrids would lead to a 6%increase in grain yield compared with Zhengdan 958,a commercially successful hybrid variety.In conclusion,our results substantiate the value of genome-wide prediction for hybrid breeding and suggest dozens of promising single crosses for developing high-yielding hybrids for Northwest China.

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

Prediction model for corrosion rate of low-alloy steels under atmospheric conditions using machine learning algorithms

This work constructed a machine learning(ML)model to predict the atmospheric corrosion rate of low-alloy steels(LAS).The material properties of LAS,environmental factors,and exposure time were used as the input,while the corrosion rate as the output.6 dif-ferent ML algorithms were used to construct the proposed model.Through optimization and filtering,the eXtreme gradient boosting(XG-Boost)model exhibited good corrosion rate prediction accuracy.The features of material properties were then transformed into atomic and physical features using the proposed property transformation approach,and the dominant descriptors that affected the corrosion rate were filtered using the recursive feature elimination(RFE)as well as XGBoost methods.The established ML models exhibited better predic-tion performance and generalization ability via property transformation descriptors.In addition,the SHapley additive exPlanations(SHAP)method was applied to analyze the relationship between the descriptors and corrosion rate.The results showed that the property transformation model could effectively help with analyzing the corrosion behavior,thereby significantly improving the generalization ability of corrosion rate prediction models.

A Physics-informed Deep-learning Intensity Prediction Scheme for Tropical Cyclones over the Western North Pacific

Accurate prediction of tropical cyclone(TC)intensity is challenging due to the complex physical processes involved.Here,we introduce a new TC intensity prediction scheme for the western North Pacific(WNP)based on a time-dependent theory of TC intensification,termed the energetically based dynamical system(EBDS)model,together with the use of a long short-term memory(LSTM)neural network.In time-dependent theory,TC intensity change is controlled by both the internal dynamics of the TC system and various environmental factors,expressed as environmental dynamical efficiency.The LSTM neural network is used to predict the environmental dynamical efficiency in the EBDS model trained using besttrack TC data and global reanalysis data during 1982–2017.The transfer learning and ensemble methods are used to retrain the scheme using the environmental factors predicted by the Global Forecast System(GFS)of the National Centers for Environmental Prediction during 2017–21.The predicted environmental dynamical efficiency is finally iterated into the EBDS equations to predict TC intensity.The new scheme is evaluated for TC intensity prediction using both reanalysis data and the GFS prediction data.The intensity prediction by the new scheme shows better skill than the official prediction from the China Meteorological Administration(CMA)and those by other state-of-art statistical and dynamical forecast systems,except for the 72-h forecast.Particularly at the longer lead times of 96 h and 120 h,the new scheme has smaller forecast errors,with a more than 30%improvement over the official forecasts.

ST-LSTM-SA:A New Ocean Sound Velocity Field Prediction Model Based on Deep Learning

The scarcity of in-situ ocean observations poses a challenge for real-time information acquisition in the ocean.Among the crucial hydroacoustic environmental parameters,ocean sound velocity exhibits significant spatial and temporal variability and it is highly relevant to oceanic research.In this study,we propose a new data-driven approach,leveraging deep learning techniques,for the prediction of sound velocity fields(SVFs).Our novel spatiotemporal prediction model,STLSTM-SA,combines Spatiotemporal Long Short-Term Memory(ST-LSTM) with a self-attention mechanism to enable accurate and real-time prediction of SVFs.To circumvent the limited amount of observational data,we employ transfer learning by first training the model using reanalysis datasets,followed by fine-tuning it using in-situ analysis data to obtain the final prediction model.By utilizing the historical 12-month SVFs as input,our model predicts the SVFs for the subsequent three months.We compare the performance of five models:Artificial Neural Networks(ANN),Long ShortTerm Memory(LSTM),Convolutional LSTM(ConvLSTM),ST-LSTM,and our proposed ST-LSTM-SA model in a test experiment spanning 2019 to 2022.Our results demonstrate that the ST-LSTM-SA model significantly improves the prediction accuracy and stability of sound velocity in both temporal and spatial dimensions.The ST-LSTM-SA model not only accurately predicts the ocean sound velocity field(SVF),but also provides valuable insights for spatiotemporal prediction of other oceanic environmental variables.

