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The impact of genomic relatedness between populations on the genomic estimated breeding values

Journal of Animal Science and Biotechnology 2018年第4期9卷 841-846页

作者： Peipei Ma Ju Huang Weijia Gong Xiujin Li Hongding Gao Qin Zhang Xiangdong Ding Chonglong Wang National Engineering Laboratory for Animal breeding Laboratory of Animal GeneticsBreeding and ReproductionMinistry of AgricultureCollege of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China Department of Animal Science School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghai 200240China Gènes DIFFSUION 3595 Route de Tourna59500 DouaiFrance Center for Quantitative Genetics and Genomics Department of Molecular Biology and GeneticsAarhus UniversityTjeleDenmark Key Laboratory of pig Molecular Quantitative Genetics Institute of Animal Husbandry and Veterinary MedicineAnhui Academy of Agricultural SciencesHefei 230031China

In genomic selection, prediction accuracy is highly driven by the size of animals in the reference population(RP).Combining related populations from different countries and regions or using a related population with large size of RP has been considered to be viable strategies in cattle breeding. The genetic relationship between related populations is important for improving the genomic predictive ability. In this study, we used 122 French bulls as test individuals. The genomic estimated breeding values(GEBVs) evaluated using French RP, America RP and Chinese RP were *** results showed that the GEBVs were in higher concordance using French RP and American RP compared with using Chinese population. The persistence analysis, kinship analysis and the principal component analysis(PCA) were performed for 270 French bulls, 270 American bulls and 270 Chinese bulls to interpret the results. All the analyses illustrated that the genetic relationship between French bulls and American bulls was closer compared with Chinese bulls. Another reason could be the size of RP in China was smaller than the other two RPs. In conclusion, using RP of a related population to predict GEBVs of the animals in a target population is feasible when these two populations have a close genetic relationship and the related population is large.

关键词： Genomic prediction Genomic relationship Joint population prediction

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The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

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Journal of Animal Science and Biotechnology 2013年第2期4卷 145-151页

作者： Guanghui Yu Hai Xiang Jikun Wang Xingbo Zhao National Engineering Laboratory for Animal breeding Ministry of Agricultural Key Laboratory of Animal Genetics Breeding and Reproduction State Key Laboratory for Agribiotechnology College of Animal Science and Technology China Agricultural University

China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences (mtDNA) from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European clade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.

关键词： Mitochondrial DNA Origin and evolution Phylogenetic analysis pig

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Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population

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Journal of Integrative Agriculture 2021年第6期20卷 1607-1614页

作者： HANG Zhe CHEN Zi-tao DIAO Shu-qi YE Shao-pan WANG Jia-ying GAO Ning YUAN Xiao-long CHEN Zan-mou ZHANG Hao LI Jia-qi Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular breeding/National Engineering Research Center for breeding Swine Industry/College of Animal Science South China Agricultural UniversityGuangzhou 510642P.R.China

In modern pig breeding programs,growth and fatness are vital economic traits that significantly influence porcine *** identify underlying variants and candidate genes associated with growth and fatness traits,a total of 1067 genotyped Duroc pigs with de-regressed estimated breeding values(DEBV)records were analyzed in a genome wide association study(GWAS)by using a single marker regression *** total,28 potential single nucleotide polymorphisms(SNPs)were associated with these traits of ***,VPS4 B,PHLPP1,and some other genes were highlighted as functionally plausible candidate genes that compose the underlying genetic architecture of porcine growth and fatness *** findings contribute to a better understanding of the genetic architectures underlying swine growth and fatness traits that can be potentially used in pig breeding programs.

关键词： pig GWAS growth trait fatness trait candidate gene

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Transcriptomic analysis elucidates the enhanced skeletal muscle mass, reduced fat accumulation, and metabolically benign liver in human follistatin-344 transgenic pigs

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Journal of Integrative Agriculture 2022年第9期21卷 2675-2690页

作者： LONG Ke-ren LI Xiao-kai ZHANG Ruo-wei GU Yi-ren DU Min-jie XING Xiang-yang DU Jia-xiang MAI Miao-miao WANG Jing JIN Long TANG Qian-zi HU Si-lu MA Ji-deng WANG Xun PAN Deng-ke LI Ming-zhou Institute of Animal Genetics and breeding College of Animal Science and TechnologySichuan Agricultural UniversityChengdu 611130P.R.China Animal breeding and Genetics Key Laboratory of Sichuan Province Pig Science InstituteSichuan Animal Science AcademyChengdu 610066P.R.China Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijing 100193P.R.China Institute of Organ Transplantation Sichuan Academy of Medical Sciences&Sichuan Provincial People's HospitalChengdu 610072P.R.China Chengdu Clonorgan Biotechnology Co. Ltd.Chengdu 610041P.R.China

