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Whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep

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Zoological research 2022年第5期43卷 695-705页

作者： De-Yin Zhang Xiao-Xue Zhang Fa-Di Li Lv-Feng Yuan Xiao-Long Li Yu-Kun Zhang Yuan Zhao Li-Ming Zhao Jiang-Hui Wang Dan Xu Jiang-Bo Cheng Xiao-Bin Yang Wen-Xin Li Chang-Chun Lin Bu-Bo Zhou Wei-Min Wang State Key Laboratory of Grassland Agro-Ecosystems Key Laboratory of Grassland Livestock Industry InnovationMinistry of Agriculture and Rural AffairsEngineering Research Center of Grassland IndustryMinistry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouGansu 730020China College of Animal Science and technology Gansu Agricultural UniversityLanzhouGansu 730070China engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in gansu province MinqinGansu 733300China Lanzhou veterinary research Institute Chinese Academy of Agricultural SciencesLanzhouGansu 730046China

The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, chinese indigenous breeds,African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group,while the chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function.Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation,energy metabolism, and growth development.Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30domesticated sheep breeds. The IFI44 c. 54413058C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.

关键词： Sheep Whole-genome resequencing Selection signature analysis Immunity IFI44 gene

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The Estimation of Soil Trace Elements Distribution and Soil-Plant-Animal Continuum in Relation to Trace Elements Status of Sheep in Huangcheng Area of Qilian Mountain Grassland,China

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Journal of Integrative Agriculture 2014年第1期13卷 140-147页

作者： WANG Hui LIU Yong-ming QI Zhi-ming WANG Sheng-yi LIU Shi-xiang LI Xia WANG Hai-jun WANG Xiao-li XIA Xin-chao ZHU Xin-qiang Key Laboratory of veterinary Pharmaceutics Development Ministry of Agriculture/Key Laboratory of New Animal Drug Project of Gansu Province/Engineering and Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province/Lanzhou Institute of Husbandry and Pharmaceutics SciencesChinese Academy of Agricultural Sciences

The purpose of the present study was to survey contents of trace elements of Cu, Mn, Fe, and Zn in the surface layer （0-20 cm） in the soil, pasture and serum of sheep in Huangcheng area of Qilian mountain grassland, China. Also the soil-plantanimal continuum was analyzed. Soil （n=300）, pasture （n=60）, and blood serum samples from sheep （n=480） were collected from Huangcheng area of Qilian mountain grassland, China. The contents of trace element in the samples were analyzed by atomic absorption spectrophotometer after digestion. The soil trace elements density distribution shows a ladder-like pattern distribution. Equations developed in the present study for prediction of Fe （R2=0.943） and Zn （R2=0.882） had significant R2 values.

关键词： trace elements minerals deficiency soil type Qilian mountain grassland correlation

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Interplays of liver fibrosis-associated microRNAs:Molecular mechanisms and implications in diagnosis and therapy

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Genes & Diseases 2023年第4期10卷 1457-1469页

作者： Hong Li Tingli Liu Yongchun Yang William C.Cho Robin J.Flynn Majid Fasihi Harandi Houhui Song Xuenong Luo Yadong Zheng State Key Laboratory of veterinary Etiological Biology Key Laboratory of Veterinary Parasitology of Gansu ProvinceLanzhou Veterinary Research InstituteChinese Academy of Agricultural SciencesLanzhouGansu 730046China Key Laboratory of Applied technology on Green-Eco-Healthy Animal Husbandry of Zhejiang province Zhejiang Provincial Engineering Laboratory for Animal Health Inspection&Internet TechnologyZhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health ManagementChina-Australia Joint Laboratory for Animal Health Big Data AnalyticsCollege of Animal Science and Technology&College of Veterinary Medicine of Zhejiang A&F UniversityHangzhouZhejiang 311300China Department of Clinical Oncology Queen Elizabeth HospitalHong Kong SAR 999077China Department of Infection Biology Institute of Infection and Global HealthUniversity of LiverpoolLiverpool L35RFUK Graduate Studies Office Department of ResearchInnovation and Graduate StudiesWaterford Institute of TechnologyX91 K0EKIreland research center for Hydatid Disease in Iran Kerman University of Medical SciencesKerman ***Iran

microRNAs(miRNAs)are a class of non-coding functional small RNA composed of 21e23 nucleotides,having multiple associations with liver fibrosis.Fibrosis-associated miRNAs are roughly classified into pro-fibrosis or anti-fibrosis types.The former is capable of activating hepatic stellate cells(HSCs)by modulating pro-fibrotic signaling pathways,mainly including TGF-b/SMAD,WNT/b-catenin,and Hedgehog;the latter is responsible for maintenance of the quiescent phenotype of normal HSCs,phenotypic reversion of activated HSCs(aHSCs),inhibition of HSCs proliferation and suppression of the extracellular matrix-associated gene expression.Moreover,several miRNAs are involved in regulation of liver fibrosis via alternative mechanisms,such as interacting between hepatocytes and other liver cells via exosomes and increasing autophagy of aHSCs.Thus,understanding the role of these miRNAs may provide new avenues for the development of novel interventions against hepatic fibrosis.

