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Genome-wide association study identifies 12 new genetic loci associated with growth traits in pigs

Journal of Integrative Agriculture 2024年第1期23卷 217-227页

作者： Mu Zeng Binhu Wang Lei Liu Yalan Yang zhonglin tang Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding/Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes School of Life Science and EngineeringFoshan UniversityFoshan 528231China Kunpeng Institute of Modern Agriculture at Foshan Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesFoshan 528200China Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture/Key Laboratory of Livestock and Poultry Multi-omics of Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Growth traits are among the most important economic traits in pigs and are regulated by polygenes with complex regulatory *** the major indicators of growth performance,the backfat thickness(BFT),loin eye area(LEA),and days to 100 kg(D100)traits are commonly used to the genetics improvement in ***,the available genetic markers for these traits are *** uncover novel loci and candidate genes associated with growth performance,we collected the phenotypic information of BFT,LEA,and D100 in 1,186 pigs and genotyped all these individuals using the Neogen GGP porcine 80K *** performed a genome-wide association study(GWAS)using 4 statistical models,including mixed linear models(MLM),fixed and random model circulating probability unification(FarmCPU),settlement of MLM under progressively exclusive relationships(SUPER),Bayesian-information and linkage-disequilibrium Iteratively nested keyway(Blink),and identified 5,3,and 6 high-confidence single nucleotide polymorphisms(SNPs)associated with BFT,LEA,and D100,*** annotation and quantitative trait locus(QTL)mapping analysis suggested that6 genes(SKAP2,SATB1,PDE7B,PPP1R16B,WNT3,and WNT9B)were potentially associated with growth performance in *** analysis suggested that the expression of Src Kinase Associated Phosphoprotein 2(SKAP2)was higher in prenatal muscles than in postnatal muscles,and the expression of Phosphodiesterase 7B(PDE7B)continuously increased during the prenatal stages and gradually decreased after birth,implying their potential roles in prenatal skeletal muscle ***,this study provides new candidate loci and genes for the genetic improvement of pigs.

关键词： GWAS pig growth trait QTL mapping skeletal muscle

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Biology of Hippo signaling pathway:Skeletal muscle development and beyond

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Journal of Integrative Agriculture 2024年第6期23卷 1825-1838页

作者： Shuqi Qin Chaocheng Li Haiyan Lu Yulong Feng Tao Guo Yusong Han Yongsheng Zhang zhonglin tang Xinjiang Characteristic Livestock Breeding and Reproduction Team College of Animal Science and TechnologyShihezi UniversityShihezi 832003China Lanzhou Veterinary Research Institute Chinese Academy of Agricultural SciencesLanzhou 730046China Kunpeng Institute of Modern Agriculture at Foshan Foshan 528226China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Global demand for farm animals and their meat products i.e.,pork,chicken and other livestock meat,is steadily *** the ongoing life science research and the rapid development of biotechnology,it is a great opportunity to develop advanced molecular breeding markers to efficiently improve animal meat production *** is an important study subject because of its crucial role in the regulation of organ *** recent years,with the increase of research on Hippo signaling pathway,the integrative application of multi-omics technologies such as genomics,transcriptomics,proteomics,and metabolomics can help promote the in-depth involvement of Hippo signaling pathway in skeletal muscle development *** Hippo signaling pathway plays a key role in many biological events,including cell division,cell migration,cell proliferation,cell differentiation,cell apoptosis,as well as cell adhesion,cell polarity,homeostasis,maintenance of the face of mechanical overload,*** influence on the development of skeletal muscle has important research value for enhancing the efficiency of animal husbandry *** this study,we traced the origin of the Hippo pathway,comprehensively sorted out all the functional factors found in the pathway,deeply analyzed the molecular mechanism of its function,and classified it from a novel perspective based on its main functional domain and mode of *** aim is to systematically explore its regulatory role throughout skeletal muscle *** specifically focus on the Hippo signaling pathway in embryonic stem cell development,muscle satellite cell fate determination,myogenesis,skeletal muscle meat production and organ size regulation,muscle hypertrophy and atrophy,muscle fiber formation and its transformation between different types,and *** roles in proliferation and regeneration are methodically summarized and analyzed *** summary and prospect of the Hippo signaling pathway within this a

