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Accuracy of genomic selection in biparental populations of flax(Linum usitatissimum L.)

The Crop Journal 2016年第4期4卷 290-303页

作者： frank m.you Helen m.Booker Scott D.Duguid Gaofeng Jia Sylvie Cloutier morden Research and Development Centre Agriculture and Agri-Food Canada Crop Development Centre Department of Plant Sciences University of Saskatchewan Ottawa Research and Development Centre Agriculture and Agri-Food Canada

Flax is an important economic crop for seed oil and stem fiber. Phenotyping of traits such as seed yield, seed quality, stem fiber yield, and quality characteristics is expensive and time consuming. Genomic selection(GS) refers to a breeding approach aimed at selecting preferred individuals based on genomic estimated breeding values predicted by a statistical model based on the relationship between phenotypes and genome-wide genetic markers. We evaluated the prediction accuracy of GS(rmP) and the efficiency of GS relative to phenotypic selection(RE) for three GS models: ridge regression best linear unbiased prediction(RR-BLUP),Bayesian LASSO(BL), and Bayesian ridge regression(BRR), for seed yield, oil content, iodine value, linoleic, and linolenic acid content with a full and a common set of genome-wide simple sequence repeat markers in each of three biparental populations. The three GS models generated similar rmPand RE, while BRR displayed a higher coefficient of determination(R^2)of the fitted models than did RR-BLUP or BL. The mean rmPand RE varied for traits with different heritabilities and was affected by the genetic variation of the traits in the *** for seed yield generated a mean RE of 1.52 across populations and marker sets, a value significantly superior to that for direct phenotypic selection. Our empirical results provide the first validation of GS in flax and demonstrate that GS could increase genetic gain per unit time for linseed breeding. Further studies for selection of training populations and markers are warranted.

关键词： Genomic selection SSR Flax Linseed Seed yield Fatty acid composition

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Inheritance of marsh spot disease resistance in cranberry common bean(Phaseolus vulgaris L.)

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The Crop Journal 2022年第2期10卷 456-467页

作者： Bosen Jia Robert L.Conner Nadeem Khan Anfu Hou Xuhua Xia frank m.you Ottawa Research and Development Centre Agriculture and Agri-Food CanadaOttawaOntario K1A 0C6Canada Department of Biology University of OttawaOttawaOntario K1N 6N5Canada morden Research and Development Centre Agriculture and Agri-Food CanadaMordenManitoba R6M 1Y5Canada

Common bean(Phaseolus vulgaris) is an annual legume crop that is grown worldwide for its edible dry seeds and tender pods. marsh spot(mS) of the seeds is a physio-genic stress disease affecting seed quality in beans. Studies have suggested that this disease involves a nutritional disorder caused by manganese deficiency, but the inheritance of resistance to this disease has not been reported. A biparental genetic population composed of 138 recombinant inbred lines(RILs) was developed from a cross between an mS resistant cultivar ‘Cran09’ and an mS susceptible cultivar ‘messina’. The 138 RILs and their two parents were evaluated for mS resistance during five consecutive years from 2015 to 2019 in sandy and heavy clay soils in morden, manitoba, Canada. The mS incidence(mSI) and the mS resistance index(mSRI) representing disease severity were shown to be both highly correlated heritable traits that had high broad-sense heritability values(H;) of 86.5% and 83.2%, respectively. No significant differences for mSI and mSRI were observed between the two soil types in all five-(mSI) or four-year(mSRI) data collection, but significant correlations among years were observed despite mS resistance was moderately affected by year. The mSIs and mSRIs displayed a right-skewed distribution, indicating a mixed genetic model involving a few major genes and polygenes. Using the joint segregation analysis method, the same four major genes with additive-epistasis effects showed the best fit for both traits, explaining 84.4% and85.3% of the phenotypic variance for mSI and mSRI, respectively. For both traits, the m1, m2, m3 and m4 acted as the favorable(resistant) alleles for the four genes where m and m represent two alleles of each gene. However, due to epistatic effects, only the individuals of the m1 m2 m3 m4 haplotype appeared to be highly resistant, whereas those of the m1 m2 m3 m4 haplotype were the most susceptible. The m4 allele significantly suppressed the additive effects of m1 m

关键词： Common bean Cranberry bean marsh spot Resistance Recombinant inbred line(RIL) Joint segregation analysis major gene Polygene