Assessments of Data-Driven Deep Learning Models on One-Month Predictions of Pan-Arctic Sea Ice Thickness

In recent years,deep learning methods have gradually been applied to prediction tasks related to Arctic sea ice concentration,but relatively little research has been conducted for larger spatial and temporal scales,mainly due to the limited time coverage of observations and reanalysis data.Meanwhile,deep learning predictions of sea ice thickness(SIT)have yet to receive ample attention.In this study,two data-driven deep learning(DL)models are built based on the ConvLSTM and fully convolutional U-net(FC-Unet)algorithms and trained using CMIP6 historical simulations for transfer learning and fine-tuned using reanalysis/observations.These models enable monthly predictions of Arctic SIT without considering the complex physical processes involved.Through comprehensive assessments of prediction skills by season and region,the results suggest that using a broader set of CMIP6 data for transfer learning,as well as incorporating multiple climate variables as predictors,contribute to better prediction results,although both DL models can effectively predict the spatiotemporal features of SIT anomalies.Regarding the predicted SIT anomalies of the FC-Unet model,the spatial correlations with reanalysis reach an average level of 89%over all months,while the temporal anomaly correlation coefficients are close to unity in most cases.The models also demonstrate robust performances in predicting SIT and SIE during extreme events.The effectiveness and reliability of the proposed deep transfer learning models in predicting Arctic SIT can facilitate more accurate pan-Arctic predictions,aiding climate change research and real-time business applications.

An adaptive physics-informed deep learning method for pore pressure prediction using seismic data

Accurate prediction of formation pore pressure is essential to predict fluid flow and manage hydrocarbon production in petroleum engineering.Recent deep learning technique has been receiving more interest due to the great potential to deal with pore pressure prediction.However,most of the traditional deep learning models are less efficient to address generalization problems.To fill this technical gap,in this work,we developed a new adaptive physics-informed deep learning model with high generalization capability to predict pore pressure values directly from seismic data.Specifically,the new model,named CGP-NN,consists of a novel parametric features extraction approach(1DCPP),a stacked multilayer gated recurrent model(multilayer GRU),and an adaptive physics-informed loss function.Through machine training,the developed model can automatically select the optimal physical model to constrain the results for each pore pressure prediction.The CGP-NN model has the best generalization when the physicsrelated metricλ=0.5.A hybrid approach combining Eaton and Bowers methods is also proposed to build machine-learnable labels for solving the problem of few labels.To validate the developed model and methodology,a case study on a complex reservoir in Tarim Basin was further performed to demonstrate the high accuracy on the pore pressure prediction of new wells along with the strong generalization ability.The adaptive physics-informed deep learning approach presented here has potential application in the prediction of pore pressures coupled with multiple genesis mechanisms using seismic data.

Flood Velocity Prediction Using Deep Learning Approach

Floods are one of the most serious natural disasters that can cause huge societal and economic losses.Extensive research has been conducted on topics like flood monitoring,prediction,and loss estimation.In these research fields,flood velocity plays a crucial role and is an important factor that influences the reliability of the outcomes.Traditional methods rely on physical models for flood simulation and prediction and could generate accurate results but often take a long time.Deep learning technology has recently shown significant potential in the same field,especially in terms of efficiency,helping to overcome the time-consuming associated with traditional methods.This study explores the potential of deep learning models in predicting flood velocity.More specifically,we use a Multi-Layer Perceptron(MLP)model,a specific type of Artificial Neural Networks(ANNs),to predict the velocity in the test area of the Lundesokna River in Norway with diverse terrain conditions.Geographic data and flood velocity simulated based on the physical hydraulic model are used in the study for the pre-training,optimization,and testing of the MLP model.Our experiment indicates that the MLP model has the potential to predict flood velocity in diverse terrain conditions of the river with acceptable accuracy against simulated velocity results but with a significant decrease in training time and testing time.Meanwhile,we discuss the limitations for the improvement in future work.