关键词： Hippo skeletal muscle organ size myogenesis C2C12 livestock animals

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miR-378a-3p responds to physical activity by modulating insulin-mediated glucose uptake and tricarboxylic acid cycle in skeletal muscle

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Genes & Diseases 2024年第3期11卷 98-101页

作者： Zishuai Wang Yilong Yao Xinhua Hou Danyang Fan Yanwen Liu Adeyinka Abiola Adetula Yalan Yang kui Li zhonglin tang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong518000China Kunpeng Institute of Modern Agriculiture at Foshan Chinese Academy of Agricultural SciencesFoshanGuangdong528226China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig BamaGuangxi 547500China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing100193China

Aerobic exercise training alters gene expression in skeletal muscle,and miRNAs significantly contribute to motion ***,the molecular mechanisms by which miRNAs regulate the response to exercise training are not well ***,we found that the abundance of miR-378a-3p in skeletal muscle significantly decreased after exercise ***-378a-3p knockout mice showed increased insulin sensitivity,insulin-mediated glucose uptake.

关键词： skeletal miR uptake

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基于颜色空间融合的电子鼻特征优化方法研究

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自动化应用 2024年第11期65卷 38-41页

作者：唐忠林陕西工业职业技术学院航空工程学院陕西咸阳712000

为了提高光电子鼻的气体区分能力,对7种气体样本进行了检测和分类实验。将敏感阵列的响应图像从RGB颜色空间向其他6种典型的颜色空间进行了转换,并通过增L减R(L-R)搜索算法,在欧式距离样本可分性判据的基础上,从新生成的7种颜色空间中... 详细信息

为了提高光电子鼻的气体区分能力,对7种气体样本进行了检测和分类实验。将敏感阵列的响应图像从RGB颜色空间向其他6种典型的颜色空间进行了转换,并通过增L减R(L-R)搜索算法,在欧式距离样本可分性判据的基础上,从新生成的7种颜色空间中优选了18个颜色通道组成融合空间。主成分分析和欧式距离可分性判据对比表明,电子鼻在融合颜色空间的气体响应特征向量的类别可分性要显著优于其他颜色空间。

关键词：颜色特征优化空间融合搜索算法电子鼻

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转食饲料对大口黑鲈幼鱼的存活率、抗氧化酶和消化酶活性及肠道菌群的影响

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中国水产科学 2024年第4期31卷 403-415页

作者：马兴宇唐忠林陈树桥周国勤徐钢春南京市水产科学研究所中国水产科学研究院淡水渔业研究中心

转食配合饲料是大口黑鲈(Micropterussalmoides)幼鱼培育的一个重要环节,为了找到大口黑鲈幼鱼适宜转食的规格以及转食对幼鱼生理生化的影响,本研究探讨了摄食丰年虫(Artemia salina)幼鱼转食饲料后,其存活率、组织抗氧化酶和消化酶活... 详细信息