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Estimation of genetic parameters and their sampling variances for quantitative traits in the type 2 modified augmented design

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The Crop Journal 2016年第2期4卷 107-118页

作者： frank m.you Qijian Song Gaofeng Jia Yanzhao Cheng Scott Duguid Helen Booker Sylvie Cloutier morden Research and Development Centre Agriculture and Agri-Food Canada Soybean Genomics and Improvement Laboratory USDA-ARS Crop Development Centre University of Saskatchewan Ottawa Research and Development Centre Agriculture and Agri-Food Canada

The type 2 modified augmented design(mAD2) is an efficient unreplicated experimental design used for evaluating large numbers of lines in plant breeding and for assessing genetic variation in a population. Statistical methods and data adjustment for soil heterogeneity have been previously described for this design. In the absence of replicated test genotypes in mAD2, their total variance cannot be partitioned into genetic and error components as required to estimate heritability and genetic correlation of quantitative traits, the two conventional genetic parameters used for breeding selection. We propose a method of estimating the error variance of unreplicated genotypes that uses replicated controls, and then of estimating the genetic parameters. Using the Delta method, we also derived formulas for estimating the sampling variances of the genetic *** simulations indicated that the proposed method for estimating genetic parameters and their sampling variances was feasible and the reliability of the estimates was positively associated with the level of heritability of the trait. A case study of estimating the genetic parameters of three quantitative traits, iodine value, oil content, and linolenic acid content, in a biparental recombinant inbred line population of flax with 243 individuals, was conducted using our statistical models. A joint analysis of data over multiple years and sites was suggested for genetic parameter estimation. A pipeline module using SAS and Perl was developed to facilitate data analysis and appended to the previously developed mAD data analysis pipeline(http://***/bioinformatics_ tools/mADPipeline/***).

关键词： Broad-sense heritability Genetic correlation Sampling variance modified augmented design

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The cloning of Rht23 revealed a point mutation in 5Dq leading to plant dwarfness and compact spike in common wheat

The cloning of Rht23 revealed a point mutation in 5Dq leadin...

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2017中国长三角遗传学大会

作者： Kaijun Zhao Jin Xiao Yu Liu Shulin Chen Chunxia Yuan Aizhong Cao frank m.you Donglei Yang An Shengmin Haiyan Wang Xiue Wang State Key Laboratory of Crop Genetics and Germplasm Enhancement Cytogenetics InstituteNanjing Agricultural University/JCIC-MCP morden Research and Development Centre Agriculture and Agri-Food Canada

The domesticated Q gene on wheat chromosome 5 A(5 AQ) encode an AP2 transcription factor,conferring characters of free-threshing and subcompact *** B and D homeoalleles of hexaploid bread wheat are thought to be either a pseudogene or expressed at a low level,*** function of the low expressed allele on chromosome 5 D(5 Dq) was still *** identified a compact spike and dwarf mutant of Sumai 3,NAUH164,by EmS mutagenesis,and the mutant gene was designated as ***23 was mapped to a physical interval of 8.5 mb on chromosome 5 DL,in which the 5 Dq was *** present study,the 5 Dq/q’ were cloned from wild type Sumai 3 and its *** comparison showed that there occurred a SNP substitution(G3147 A) in the 5 Dq ORF-region,which has been proved as the binding site of *** SNP resulted in an Ala416 Thr mutation and changed the structure of 5 Dq *** expression change was observed for 5 AQ in the wild type and the *** the 5 Dq expression was significantly up-regulated in leaves,stems and spikes of NAUH164 than those in Sumai *** in the wild type Sumai 3,the Ta-miR172 expression was down regulated in leaf,stem and spike of the *** may due to the induced mismatch to *** further study the relationship of 5 Dq’ with Rht23,a SNP-based co-dominant marker,was *** analysis using a(NAUH164×Alondra’s) RIL population showed that the marker allele was co-segregated with the Rht23 mutant *** results suggest that Rht23 was a 5 Dq point mutation,which led to plant dwarf and compact spike *** results provided the evidence that the Q homolog on chromosome 5 D also has pleiotropic effect in regulation of plant architecture.