关键词： Diagnosis Hepatic stellate cell Liver fibrosis miRNA Therapy

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Genetic characterization of antimicrobial resistance in Staphylococcus aureus isolated from bovine mastitis cases in Northwest China

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Journal of Integrative Agriculture 2016年第12期15卷 2842-2847页

作者： YANG Feng WANG Qi WANG Xu-rong WANG Ling LI Xin-pu LUO Jin-yin ZHANG Shi-dong LI Hong-sheng Key Laboratory of veterinary Pharmaceutical Development Ministry of Agriculture/Engineering & Technology Research Center of Traditional Chinese Veterinary Medicine of Gansu Province/Lanzhou Institute of Husbandry and Pharmaceutical SciencesChinese Academy of Agricultural Sciences State Key Laboratory of Applied Organic Chemistry Lanzhou University

Staphylococcus aureus is the most common etiological pathogen of bovine mastitis. The resistant strains make the disease difficult to cure. The aim of this study was to characterize the genetic nature of the antimicrobial resistance in S. aureus cultured from bovine mastitis in Northwest China in 2014. A total of 44 S. aureus were isolated for antimicrobial resistance and resistance-related genes. Antimicrobial resistance was determined by disc diffusion and the corresponding resistance genes were detected by PCR. Phenotype indicated that S. aureus isolates were resistant to penicillin （84.09%）, erythromycin （20.45%）, tetracycline （15.91%）, gentamicin （9.09%）, tobramycin （6.82%）, kanamycin （6.82%） and methicillin （2.27%）. 9.09% of the S. aureus isolates were classified as multidrug resistant. In addition, genotypes showed that the isolates were resistant to rifampicin （100%, rpoB）, penicillin （95.45%, blaZ）, tetracycline （22.73%, tetK, tetM, alone or in combination）, erythromycin （22.73%, ermB or ermC）, gentamicin/tobramycin/kanamycin （2.27%, aacA-aphD）, methicillin （2.27%, mecA） and vancomycin （2.27%, vanA）. Resistance to tetracycline was attributed to the genes tetK and tetM （r=0.558, P〈0.001）. This study noted high-level geno- and phenotypic antimicrobial resistance in S. aureus isolates from bovine mastitis cases in Northwest China.

关键词： bovine mastitis Staphylococcus aureus antimicrobial resistance phenotype genotype

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Detection of antimicrobial resistance and virulence-related genes in Streptococcus uberis and Streptococcus parauberis isolated from clinical bovine mastitis cases in northwestern China

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Journal of Integrative Agriculture 2020年第11期19卷 2784-2791页

作者： ZHANG Hang YANG Feng LI Xin-pu LUO Jin-yin WANG Ling ZHOU Yu-long YAN Yong WANG Xurong LI Hong-sheng Lanzhou Institute of Husbandry and Pharmaceutical Sciences Chinese Academy of Agricultural Sciences/Key Lab of Veterinary Pharmaceutical DevelopmentMinistry of Agriculture and Rural Affairs/Engineering and Technology Research Center of Traditional Chinese Veterinary MedicineLanzhou 730050P.R.China

The objectives of this study were to investigate antimicrobial resistance of Streptococcus uberis and Streptococcus parauberis isolated from cows with bovine clinical mastitis in China and to examine the distribution of resistance-and virulence-related gene patterns.Antimicrobial susceptibility was determined by the E-test.Genes encoding antimicrobial resistance and invasiveness factors were examined by PCR.A total of 27 strains were obtained from 326 mastitis milk samples.Streptococcus parauberis isolates(n=11)showed high resistance to erythromycin(90.9%),followed by tetracycline(45.5%),chloramphenicol(36.4%)and clindamycin(27.3%).Streptococcus uberis isolates(n=16)were highly resistant to tetracycline(81.3%)and clindamycin(62.5%).Both species were susceptible to ampicillin.The most prevalent resistance gene in S.uberis was tetM(80.0%),followed by blaZ(62.5%)and ermB(62.5%).However,tetM,blaZ,and ermB genes were only found in 27.3,45.5,and 27.3%,respectively,of S.parauberis.In addition,all of the isolates carried at least one selected virulence-related gene.The most prevalent virulence-associated gene pattern in the current study was sua+pauA/skc+gapC+hasC detected in 22.2%of the strains.One S.uberis strain carried 7 virulence-associated genes and belonged to the sua+pauA/skc+gapC+cfu+hasA+hasB+hasC pattern.More than 59.3%of analysed strains carried 4 to 7 virulence-related genes.Our findings demonstrated that S.parauberis and S.uberis isolated from clinical bovine mastitis cases in China exhibited diverse molecular ecology,and that the strains were highly resistant to antibiotics commonly used in the dairy cow industry.The data obtained in the current study contribute to a better understanding of the pathogenesis of bacteria in mastitis caused by these pathogens,and the findings are relevant to the development of multivalent vaccines and targeted prevention procedures.

