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An overview of detecting gene-trait associations by integrating GWAS summary statistics and eQTLs

Science china(Life Sciences) 2024年第6期67卷 1133-1154页

作者： Yang Zhang Mengyao Wang Zhenguo Li Xuan Yang Keqin Li Ao Xie Fang Dong Shihan Wang Jianbing Yan Jianxiao Liu National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Smart Farming for agricultural Animals Huazhong Agricultural UniversityWuhan 430070China Hubei Key Laboratory of agricultural Bioinformatics Huazhong Agricultural UniversityWuhan 430070China College of Informatics Huazhong Agricultural UniversityWuhan 430070China College of Life Sciences Nankai UniversityTianjin 300071China

Detecting genes that affect specific traits(such as human diseases and crop yields)is important for treating complex diseases and improving crop quality.A genome-wide association study(GWAS)provides new insights and directions for understanding complex traits by identifying important single nucleotide polymorphisms.Many GWAS summary statistics data related to various complex traits have been gathered recently.Studies have shown that GWAS risk loci and expression quantitative trait loci(e QTLs)often have a lot of overlaps,which makes gene expression gradually become an important intermediary to reveal the regulatory role of GWAS.In this review,we review three types of gene-trait association detection methods of integrating GWAS summary statistics and e QTLs data,namely colocalization methods,transcriptome-wide association study-oriented approaches,and Mendelian randomization-related methods.At the theoretical level,we discussed the differences,relationships,advantages,and disadvantages of various algorithms in the three kinds of gene-trait association detection methods.To further discuss the performance of various methods,we summarize the significant gene sets that influence highdensity lipoprotein,low-density lipoprotein,total cholesterol,and triglyceride reported in 16 studies.We discuss the performance of various algorithms using the datasets of the four lipid traits.The advantages and limitations of various algorithms are analyzed based on experimental results,and we suggest directions for follow-up studies on detecting gene-trait associations.

关键词： gene-trait association GWAS eQTL colocalization transcriptome-wide association study(TWAS) Mendelian randomization(MR)

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The evolution,pathogenicity and transmissibility of quadruple reassortant H1N2 swine influenza virus in china:A potential threat to public health

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Virologica Sinica 2024年第2期39卷 205-217页

作者： Xinxin Cui Jinhuan Ma Zifeng Pang Lingzhi Chi Cuishan Mai Hanlin Liu Ming Liao Hailiang Sun College of Veterinary Medicine South China Agricultural UniversityGuangzhou510642China Key Laboratory of Zoonosis Control and Prevention of Guangdong Province South China Agricultural UniversityGuangzhou510642China National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control South China Agricultural UniversityGuangzhou510642China Shandong Vocational Animal Science and Veterinary College Weifang261061China institute of Animal Health Guangdong Academy of Agricultural SciencesGuangzhou510640China

Swine are regarded as“intermediate hosts”or“mixing vessels”of influenza viruses,capable of generating strains with pandemic potential.From 2020 to 2021,we conducted surveillance on swine H1N2 influenza(swH1N2)viruses in swine farms located in Guangdong,Yunnan,and Guizhou provinces in southern china,as well as Henan and Shandong provinces in northern china.We systematically analyzed the evolution and pathogenicity of swH1N2 isolates,and characterized their replication and transmission abilities.The isolated viruses are quadruple reassortant H1N2 viruses containing genes from pdm/09 H1N1(PB2,PB1,PA and NP genes),triple-reassortant swine(NS gene),Eurasian Avian-like(HA and M genes),and recent human H3N2(NA gene)lineages.The NA,PB2,and NP of SW/188/20 and SW/198/20 show high gene similarities to A/Guangdong/Yue Fang277/2017(H3N2).The HA gene of swH1N2 exhibits a high evolutionary rate.The five swH1N2 isolates replicate efficiently in human,canine,and swine cells,as well as in the turbinate,trachea,and lungs of mice.A/swine/Shandong/198/2020 strain efficiently replicates in the respiratory tract of pigs and effectively transmitted among them.Collectively,these current swH1N2 viruses possess zoonotic potential,highlighting the need for strengthened surveillance of swH1N2 viruses.