关键词： Common wheat Q gene Rht23 mutagenesis Single nucleotide polymorphism(SNP)

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Sequencing a Juglans regia×*** hybrid yields high-quality genome assemblies of parental species

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Horticulture Research 2019年第1期6卷 1271-1286页

作者： Tingting Zhu Le Wang frank m.you Juan C.Rodriguez Karin R.Deal Limin Chen Jie Li Sandeep Chakraborty Bipin Balan Cai-Zhong Jiang Patrick J.Brown Charles ALeslie mallikarjuna KAradhya Abhaya m.Dandekar Patrick E.mcGuire Daniel Kluepfel Jan Dvorak ming-Cheng Luo Department of Plant Sciences University of CaliforniaDavisCA 95616USA Ottawa Research and Development Centre Agriculture and Agri-Food CanadaOttawaON K1A 0C6Canada Genome Center University of CaliforniaDavisCA 95616USA Crops Pathology and Genetics Research Unit USDA-ARSDavisCA 95616USA National Clonal Germplasm Repository USDA-ARSDavisCA 95616USA

members of the genus Juglans are monecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes,which greatly complicates genome sequence *** genomes of interspecific hybrids are usually comprised of haploid genomes of parental *** exploited this attribute of interspecific hybrids to avoid heterozygosity and sequenced an interspecific hybrid Juglans microcarpa×*** using a novel combination of single-molecule sequencing and optical genome mapping *** resulting assemblies of both genomes were remarkably complete including chromosome termini and centromere *** termini consisted of arrays of telomeric repeats about 8 kb long and heterochromatic subtelomeric regions about 10 kb *** centromeres consisted of arrays of a centromere-specific Gypsy retrotransposon and most contained genes,many of them *** genomes evolved by a whole-genome-duplication dating back to the Cretaceous-Paleogene boundary and consist of two subgenomes,which were fractionated by numerous short gene deletions evenly distributed along the length of the *** was shown to be asymmetric with one subgenome exhibiting greater gene loss than the *** asymmetry of the process is ongoing and mirrors an asymmetry in gene expression between the *** the importance of ***×*** hybrids as potential walnut rootstocks,we catalogued disease resistance genes in the parental genomes and studied their chromosomal *** also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.

关键词： Juglans parental evenly

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Improved Quantile Convolutional and Recurrent Neural Networks for Electric Vehicle Battery Temperature Prediction

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Big Data mining and Analytics 2024年第2期7卷 512-530页

作者： Andreas m.Billert Runyao Yu Stefan Erschen michael Frey frank Gauterin Karlsruhe Institute of Technology(KIT) Institute of Vehicle System TechnologyKarlsruhe 76131Germanyand also with Bayerische Motoren Werke(BMW)AGMunich 80788Germany Technical University of munich(TUm) Munich 80333Germany BmW AG Munich 80788Germany KIT Institute of Vehicle System TechnologyKarlsruhe 76131Germany

The battery thermal management of electric vehicles can be improved using neural networks predicting quantile sequences of the battery *** work extends a method for the development of Quantile Convolutional and Quantile Recurrent Neural Networks(namely Q*NN).Fleet data of 225629 drives are clustered and balanced,simulation data from 971 simulations are augmented before they are combined for training and *** Q*NN hyperparameters are optimized using an efficient Bayesian optimization,before the Q*NN models are compared with regression and quantile regression models for four *** analysis of point-forecast and quantile-related metrics shows the superior performance of the novel Q*NN *** median predictions of the best performing model achieve an average RmSE of 0.66°C and R^(2) of *** predicted 0.99 quantile covers 98.87%of the true values in the test *** conclusion,this work proposes an extended development and comparison of Q*NN models for accurate battery temperature prediction.

关键词： deep learning battery temperature convolutional and recurrent neural network quantile forecasting

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Solving traffic data occlusion problems in computer vision algorithms using DeepSORT and quantum computing

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Journal of Traffic and Transportation Engineering(English Edition) 2024年第1期11卷 1-15页

作者： frank Ngeni Judith mwakalonge Saidi Siuhi Department of Engineering South Carolina State UniversityOrangeburgSC 29117USA