关键词： bovine mastitis Streptococcus uberis Streptococcus parauberis antimicrobial resistance virulence gene

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Evolution and molecular epidemiology of foot-and-mouth disease virus in China

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chinese Science Bulletin 2011年第21期56卷 2191-2201页

作者： BAI XingWen LI PingHua BAO HuiFang LIU ZaiXin LI Dong LU ZengJun CAO YiMei SHANG YouJun SHAO JunJun CHANG HuiYun LUO JianXun LIU XiangTao State Key Laboratory of veterinary Etiological Biology National Foot-and-Mouth Disease Reference LaboratoryEngineering Research Center of Biological Detection of Gansu ProvinceLanzhou Veterinary Research InstituteChinese Academy of Agricultural SciencesLanzhou 730046China

Foot-and-mouth disease (FMD),caused by foot-and-mouth disease virus (FMDV),is considered one of the most important viral diseases of cloven-hoofed animals,causing severe economic losses in affected regions of the world.Three serotypes (A,O,and Asia 1) of FMDV have been identified in China since 1958.In addition,the occurrence of novel subtypes within these serotypes has made the epidemiology of FMDV more complicated over the last few years.In this review,we summarize the history and the current epidemiological situation in China,genetic diversity (e.g.,quasispecies dynamics,antigenic heterogeneity,and functional constraints),intertypic recombination,and the evidence for positive selection of different FMDV serotypes.We also assess these genetic data to understand the origin,evolution,and transmission of FMDV,the findings of which may be useful in developing control measures for future epidemics.

关键词：分子流行病学病毒性传染病中国口蹄疫病毒演变 FMDV 偶蹄类动物遗传多样性

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Application of traditional chinese veterinary medicine in Sheep Green Breeding

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Animal Husbandry and Feed Science 2017年第5期9卷 293-297,338页

作者： Luo Chaoying Li Jinyu Wang Guibo Lanzhou Institute of Husbandry & Pharmaceutics Science CAAS Lanzhou 730050 China engineering & technology research center of traditional chinese veterinary medicine of gansu province Lanzhou 730050 China

Disease control and health care with traditional chinese veterinary medicine( TCVM) has attracted more and more attention in sheep green breeding. To promote healthy and smooth development of the work,the relationships between TCVM and antibiotics,and between TCVM and vaccines,were reviewed and analyzed. It was thought that TCVM and western medicine,such as antibiotics and vaccines,etc.,have their own characteristics and advantages,and should be mutually complemented rather than replaced. We should pay attention to the characteristics and advantages of the wholism concept and syndrome differentiation and treatment( diagnosis and treatment based on an overall analysis of the illness and the patient's condition) of TCVM,to develop and use TCVM health care agent or vaccine adjuvant,and their pertinence was improved according to different growth stages and physiological and pathological characteristics. Diagnosis and treatment based on an overall analysis of the illness and the population patient's condition must be attached importance to optimize the mode of administration,in order to adapt to disease prevention and control requirements in intensive and scale breeding of sheep.

关键词： Sheep green breeding Healthcare traditional chinese veterinary medicine (TCVM) Antibiotics Vaccines

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Genome-wide association study for numbers of vertebrae in Dezhou donkey population reveals new candidate genes

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Journal of Integrative Agriculture 2023年第10期22卷 3159-3169页

作者： SUN Yan LI Yu-hua ZHAO Chang-heng TENG Jun WANG Yong-hui WANG Tian-qi SHI Xiaoyuan LIU Zi-wen LI Hai-jing WANG Ji-jing WANG Wen-wen NING Chao WANG Chang-fa ZHANG Qin Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention College of Animal Science and TechnologyShandong Agricultural UniversityTai’an 271018P.R.China Liaocheng research Institute of Donkey High-Efficiency Breeding and Ecological Feeding Liaocheng UniversityLiaocheng 252059P.R.China National engineering research center for Gelatin-Based traditional chinese medicine Dong-E E-Jiao Co.Ltd.Liaocheng 252200P.R.China Shandong Provincial Key Laboratory of Animal Disease Control and Breeding Institute of Animal Science and Veterinary MedicineShandong Academy of Agricultural SciencesJinan 250100P.R.China