转食配合饲料是大口黑鲈(Micropterussalmoides)幼鱼培育的一个重要环节,为了找到大口黑鲈幼鱼适宜转食的规格以及转食对幼鱼生理生化的影响,本研究探讨了摄食丰年虫(Artemia salina)幼鱼转食饲料后,其存活率、组织抗氧化酶和消化酶活性及肠道菌群的变化。实验选取了平均体长分别为(1.06±0.02)cm、(2.04±0.03)cm、(3.02±0.04) cm、(4.05±0.04) cm、(5.01±0.04) cm共5种规格幼鱼,设为体长1 cm、2 cm、3 cm、4 cm、5 cm组进行转食实验,统计了幼鱼自然死亡率、存活率和残食率。通过酶活测定方法对比分析了转食前后幼鱼肝脏与肌肉组织的抗氧化酶活性变化及胃、肠道和幽门盲囊组织的消化酶活性变化。通过高通量测序方法对比分析了转食前后幼鱼肠道菌群的变化。结果显示:(1)体长1cm幼鱼转食死亡率、残食率最高,存活率最低,分别为60.31%、30.85%和8.84%;体长4cm、5cm幼鱼死亡率和残食率为0,存活率为100%,表明规格越大死亡率和残食率越低,存活率越高。(2)转食后肝脏与肌肉的过氧化物歧化酶(SOD)活性分别升高了86.97%和16.62%(P<0.05),肝脏过氧化氢酶(CAT)活性下降了58.60%(P<0.05)。(3)转食对肠道中消化酶活性影响最为显著,转食后肠道中胰蛋白酶、脂肪酶及淀粉酶活性均显著下降,分别为50.11%、40.71%和42.79%(P<0.05);胃中胰蛋白酶活性下降了18.33%(P<0.05),幽门盲囊中消化酶活性无显著性变化。(4)转食后肠道放线菌门(Actinobacteriota)显著下降(40.91%vs13.33%),厚壁菌门(Firmicutes)显著上升(14.03%vs64.60%);属水平上转食前优势菌为分支杆菌属(Mycobacterium, 24.73%)、微杆菌属(Microbacterium, 10.25%)和副球菌属(Paracoccus, 10.05%),转食后优势菌为乳球菌属(Lactococcus, 14.96%)、支原体属(Mycoplasma, 13.55%)和芽孢杆菌属(Bacillus, 9.32%);转食前后共有不同水平的51个细菌类群发生显著性差异。结果表明,幼鱼最佳转食规格为体长3～4 cm,转食产生的应激反应引起了组织氧化损伤,降低了消化酶的活性,肠道优势菌群发生显著的转变。本研究可为提高大口黑鲈幼鱼转食存活率及添加外源辅助消化物质研究提供参考。

关键词：大口黑鲈幼鱼转食存活率抗氧化酶消化酶肠道菌群

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Coordinated transcriptional and post-transcriptional epigenetic regulation during skeletal muscle development and growth in pigs

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Journal of Animal Science and Biotechnology 2023年第2期14卷 564-577页

作者： Du Zhang Shumei Wu Xinxin Zhang Shuqiang Ren zhonglin tang Fei Gao Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China College of Animal Sciences South China Agricultural UniversityGuangdong Provincial Key Lab of Agro-animal Genomics and Molecular BreedingNational Engineering Research Center for Breeding Swine IndustryGuangzhou 510642China Kunpeng Institute of Modern Agriculture at Foshan Chinese Academy of Agricultural SciencesFoshan 528226China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig Bama 547500China Comparative Pediatrics and Nutrition Department of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark.

Background:N6-methyladenosine(m^(6)A)and DNA 5-methylcytosine(5mC)methylation plays crucial roles in diverse biological processes,including skeletal muscle development and *** studies unveiled a potential link between these two systems,implicating the potential mechanism of coordinated transcriptional and post-transcrip-tional regulation in porcine prenatal myogenesis and postnatal skeletal muscle ***:Immunofluorescence and co-IP assays were carried out between the 5mC writers and m^(6)A writers to investigate the molecular basis ***-scale in-house transcriptomic data were compiled for applying weighted correlation network analysis(WGCNA)to identify the co-expression patterns of m^(6)A and 5mC regulators and their potential role in pig ***-genome bisulfite sequencing(WGBS)and methylated RNA immu-noprecipitation sequencing(MeRIP-seq)were performed on the skeletal muscle samples from Landrace pigs at four postnatal growth stages(days 30,60,120 and 180).Results:Significantly correlated expression between 5mC writers and m^(6)A writers and co-occurrence of 5mC and m^(6)A modification were revealed from public datasets of C2C12 *** protein-protein interactions between the DNA methylase and the m^(6)A methylase were observed in mouse myoblast ***,by analyzing tran-scriptome data comprising 81 pig skeletal muscle samples across 27 developmental stages,we identified a 5mC/m^(6)A epigenetic module eigengene and decoded its potential functions in pre-or post-transcriptional regulation in postnatal skeletal muscle development and growth of *** integrative multi-omics analyses on the WGBS methylome data and MeRIP-seq data for both m^(6)A and gene expression profiles revealed a genome/transcriptome-wide correlated dynamics and co-occurrence of 5mC and m^(6)A modifications as a consequence of 5mC/m^(6)A crosstalk in the postnatal myogenesis progress of ***,we identified a group of myogenesis-relat