Follistatin(FST) is an important regulator of skeletal muscle growth and adipose deposition through its ability to bind to several members of the transforming growth factor-β(TGF-β) superfamily, and thus may be a good candidate for future animal breeding programs. However, the molecular mechanisms underlying the phenotypic changes have yet to be clarified in pig. We generated transgenic(TG) pigs that express human FST specifically in skeletal muscle tissues and characterized the phenotypic changes compared with the same tissues in wild-type pigs. The TG pigs showed increased skeletal muscle growth, decreased adipose deposition, and improved metabolism status(Ppigs. Gene set enrichment analysis revealed that genes related to lipid synthesis, lipid catabolism, and lipid storage were down-regulated(Ppigs for subcutaneous fat, whereas genes related to lipid catabolism were significantly up-regulated(Ppigs for retroperitoneal fat compared with their expression levels in wild-type pigs. In liver, genes related to the TGF-β signaling pathway were over-represented in the TG pigs, which is consistent with the inhibitory role of FST in regulating TGF-β signaling. Together, these results provide new insights into the molecular mechanisms underlying the phenotypic changes in pig.

关键词： follistatin transgenic pig transcriptome skeletal muscle liver adipose

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Exploring the genetic features and signatures of selection in South China indigenous pigs

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Journal of Integrative Agriculture 2021年第5期20卷 1359-1371页

作者： DIAO Shu-qi XU Zhi-ting YE Shao-pan HUANG Shu-wen TENG Jin-yan YUAN Xiao-long CHEN Zan-mou ZHANG Hao LI Jia-qi ZHANG Zhe Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular breeding/National Engineering Research Center for breeding Swine Industry/College of Animal Science South China Agricultural UniversityGuangzhou 510642P.R.China

To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs,259 pigs from six populations were genotyped using single-nucleotide polymorphism(SNP)*** component analysis(PCA),effective population size(Ne),linkage disequilibrium(LD),and signatures of selection were explored and investigated among the six pig *** results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations *** LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations,while it was 0.32 for the Duroc ***,the LD of all six pig populations showed the opposite order at long distances(>5 Mb).Furthermore,15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs,while eight potential signatures of selection associated with growth traits were detected in Duroc *** work provides valuable insights for the utilization and conservation of South China indigenous pigs.

关键词： pigs population structure effective population size SNP

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Isolation, cDNA sequence analysis and tissue expression profile of a novel swine gene differentially expressed in the Longissimus dorsi muscle tissues from Large White x Meishan cross combination

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Progress in Natural Science:Materials International 2005年第12期15卷 1073-1078页

作者： LIU Yonggang,LEI Minggang,XIONG Yuanzhu and DENG Changyan Key Laboratory of Swine Genetics and breeding,Ministry of Agriculture,Huazhong Agricultural University,Wuhan 430070,China Key Laboratory of Swine Genetics and breeding Ministry of Agriculture Huazhong Agricultural University Wuhan 430070 China

In order to study the molecular mechanism of heterosis in pigs,the mRNA differential display technique was performed to investigate the differences in gene expression in the Longissimus dorsi muscle tissues from Large White×Meishan cross combination. One novel gene differentially expressed between the hybrids and the purebreds was isolated and subsequently identified using semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR) and its complete cDNA sequence was obtained using the rapid amplification of cDNA ends (RACE) *** nucleotide sequence of the gene is not homologous to any of the known porcine *** sequence prediction revealed that the open reading frame of this gene encodes a protein of 188 amino acids that contains the putative conserved domain of the PRAl family protein and this protein has high homology with the PRA1 family protein 3 of three species-rat (88% ),human (88%),and mouse (87%),-so that it can be defined as swine PRA1 family protein *** phylogenetic tree analysis revealed that the swine PRA1 family protein 3 has a closer genetic relationship with the human PRA1 family protein 3 than with those of mouse and rat. The tissue expression analysis indicated that swine PRA1family protein 3 gene is highly-expressed in muscle and fat,moderately in spleen, weakly in heart,kidney,ovary,lung,and almost not expressed in small intestine and *** function of this gene and the relationship between this gene and heterosis are also discussed.