Inaccuracies of traffic sensors during traffic counting and vehicle classification have persisted as transportation agencies have been prompted to calibrate sensors *** of multiple objects,heavy occlusions,and similar appearances in congested places are some causes of computer vision model *** paper used the YOLOv5 model for detection and the DeepSORT model for tracking *** to the nature of the reported problem caused by many misses and mismatches,the power of quantum computing with the alternating direction method of multipliers(ADmm)optimizer was leveraged.A basic Kalman filter and the Hungarian algorithm features were used in combination with a quantum optimizer to present robust multiple object tracking(mOT)*** hybrid combination of the classical and quantum model has fastened learning the occludes during frame matching of tracks and detections by generating minimum quantum cost function *** with the existing models indicated a significant increase in the primary mOT metric multiple object tracking accuracy(mOTA)by 16%more than the regular YOLOv5-DeepSORT model when using a quantum ***,a 6%multiple object tracking precision(mOTP)increases and a 6%identification metrics(F_(1))score increase were observed using the quantum optimizer with identity switching reduced from 6 to *** model is expected to assist transportation officials in improving the accuracy of traffic counts and vehicle classification and reduce the need for regular computer vision software calibration.

关键词： Traffic classification Traffic counting DeepSORT YOLOv5 Quantum computing

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Physics-constrained graph modeling for building thermal dynamics

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Energy and AI 2024年第2期16卷 150-157页

作者： Ziyao Yang Amol D.Gaidhane Ján Drgoňa Vikas Chandan mahantesh m.Halappanavar frank Liu Yu Cao School of Electrical Computer and Energy EngineeringArizona State UniversityTempeAZ 85287USA Pacific Northwest National Laboratory RichlandWA 99354USA Oak Ridge National Laboratory Oak RidgeTN 37830USA

In this paper,we propose a graph model embedded with compact physical equations for modeling the thermal dynamics of *** principles of heat flow across various components in the building,such as walls and doors,fit the message-passing strategy used by Graph Neural networks(GNNs).The proposed method is to represent the multi-zone building as a graph,in which only zones are considered as nodes,and any heat flow between zones is modeled as an edge based on prior knowledge of the building ***,the thermal dynamics of these components are described by compact models in the *** are further employed to train model parameters from collected *** model training,our proposed method enforces physical constraints(e.g.,zone sizes and connections)on model parameters and propagates the penalty in the loss function of *** constraints are essential to ensure model robustness and *** evaluate the effectiveness of the proposed modeling approach on a realistic dataset with multiple *** results demonstrate a satisfactory accuracy in the prediction of multi-zone ***,we illustrate that the new model can reliably learn hidden physical parameters with incomplete data.

关键词： Physics-constrained learning Graph Neural Networks Compact model Building thermal dynamics

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Fenofibrate-promoted hepatomegaly and liver regeneration are PPARα-dependent and partially related to the YAP pathway

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Acta Pharmaceutica Sinica B 2024年第7期14卷 2992-3008页

作者： Shicheng Fan Yue Gao Pengfei Zhao Guomin Xie Yanying Zhou Xiao Yang Xuan Li Shuaishuai Zhang frank JGonzalez Aijuan Qu min Huangb Huichang Bi NmPA Key Laboratory for Research and Evaluation of Drug metabolism&Guangdong Provincial Key Laboratory of New Drug Screening&Guangdong-Hongkong-macao Joint Laboratory for New Drug Screening School of Pharmaceutical SciencesSouthern Medical UniversityGuangzhou 510515China Guangdong Provincial Key Laboratory of New Drug Design and Evaluation School of Pharmaceutical SciencesSun Yat-sen UniversityGuangzhou 510006China Department of Physiology and Pathophysiology School of Basic Medical SciencesCapital Medical UniversityBeijing 100069China Laboratory of metabolism Center for Cancer ResearchNational Cancer InstituteNational Institutes of HealthBethesdaMD 20892USA The State Key Laboratory of Chemical Oncogenomics School of Chemical Biology and BiotechnologyShenzhen Graduate School of Peking UniversityShenzhen 518055China

Fenofibrate,a peroxisome proliferator-activated receptor α(PPARα)agonist,is widely prescribed for hyperlipidemia *** studies also showed that it has therapeutic potential in various liver ***,its effects on hepatomegaly and liver regeneration and the involved mechanisms remain ***,the study showed that fenofibrate significantly promoted liver enlargement and regeneration post-partial hepatectomy in mice,which was dependent on hepatocyteexpressed PPARα.Yes-associated protein(YAP)is pivotal in manipulating liver growth and *** further identified that fenofibrate activated YAP signaling by suppressing its K48-linked ubiquitination,promoting its K63-linked ubiquitination,and enhancing the interaction and transcriptional activity of the YAP-TEAD *** inhibition of YAP-TEAD interaction using verteporfin or suppression of YAP using AAV Yap shRNA in mice significantly attenuated fenofibrate-induced *** factors,such as mYC,KRT23,RAS,and RHOA,might also participate in fenofibrate-promoted hepatomegaly and liver *** studies demonstrate that fenofibratepromoted liver enlargement and regeneration are PPARα-dependent and partially through activating the YAP signaling,with clinical implications of fenofibrate as a novel therapeutic agent for promoting liver regeneration.