Mapping Network-Coordinated Stacked Gated Recurrent Units for Turbulence Prediction

Accurately predicting fluid forces acting on the sur-face of a structure is crucial in engineering design.However,this task becomes particularly challenging in turbulent flow,due to the complex and irregular changes in the flow field.In this study,we propose a novel deep learning method,named mapping net-work-coordinated stacked gated recurrent units(MSU),for pre-dicting pressure on a circular cylinder from velocity data.Specifi-cally,our coordinated learning strategy is designed to extract the most critical velocity point for prediction,a process that has not been explored before.In our experiments,MSU extracts one point from a velocity field containing 121 points and utilizes this point to accurately predict 100 pressure points on the cylinder.This method significantly reduces the workload of data measure-ment in practical engineering applications.Our experimental results demonstrate that MSU predictions are highly similar to the real turbulent data in both spatio-temporal and individual aspects.Furthermore,the comparison results show that MSU predicts more precise results,even outperforming models that use all velocity field points.Compared with state-of-the-art methods,MSU has an average improvement of more than 45%in various indicators such as root mean square error(RMSE).Through comprehensive and authoritative physical verification,we estab-lished that MSU’s prediction results closely align with pressure field data obtained in real turbulence fields.This confirmation underscores the considerable potential of MSU for practical applications in real engineering scenarios.The code is available at https://github.com/zhangzm0128/MSU.

Product quality prediction based on RBF optimized by firefly algorithm

With the development of information technology,a large number of product quality data in the entire manufacturing process is accumulated,but it is not explored and used effectively.The traditional product quality prediction models have many disadvantages,such as high complexity and low accuracy.To overcome the above problems,we propose an optimized data equalization method to pre-process dataset and design a simple but effective product quality prediction model:radial basis function model optimized by the firefly algorithm with Levy flight mechanism(RBFFALM).First,the new data equalization method is introduced to pre-process the dataset,which reduces the dimension of the data,removes redundant features,and improves the data distribution.Then the RBFFALFM is used to predict product quality.Comprehensive expe riments conducted on real-world product quality datasets validate that the new model RBFFALFM combining with the new data pre-processing method outperforms other previous me thods on predicting product quality.

Leveraging the potential of big genomic and phenotypic data for genome-wide association mapping in wheat

Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing.Combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of interoperability.In this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading date.We explored strategies for integrating these data and subsequently the resulting potential for GWAS.Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic data.In this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our case.Contrary to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental series.However,the predictive power based on the marker-trait associations of the integrated data set was higher across data sets.Therefore,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS.The results encourage further efforts to standardize and share data in the plant breeding community.

A modified stochastic model for LS+AR hybrid method and its application in polar motion short-term prediction

Short-term(up to 30 days)predictions of Earth Rotation Parameters(ERPs)such as Polar Motion(PM:PMX and PMY)play an essential role in real-time applications related to high-precision reference frame conversion.Currently,least squares(LS)+auto-regressive(AR)hybrid method is one of the main techniques of PM prediction.Besides,the weighted LS+AR hybrid method performs well for PM short-term prediction.However,the corresponding covariance information of LS fitting residuals deserves further exploration in the AR model.In this study,we have derived a modified stochastic model for the LS+AR hybrid method,namely the weighted LS+weighted AR hybrid method.By using the PM data products of IERS EOP 14 C04,the numerical results indicate that for PM short-term forecasting,the proposed weighted LS+weighted AR hybrid method shows an advantage over both the LS+AR hybrid method and the weighted LS+AR hybrid method.Compared to the mean absolute errors(MAEs)of PMX/PMY sho rt-term prediction of the LS+AR hybrid method and the weighted LS+AR hybrid method,the weighted LS+weighted AR hybrid method shows average improvements of 6.61%/12.08%and 0.24%/11.65%,respectively.Besides,for the slopes of the linear regression lines fitted to the errors of each method,the growth of the prediction error of the proposed method is slower than that of the other two methods.