关键词： Swine influenza virus(SIV) H1N2 Evolution Replication Pathogenicity Zoonotic potential

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Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

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Journal of Animal Science and Biotechnology 2024年第1期15卷 68-87页

作者： Wencheng Zong Jinbu Wang Runze Zhao Naiqi Niu Yanfang Su Ziping Hu Xin Liu Xinhua Hou Ligang Wang Lixian Wang Longchao Zhang State Key Laboratory of Animal Biotech Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China College of Animal Science Shanxi Agricultural UniversityJinzhong 030801China College of Animal Science and Technology Qingdao Agricultural UniversityQingdao 266109China

Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

关键词： Body size GWAS Pig Skeleton Structural variations

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Pig pangenome graph reveals functional features of non‑reference sequences

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Journal of Animal Science and Biotechnology 2024年第3期15卷 956-970页

作者： Jian Miao Xingyu Wei Caiyun Cao Jiabao Sun Yuejin Xu Zhe Zhang Qishan Wang Yuchun Pan Zhen Wang College of Animal Sciences Zhejiang UniversityHangzhou 310058ZhejiangChina Yazhou Bay Science and Technology City Hainan Institute of Zhejiang UniversityYazhou DistrictBuilding 11Yongyou Industrial ParkSanya 572025HainanChina

Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

关键词： Heat tolerance Immune ability Non-reference sequences Pig pangenome

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Multiparameter Numerical Investigation of Two Types of Moving Interactions Between the Deep-Sea Mining Vehicle Track Plate and Seabed Soil:Digging and Rotating Motions

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china Ocean Engineering 2024年第3期38卷 408-423页

作者： SUN Peng-fei LYU Hai-ning YANG Jian-min XU Zhi-yong State Key Laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China Yazhou Bay institute of Deepsea SCI-TECH Shanghai Jiao Tong UniversitySanya 572024China institute of Marine Equipment Shanghai Jiao Tong UniversityShanghai 200240China

To ensure the safe performance of deep-sea mining vehicles(DSMVs),it is necessary to study the mechanical characteristics of the interaction between the seabed soil and the track plate.The rotation and digging motions of the track plate are important links in the contact between the driving mechanism of the DSMV and seabed soil.In this study,a numerical simulation is conducted using the coupled Eulerian–Lagrangian(CEL)large deformation numerical method to investigate the interaction between the track plate of the DSMV and the seabed soil under two working conditions:rotating condition and digging condition.First,a soil numerical model is established based on the elastoplastic mechanical characterization using the basic physical and mechanical properties of the seabed soil obtained by in situ sampling.Subsequently,the soil disturbance mechanism and the dynamic mechanical response of the track plate under rotating and digging conditions are obtained through the analysis of the sensitivity of the motion parameters,the grouser structure,the layered soil features and the soil heterogeneity.The results indicate that the above parameters remarkably influence the interaction between the DSMV and the seabed soil.Therefore,it is important to consider the rotating and digging motion of the DSMV in practical engineering to develop a detailed optimization design of the track plate.

关键词： deep-sea mining vehicle rotating motion digging motion track plate-seabed soil interaction CEL numerical method

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Dynamic changes in physicochemical property,biogenic amines content and microbial diversity during the fermentation of Sanchuan ham

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Food Science and Human Wellness 2024年第1期13卷 506-516页

作者： Zhongai Chen Hong Chen Huan Du Cong Chen Kaixiang Lu Qiaoli Xue Yongjin Hu College of Food Science and Technology Yunnan Agricultural UniversityKunming 650000China institute of Food Processing Guizhou Academy of Agricultural SciencesGuiyang 550006China Editorial Department of Journal of Yunnan agricultural university Yunnan Agricultural UniversityKunming 650000China

Sanchuan ham is appreciated in Yunnan Province,china,for its characteristic flavor and taste,while the microbial community structure and biogenic amines content remain unclear during fermentation processes.In this study,we explored the physicochemical property,biogenic amines concentration and microbial diversity of external and internal Sanchuan ham by high-throughput sequencing during the processing of Sanchuan ham.Results showed that the nitrite remained at a stable level of 0.15 mg/kg which was significantly lower than the national health standard safety level of 20 mg/kg.In addition,compared with fresh hams,the content of total free amino acids in ripe Sanchuan ham has grown 14 folds;sour and bitter were the main tastes of Sanchuan ham.Notably,the concentration of cadaverine was the highest of all biogenic amines during the entire fermentation period.At the bacterial phyla level,Firmicutes and Actinobacteria were the two main phyla,while at the genus level,Staphylococcus was a significant strain throughout the whole fermentation.Moreover,the dry stage has a great impact on the succession change of microbial community structure.Simultaneously,the change trends and composition of bacteria in the interior have slight discrepancies with those of the exterior of Sanchuan ham.