关键词： Fenofibrate PPARa Hepatomegaly Partial hepatectomy Liver regeneration YAP TEAD Ubiquitination

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Exome sequencing identifies a likely causative variant in 53%of families with ciliopathy-related features on renal ultrasound after excluding NPHP1 deletions

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Genes & Diseases 2024年第5期11卷 40-43页

作者： Konstantin Deutsch Verena Klambt Thomas m.Kitzler Tilman Jobst-Schwan Ronen Schneider Florian Buerger Steve Seltzsam Sherif El Desoky Jameela A.Kari Farkhanda Hafeez maria Szczepanska Loai A.Eid Hazem S.Awad muna Al-Saffar Neveen A.Soliman Velibor Tasic Camille Nicolas-frank Kirollos yousef Luca m.Schierbaum Sophia Schneider Abdul Halawi Izzeldin Elmubarak Katharina Lemberg Shirlee Shril Shrikant m.mane Nancy Rodig Friedhelm Hildebrandt Division of Nephrology Department of PediatricsBoston Children’s HospitalHarvard Medical SchoolBostonMA 02215USA Department of Pediatric Gastroenterology Nephrology and Metabolic DiseasesCharite Universitatsmedizin BerlinBerlin 13353Germany Berlin Institute of Health at Charitee Universitatsmedizin Berlin BIH Biomedical Innovation AcademyBIH Charite Clinician Scientist ProgramBerlin 10178Germany Department of Nephrology and Hypertension FriedrichAlexander-Universitat Erlangen-NurnbergErlangen 91054Germany Department of Pediatrics Faculty of Medicine King Abdulaziz UniversityPediatric Nephrology Center of ExcellenceKing Abdulaziz University HospitalJeddah 21589Saudi Arabia Department of Pediatric Nephrology The Children’s Hospital and Institute of Child HealthLahore 54000Pakistan Department of Pediatrics Faculty of Medical Sciences in ZabrzeMedical University of Silesia in KatowiceKatowice 40-752Poland Dubai Hospital and Al-Jalila Children’s Specialty Hospital Kidney Center of ExcellenceDubai 4545United Arab Emirates Department of Genetics and Genomics UAE UniversityAbu Dhabi 15551United Arab Emirates Department of Pediatrics Division of Genetics and GenomicsBoston Children’s HospitalHarvard Medical SchoolBostonMA 02215USA Department of Pediatrics Center of Pediatric Nephrology and TransplantationKasr Al Ainy School of MedicineCairo UniversityCairo 11562Egypt Egypt Center for Research and Regenerative medicine(ECRRm) Cairo 11511Egypt medical Faculty Skopje University Children’s HospitalSkopje 1000North Macedonia Department of Genetics Yale University School of MedicineNew HavenCT 06520USA

Nephronophthisis-related ciliopathies(NPHP-RC)represent one of the most common causes of chronic kidney disease in the first three decades of life and are characterized by a broad genetic and clinical heterogeneity.1 To date,more than 90 genes have been identified that cause autosomalrecessive NPHP-RC if mutated,accounting for up to 60%of cases.1 Among these,homozygous deletions of NPHP1 are the most common *** genes localize to primary cilia,basal bodies,or the centrosome and lead to a primary ciliary disruption if mutated,thereby causing a broad phenotypical spectrum.1 Patients that suffer from NPHP-RC can either have an isolated renal phenotype,such as polyuria,polydipsia,decreased urinary concentration ability,and secondary enuresis due to loss of tubular function,or present with extrarenal symptoms including retinal degeneration,cerebellar vermis hypoplasia,or hepatic *** are often diagnosed in early adolescence,reaching end-stage renal disease before 25 years of age,but early onset and rapidly progressive forms of NPHP-RC also exist.1 Renal ultrasound indicates kidneys of normal or reduced renal length with increased echogenicity and corticomedullary cysts.

关键词： degeneration urinary likely

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