Analysis of risk factors leading to anxiety and depression in patients with prostate cancer after castration and the construction of a risk prediction model

BACKGROUND Cancer patients often suffer from severe stress reactions psychologically,such as anxiety and depression.Prostate cancer(PC)is one of the common cancer types,with most patients diagnosed at advanced stages that cannot be treated by radical surgery and which are accompanied by complications such as bodily pain and bone metastasis.Therefore,attention should be given to the mental health status of PC patients as well as physical adverse events in the course of clinical treatment.AIM To analyze the risk factors leading to anxiety and depression in PC patients after castration and build a risk prediction model.METHODS A retrospective analysis was performed on the data of 120 PC cases treated in Xi'an People's Hospital between January 2019 and January 2022.The patient cohort was divided into a training group(n=84)and a validation group(n=36)at a ratio of 7:3.The patients’anxiety symptoms and depression levels were assessed 2 wk after surgery with the Self-Rating Anxiety Scale(SAS)and the Selfrating Depression Scale(SDS),respectively.Logistic regression was used to analyze the risk factors affecting negative mood,and a risk prediction model was constructed.RESULTS In the training group,35 patients and 37 patients had an SAS score and an SDS score greater than or equal to 50,respectively.Based on the scores,we further subclassified patients into two groups:a bad mood group(n=35)and an emotional stability group(n=49).Multivariate logistic regression analysis showed that marital status,castration scheme,and postoperative Visual Analogue Scale(VAS)score were independent risk factors affecting a patient's bad mood(P<0.05).In the training and validation groups,patients with adverse emotions exhibited significantly higher risk scores than emotionally stable patients(P<0.0001).The area under the curve(AUC)of the risk prediction model for predicting bad mood in the training group was 0.743,the specificity was 70.96%,and the sensitivity was 66.03%,while in the validation group,the AUC,specificity,and sensitivity were 0.755,66.67%,and 76.19%,respectively.The Hosmer-Lemeshow test showed aχ^(2) of 4.2856,a P value of 0.830,and a C-index of 0.773(0.692-0.854).The calibration curve revealed that the predicted curve was basically consistent with the actual curve,and the calibration curve showed that the prediction model had good discrimination and accuracy.Decision curve analysis showed that the model had a high net profit.CONCLUSION In PC patients,marital status,castration scheme,and postoperative pain(VAS)score are important factors affecting postoperative anxiety and depression.The logistic regression model can be used to successfully predict the risk of adverse psychological emotions.

Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

Geophysical prediction of organic matter abundance in source rocks based on geochemical analysis:A case study of southwestern Bozhong Sag,Bohai Sea,China

The Bozhong Sag is the largest petroliferous sag in the Bohai Bay Basin,and the source rocks of Paleogene Dongying and Shahejie Formations were buried deeply.Most of the drillings were located at the structural high,and there were few wells that met good quality source rocks,so it is difficult to evaluate the source rocks in the study area precisely by geochemical analysis only.Based on the Rock-Eval pyrolysis,total organic carbon(TOC)testing,the organic matter(OM)abundance of Paleogene source rocks in the southwestern Bozhong Sag were evaluated,including the lower of second member of Dongying Formation(E_(3)d2L),the third member of Dongying Formation(E_(3)d_(3)),the first and second members of Shahejie Formation(E_(2)s_(1+2)),the third member of Shahejie Formation(E_(2)s_(3)).The results indicate that the E_(2)s_(1+2)and E_(2)s_(3)have better hydrocarbon generative potentials with the highest OM abundance,the E_(3)d_(3)are of the second good quality,and the E_(3)d2L have poor to fair hydrocarbon generative potential.Furthermore,the well logs were applied to predict TOC and residual hydrocarbon generation potential(S_(2))based on the sedimentary facies classification,usingΔlogR,generalizedΔlogR,logging multiple linear regression and BP neural network methods.The various methods were compared,and the BP neural network method have relatively better prediction accuracy.Based on the pre-stack simultaneous inversion(P-wave impedance,P-wave velocity and density inversion results)and the post-stack seismic attributes,the three-dimensional(3D)seismic prediction of TOC and S_(2)was carried out.The results show that the seismic near well prediction results of TOC and S_(2)based on seismic multi-attributes analysis correspond well with the results of well logging methods,and the plane prediction results are identical with the sedimentary facies map in the study area.The TOC and S_(2)values of E_(2)s_(1+2)and E_(2)s_(3)are higher than those in E_(3)d_(3)and E_(3)d_(2)L,basically consistent with the geochemical analysis results.This method makes up the deficiency of geochemical methods,establishing the connection between geophysical information and geochemical data,and it is helpful to the 3D quantitative prediction and the evaluation of high-quality source rocks in the areas where the drillings are limited.

Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

Genome-Wide Association Study of Cooked Rice Textural Attributes and Starch Physicochemical Properties in indica Rice

Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical properties.However,the genetic bases of grain texture and starch properties in rice have not been fully understood.We conducted a genome-wide association study for apparent amylose content(AAC),starch pasting viscosities,and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome Project.We identified 26 QTLs in the whole population and detected single nucleotide polymorphisms(SNPs)with the lowest P-value at the Waxy(Wx)locus for all traits except pasting temperature and cohesiveness.Additionally,we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6(SSG6)locus for AAC,setback(SB),hardness,adhesiveness,chewiness(CHEW),gumminess(GUM),and resilience.We subsequently divided the population using a SNP adjacent to the Waxy locus,and identified 23 QTLs and 12 QTLs in two sub-panels,WxT and WxA,respectively.In these sub-panels,SSG6 was also identified to be associated with pasting parameters,including peak viscosity,hot paste viscosity,cold paste viscosity,and consistency viscosity.Furthermore,a candidate gene encoding monosaccharide transporter 5(OsMST5)was identified to be associated with AAC,breakdown,SB,CHEW,and GUM.In total,39 QTLs were co-localized with known genes or previously reported QTLs.These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.

Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat(Triticum aestivum L.)

Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.

An attention-based teacher-student model for multivariate short-term landslide displacement prediction incorporating weather forecast data

Predicting the displacement of landslide is of utmost practical importance as the landslide can pose serious threats to both human life and property.However,traditional methods have the limitation of random selection in sliding window selection and seldom incorporate weather forecast data for displacement prediction,while a single structural model cannot handle input sequences of different lengths at the same time.In order to solve these limitations,in this study,a new approach is proposed that utilizes weather forecast data and incorporates the maximum information coefficient(MIC),long short-term memory network(LSTM),and attention mechanism to establish a teacher-student coupling model with parallel structure for short-term landslide displacement prediction.Through MIC,a suitable input sequence length is selected for the LSTM model.To investigate the influence of rainfall on landslides during different seasons,a parallel teacher-student coupling model is developed that is able to learn sequential information from various time series of different lengths.The teacher model learns sequence information from rainfall intensity time series while incorporating reliable short-term weather forecast data from platforms such as China Meteorological Administration(CMA)and Reliable Prognosis(https://rp5.ru)to improve the model’s expression capability,and the student model learns sequence information from other time series.An attention module is then designed to integrate different sequence information to derive a context vector,representing seasonal temporal attention mode.Finally,the predicted displacement is obtained through a linear layer.The proposed method demonstrates superior prediction accuracies,surpassing those of the support vector machine(SVM),LSTM,recurrent neural network(RNN),temporal convolutional network(TCN),and LSTM-Attention models.It achieves a mean absolute error(MAE)of 0.072 mm,root mean square error(RMSE)of 0.096 mm,and pearson correlation coefficients(PCCS)of 0.85.Additionally,it exhibits enhanced prediction stability and interpretability,rendering it an indispensable tool for landslide disaster prevention and mitigation.