关键词： Sanchuan ham Nitrite cont ent Free amino acids Cadaverine Staphylococcus

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Protocol-Based Non-Fragile State Estimation for Delayed Recurrent Neural Networks Subject to Replay Attacks

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IEEE/CAA Journal of Automatica Sinica 2024年第1期11卷 249-251页

作者： Fan Yang Hongli Dong Yuxuan Shen Xuerong Li Dongyan Dai the Artificial Intelligence Energy Research institute Northeast Petroleum UniversityDaqing 163318 the Heilongjiang Provincial Key Laboratory of Networking and Intelligent Control Northeast Petroleum UniversityDaqing 163318 the sanya Offshore Oil&Gas Research institute Sanya 572025China IEEE

Dear Editor, This letter focuses on the protocol-based non-fragile state estimation problem for a class of recurrent neural networks(RNNs). With the development of communication technology, the networked systems have ... 详细信息

关键词： network communication estimation

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Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

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aBIOTECH 2024年第1期5卷 71-93页

作者： Baizhi Chen Yan Shi Yuchen Sun Lu Lu Luyao Wang Zijian Liu Shifeng Cheng agricultural Genomics institute at Shenzhen(AGIS) Chinese Academy of Agricultural Sciences(CAAS)ShenzhenChina

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw materials.The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding.Notably,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress resistance.However,a considerable gap remains between pea functional genomics and molecular breeding.This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

关键词： Pea Genome study Agronomic traits Breeding

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Changes in milk fat globule membrane proteins along lactation stage of Laoshan dairy goat

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Journal of Integrative Agriculture 2024年第5期23卷 1737-1748页

作者： Chuozi Liang Zhongna Yu Guangming Zhu Yixuan Li Xueheng Sun Hongning Jiang Qijing Du Rongbo Fan Jun Wang Yongxin Yang Rongwei Han College of Food Science and Engineering Qingdao Agricultural UniversityQingdao 266109China Bathurst Future Agri-Tech institute Qingdao Agricultural UniversityQingdao 266109China Haidu Cllege Qingdao Agricultural UniversityQingdao 266109China

The milk fat globule membrane(MFGM)is a complex structure with numerous functions,and its composition is affected by many factors.There have been few systematic investigations on goat MFGM proteome profiling during lactation.Individual milk samples from 15 healthy dairy goats were obtained at six lactation time points for investigation of the MFGM proteome using both data-independent acquisition(DIA)and data-dependent acquisition(DDA)proteomics techniques combined with multivariate statistical analysis.Using the DIA method,890 variably abundant MFGM proteins were discovered throughout the lactation cycle.From 1 to 240 d,butyrophilin subfamily 1 member A1,lipoprotein lipase,perilipin-2,and adipose triglyceride lipase were upregulated,while APOE,complement C3,clusterin,and IgG were downregulated.Furthermore,from 1 to 90 d,annexin A1,annexin A2,and antithrombin-ll were downregulated,then upregulated by d 240.Albumin had a high degree of connectedness,indicating that it was a key protein,according to protein-protein interaction research.Overall,our findings gave new insights into the biological features of MFGM protein in goat milk throughout lactation,which may aid in the creation of specialized MFGM products and infant formula.

关键词： goat milk fat globule membrane protein data-independent acquisition(DIA) data-dependent acquisition(DDA) lactation proteomics

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The temporal-spatial expression and functional analysis of three gustatory receptor genes in Solenopsis invicta using sweet and bitter compounds

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Insect Science 2024年第2期31卷 448-468页

作者： Muhammad Irfan Waris Yanyuan Lei Guojun Qi Ziying Guan Abdul Rashied Jie Chen Lihua Lyu institute of Plant Protection Guangdong Academy of Agricultural SciencesGuangdong Provincial Key Laboratory of High Technology for Plant ProtectionGuangzhouChina Department of Entomology College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina

The insect gustatory system participates in identifying potential food sources and avoiding toxic compounds.During this process,gustatory receptors(GRs)recognize feeding stimulant and deterrent compounds.However,the GRs involved in recognizing stimulant and deterrent compounds in the red imported fire ant,Solenopsis invicta,remain unknown.Therefore,we conducted a study on the genes SinvGR1,SinvGR32b,and SinvGR28a to investigate the roles of GRs in detecting feeding stimulant and deterrent compounds.In this current study,we found that sucrose and fructose are feeding stimulants and the bitter compound quinine is a feeding deterrent.The fire ant workers showed significant behavior changes to avoid the bitter taste in feeding stimulant compounds.Reverse transcription quantitative real-time polymerase chain reaction results from developmental stages showed that the SinvGR1,SinvGR32b,and SinvGR28a genes were highly expressed in fire ant workers.Tissue-specific expression profiles indicated that SinvGR1,SinvGR32b,and SinvGR28a were specifically expressed in the antennae and foreleg tarsi of workers,whereas SinvGR32b gene transcripts were also highly accumulated in the male antennae.Furthermore,the silencing of SinvGRI or SinvGR32b alone and the co-silencing of both genes disrupted worker stimulation and feeding on sucrose and fructose.The results also showed that SinvGR28a is required for avoiding quinine,as workers with knockdown of the SinvGR28a gene failed to avoid and fed on quinine.This study first identified stimulant and deterrent compounds of fire ant workers and then the GRs involved in the taste recognition of these compounds.This study could provide potential target gustatory genes for the control of the fire ant.

关键词： behavioral responses feeding assays gustatory receptors RNA interference Solenopsis invicta temporal-spatial expression

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