Numbers of vertebrae is an important economic trait associated with body size and meat productivity in animals.However,the genetic basis of vertebrae number in donkey remains to be well understood.The aim of this study was to identify candidate genes affecting the number of thoracic(TVn)and the number of lumbar vertebrae(LVn)in Dezhou donkey.A genome-wide association study was conducted using whole genome sequence data imputed from low-coverage genome sequencing.For TVn,we identified 38 genome-wide significant and 64 suggestive SNPs,which relate to 7 genes(NLGN1,DCC,SLC26A7,TOX,WNT7A,LOC123286078,and LOC123280142).For LVn,we identified 9 genome-wide significant and 38 suggestive SNPs,which relate to 8 genes(GABBR2,FBXO4,LOC123277146,LOC123277359,BMP7,B3GAT1,EML2,and LRP5).The genes involve in the Wnt and TGF-βsignaling pathways and may play an important role in embryonic development or bone formation and could be good candidate genes for TVn and LVn.

关键词： numbers of vertebrae GWAS genotype imputation Dezhou donkey

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Simultaneous estimation of surface soil moisture and soil properties with a dual ensemble Kalman smoother

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Science China Earth Sciences 2015年第12期58卷 2327-2339页

作者： CHU Nan HUANG ChunLin LI Xin DU PeiJun School of Environment Science and Spatial Informatics China University of Mining and Technology Key Laboratory of Remote Sensing of gansu province Cold and Arid Regions Environmental and Engineering Research InstituteChinese Academy of Sciences Heihe Remote Sensing Experimental research Station Cold and Arid Regions Environmental and Engineering Research InstituteChinese Academy of Sciences CAS center for Excellence in Tibetan Plateau Earth Sciences Chinese Academy of Sciences

In this paper, a new state-parameter estimation approach is presented based on the dual ensemble Kalman smoother(DEn KS) and simple biosphere model(Si B2) to sequentially estimate both the soil properties and soil moisture profile by assimilating surface soil moisture observations. The Arou observation station, located in the upper reaches of the Heihe River in northwestern China, was selected to test the proposed method. Three numeric experiments were designed and performed to analyze the influence of uncertainties in model parameters, atmospheric forcing, and the model's physical mechanics on soil moisture estimates. Several assimilation schemes based on the ensemble Kalman filter(En KF), ensemble Kalman smoother(En KS), and dual En KF(DEn KF) were also compared in this study. The results demonstrate that soil moisture and soil properties can be simultaneously estimated by state-parameter estimation methods, which can provide more accurate estimation of soil moisture than traditional filter methods such as En KF and En KS. The estimation accuracy of the model parameters decreased with increasing error sources. DEn KS outperformed DEn KF in estimating soil moisture in most cases, especially where few observations were available. This study demonstrates that the DEn KS approach is a useful and practical way to improve soil moisture estimation.

关键词：卡尔曼平滑土壤水分土壤性质集合参数估计方法平滑器卡尔曼滤波模型参数

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An equine disease diagnosis expert system based on improved reasoning of evidence credibility

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Information Processing in Agriculture 2019年第3期6卷 414-423页

作者： Hongyan Gao Guimiao Jiang Xiang Gao Jianhua Xiao Hongbin Wang Department of veterinary Surgery Northeast Agricultural UniversityHarbin 150030China National engineering research center for Gelatin-based traditional chinese medicine Dong-E-E-Jiao Co.Ltd.Liaocheng 252201China

In China,there is a troubling shortage of well-trained equine veterinarians,leaving the needs of many equine farmers unmet.This is especially true with respect to the diagnosis of equine diseases.To solve this shortcoming,an equine disease diagnosis expert system was developed.For the aspect of knowledge representation,the structure of equine disease diagnosis knowledge was analyzed using an ontology system.Next,the clinical signs were described using an object-attribute-value(O-A-V)format,and the knowledge representation was then expressed using production rules.With respect to the reasoning mechanism,the weights of the clinical signs and promoted confidence factors(PCF)were combined to express information and rules pertaining to clinical signs with an associated level of uncertainty.The model was established based on improved reasoning of evidence credibility.Finally,using the *** platform and the SQL Server 2008 database,the equine disease diagnosis expert system based on the B/S structure has been developed,and is capable of reliably diagnosing 40 of the most common equine diseases.A functional evaluation of the system was conducted,and the diagnostic accuracy was observed to be 88%.This study demonstrates a bright prospect for the popularization and application of the system through continuous system maintenance and knowledge-based updates.

关键词： Equine disease Diagnosis Expert system Object-based ontology Evidence credibility

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