关键词： DNA methylation Epigenetic modification Epigenomic analysis 5mC regulators m^(6)A methylation m^(6)A regulators Myogenesis

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一种基于薄膜式力敏电阻的咬合力检测系统的设计与测试

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医疗装备 2024年第13期37卷 7-10,14页

作者：唐忠林雷宏伟李向东陕西工业职业技术学院航空工程学院陕西咸阳712000 西安苏茂医疗科技有限公司陕西西安710077 解放军95685部队云南昆明650600

咬合力是衡量咀嚼功能的重要指标,目前临床尚无广泛使用的咬合力检测产品。该研究利用薄膜式力敏电阻(FSR)作为传感器,采用高精度数据采集卡和LabWindows/CVI程序设计了一种咬合力检测系统,并在50~500 N压力范围内进行了压力-电压响应... 详细信息

咬合力是衡量咀嚼功能的重要指标,目前临床尚无广泛使用的咬合力检测产品。该研究利用薄膜式力敏电阻(FSR)作为传感器,采用高精度数据采集卡和LabWindows/CVI程序设计了一种咬合力检测系统,并在50~500 N压力范围内进行了压力-电压响应特性测试和真人咬合测试。结果显示,该系统具有良好的线性响应,压力测量的平均相对误差为8.2%,灵敏度为344.827N/V,分辨率为1.68N,且咬合安装方便,可明显区分5名受试人员的咬合力差异,具备实际应用潜力。

关键词：力敏电阻咬合力虚拟仪器软件口腔检测系统

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Single-cell analysis reveals the lncRNA-MEG3/miRNA-133a-3p/PRRT2 axis regulates skeletal muscle regeneration and myogenesis

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Genes & Diseases 2023年第2期10卷 359-362页

作者： Yilong Yao Zishuai Wang Yun Chen Lei Liu Liyuan Wang Guoqiang Yi Yalan Yang Dazhi Wang Kui Li zhonglin tang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518000China Kunpeng Institute of Modern Agriculture at Foshan FoshanGuangdong 528226China Center for Regenerative Medicine University of South Florida Health Heart Institute Morsani College of MedicineUniversity of South FloridaFL 33602USA Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518000China GuangXi Engineering Centre for Resource Development of Bama Xiang Pig BamaGuangxi 547500China State Key Laboratory of Animal Nutrition Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China

Skeletal muscle is the largest motor and metabolic organ of the body, which has a robust capacity for regeneration following injury or disease. Delayed regeneration after skeletal muscle injury reduces muscle contractility and leads to dysfunction of innervation. Therefore, identifying the regulation components in skeletal muscle regeneration and determining their molecular mechanisms are important to discover novel therapeutic markers for muscular diseases. Long non-coding RNA (LncRNA) has been implicated in skeletal muscle regeneration. Recent developed single-cell RNA sequencing (scRNA-seq) provides a higher resolution of cellular differences than bulk RNA-seq. Here, we re-analyzed single-cell transcriptomes data of skeletal muscle regeneration and identified lncRNA maternally expressed gene 3 (lncRNA-MEG3) was highly expressed in muscle satellite cells (MuSCs). Further study showed that lncRNA-MEG3 regulates skeletal muscle regeneration via sponging miR-133a-3p to regulate proline-rich transmembrane protein 2 (PRRT2) expression level. These results suggested that lncRNA-MEG3 might be a potential target for skeletal muscle diseases.