关键词： pig heterosis Longissimus dorsi mRNA differential display RACE PRA1 family protein 3

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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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cDNA Cloning,Sequence Analysis of the Porcine LIM and Cysteine-rich Domain 1 Gene

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Acta Biochimica et Biophysica Sinica 2005年第12期37卷 843-850页

作者： Jun WANG Chang-Yah DENG Yuan-Zhu XIONG Bo ZUO Lei XING Feng-E LI Ming-Gang LEI Rong ZHENG Si-Wen JIANGKey Laboratiry of Swine Genetics and breeding,Ministry of Agriculture.College of Animal Sciences,Huazhong Agricultural University.Wuhan 430070,China Key Laboratory of Swine Genetics and breeding Ministry of Agriculture College of Animal Sciences Huazhong Agricultural UniversityWuhan 430070 China

LIM domain proteins are important regulators in cell growth,cell fate determination,celldifferentiation and remodeling of the cell cytoskeleton by their interaction with various structural proteins,kinases and transcriptional *** molecular biology combined with in silico cloning,we havecloned the complete coding sequence of pig LIM and the cysteine-rich domain 1 gene (LMCD1) whichencodes a 363 amino acid *** estimated molecular weight of the LMCD1 protein is 40,788 Da witha pI of *** was found to be highly expressed in both skeletal muscle and cardiac *** revealed that the deduced protein sequence shares 86%,91% and 93% homology with that of itshuman,mouse and rat counterparts,*** LMCD 1 protein was predicted by bioinformaticssoftware to contain a novel cysteine-rich domain in the N-terminal region,two LIM domains in theC-terminal region,nine potential protein kinase C phosphorylation sites,seven casein kinase Ⅱ phosphorylationsites,a tyrosine kinase phosphorylation site,seven N-glycosylation and N-myristoylation sites and a singlepotential N-glycosylation site,which is similar to the protein’s human *** tree wasconstructed by aligning the amino acid sequences of the LIM domain trom different *** addition,fourbase mutations were detected by comparing the sequences of Large White pigs with those of ChineseMeishan *** G294A mutation site was confirmed by polymerase chain reaction-single-strandconformation polymorphism *** allele frequencies were studied in five pig breeds.

关键词： LIM and cysteine-rich domain 1(LMCD1) SSCP PCR gene expression data analysis

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Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

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Journal of Animal Science and Biotechnology 2021年第2期12卷 492-507页

作者： Jingya Xu Yuhua Fu Yan Hu Lilin Yin Zhenshuang Tang Dong Yin Mengjin Zhu Mei Yu Xinyun Li Yang Zhou Shuhong Zhao Xiaolei Liu Key Laboratory of Agricultural Animal Genetics Breeding and ReproductionMinistry of Education&Key Laboratory of Swine Genetics and BreedingMinistry of Agriculture&College of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiPR China

Background:A large number of pig breeds are distributed around the world,their features and characteristics vary among breeds,and they are valuable *** the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig ***:In this study,we performed GWAS using a standard mixed linear model with three types of genome variants(SNP,InDel,and CNV)that were identified from public,whole-genome,sequencing data *** used 469 pigs of 57 breeds,and we identified and analyzed approximately 19 million SNPs,1.8 million InDels,and 18,016 *** defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes,which included coat color,ear shape,gradient zone,body weight,body length,and body height.A total of 37 candidate genes was identified,which included 27 that were reported previously(e.g.,PLAG1 for body weight),but the other 10 were newly detected candidate genes(e.g.,ADAMTS9 for coat color).Conclusion:Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

关键词： Breed feature CNV GWAS InDel pig SNP

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Development and evaluation of neutralizing antibodies for cross-protection against West Nile virus and Japanese encephalitis virus

Infectious Medicine

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Infectious Medicine 2023年第3期2卷 212-223页

作者： Meng-Jie Yang Hao-Ran Luo Zhen-Yu Fan Yu-Xiang Feng Ning Wei Bi-Bo Zhu Jing Ye Sheng-Bo Cao You-Hui Si National Key Laboratory of Agricultural Microbiology College of Veterinary MedicineHuazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory Wuhan 430070China Frontiers Science Center for Animal breeding and Sustainable Production Huazhong Agricultural UniversityWuhan 430070China The Cooperative Innovation Center for Sustainable pig Production Huazhong Agricultural UniversityWuhan 430070China

Background:West Nile virus is a severe zoonotic pathogen that can cause severe central nervous system symptoms in humans and horses,and is fatal for birds,chickens and other *** no specific drugs or vaccines available,antibody-based therapy is a promising *** study aims to develop neutralizing antibodies against West Nile virus and assess their cross-protective potential against Japanese encephalitis ***:Monoclonal antibodies against WNV and JEV were isolated by hybridoma *** therapeutic efficacy of these antibodies was evaluated using a mouse model,and a humanized version of the monoclonal antibody was generated for potential human ***:In this study,we generated eight monoclonal antibodies that exhibit neutralizing activity against *** therapeutic effects against WNV were validated both in vivo and in *** these antibodies,C9-G11-F3 also exhibited cross-protective activity against *** also humanized the antibody to ensure that it could be used for WNV infection treatment in ***:This study highlights the importance of neutralizing antibodies as a promising approach for pro-tection against West Nile virus infection and suggests their potential utility in the development of therapeutic interventions.

关键词： West Nile virus Neutralizing antibodies Cross protection Therapeutic antibodies Humanization

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