关键词： MEG3 skeletal muscular

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MiR-743a-5p regulates differentiation of myoblast by targeting Mob1b in skeletal muscle development and regeneration

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Genes & Diseases 2022年第4期9卷 1038-1048页

作者： YongSheng Zhang YiLong Yao ZiShuai Wang Dan Lu YuanYuan Zhang Adeyinka Abiola Adetula SiYuan Liu Min Zhu YaLan Yang XinHao Fan MuYa Chen YiJie tang Yun Chen YuWen Liu GuoQiang Yi zhonglin tang Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124PR China Genome Analysis Laboratory of the Ministry of Agriculture Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518124PR China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193PR China

The microRNAs (miRNAs) play an important role in regulating myogenesis by targeting mRNA. However, the understanding of miRNAs in skeletal muscle development and diseases is unclear. In this study, we firstly performed the transcriptome profiling in differentiating C2C12 myoblast cells. Totally, we identified 187 miRNAs and 4260 mRNAs significantly differentially expressed that were involved in myoblast differentiation. We carried out validation of microarray data based on 5 mRNAs and 5 miRNAs differentially expressed and got a consistent result. Then we constructed and validated the significantly up- and down-regulated mRNA-miRNA interaction networks. Four interaction pairs (miR-145a-5p-Fscn1, miR-200c-5p-Tmigd1, miR-27a-5p-Sln and miR-743a-5p-Mob1b) with targeted relationships in differentiated myoblast cells were demonstrated. They are all closely related to myoblast development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated cell cycle signals important for exploring skeletal muscle development and disease. Functionally, we discovered that miR-743a targeting gene Mps One Binder Kinase Activator-Like 1B (Mob1b) gene in differentiated C2C12. The up-regulated miR-743a can promote the differentiation of C2C12 myoblast. While the down-regulated Mob1b plays a negative role in differentiation. In addition, the expression profile of miR-743a and Mob1b are consistent with skeletal muscle recovery after Cardiotoxin (CTX) injury. Our study revealed that miR-743a-5p regulates myoblast differentiation by targeting Mob1b involved in skeletal muscle development and regeneration. Our findings made a further exploration for mechanisms in myogenesis and might provide potential possible miRNA-based target therapies for skeletal muscle regeneration and disease in the near future.

关键词： Differentiation miR 743a-5p Mob 1b Myoblast Skeletal muscle .Transcriptome

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Longitudinal epitranscriptome profiling reveals the crucial role of N^(6)-methyladenosine methylation in porcine prenatal skeletal muscle development

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Journal of Genetics and Genomics 2020年第8期47卷 465-476页

作者： Xinxin Zhang Yilong Yao Jinghua Han Yalan Yang Yun Chen zhonglin tang Fei Gao Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen518124China Comparative Pediatrics and Nutrition Department of Veterinary and Animal SciencesFaculty of Health and Medical SciencesUniversity of CopenhagenFrederiksbergDK-2000Denmark Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijing100193China

N6-methyladenosine(m6A)represents the most abundantly occurring m RNA modification and is involved in the regulation of skeletal muscle ***,the status and function of m6A methylation in prenatal myogenesis remains *** this study,we first demonstrated that knockdown of METTL14,an m6A methyltransferase,inhibited the differentiation and promoted the proliferation of C2 C12 myoblast ***,using a refined m6A-specific methylated RNA immunoprecipitation(RIP)with next generation sequencing(Me RIP-seq)method that is optimal for use with samples containing small amounts of RNA,we performed transcriptome-wide m6A profiling for six prenatal skeletal muscle developmental stages spanning two important waves of porcine *** results revealed that,along with a continuous decrease in the m RNA expression of the m6A reader protein insulin-like growth factor 2 m RNA-binding protein 1(IGF2 BP1),the m6A methylome underwent highly dynamic changes across different development stages,with most of the affected genes being enriched in pathways related to skeletal muscle *** immunoprecipitation confirmed that IGF2 BP1 targets 76 genes involved in pathways associated with muscle development,including the key marker genes MYH2 and Myo ***,small interfering RNA(si RNA)-mediated knockdown of IGF2 BP1 induced phenotypic changes in C2C12 myoblasts similar to those observed with knockdown of *** conclusion,we clarified the dynamics of m6A methylation and identified key genes involved in the regulatory network of porcine skeletal muscle development.

关键词： N^(6)-methyladenosine IGF2BP1 Myoblast Skeletal muscle

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