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Porcine methionine sulfoxide reductase B3:molecular cloning,tissue-specific expression profiles,and polymorphisms associated with ear size in Sus scrofa

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Journal of Animal Science and Biotechnology 2016年第2期7卷 149-157页

作者： Yuebo zhang Jing Liang longchao zhang Ligang Wang Xin Liu Hua Yan Kebin Zhao Huibi Shi Tian zhang Na Li Lei Pu Lixian Wang Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation Ministry of AgricultureInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China Jilin Academy of Agricultural Sciences Changchun 130033China

Background： In Sus scrofa, methionine sulfoxide reductase B3（MSRB3） is a crucial candidate gene for ear size, and an important conformational trait of pig breeds. However, challenges in MSRB3 c DNA amplification have prevented further identification of MSRB3 allelic variants influencing pig ear ***： We cloned a full-length c DNA sequence of porcine MSRB3 by rapid-amplification of c DNA ends. The3,765-bp gene contained a 5＇-untranslated region（UTR）（190 bp）, a coding region（552 bp）, and a 3＇-UTR（3,016 bp） and shared 84 %, 84 %, 87 %, 86 %, and 70 % sequence identities with human, orangutan, mouse, chicken, and zebrafish,respectively. The gene encoded a 183-amino acid protein, which shared 88 %, 91 %, 89 %, 86 %, and 67 % identities with human, orangutan, mouse, chicken, and zebrafish, respectively. Tissue expression analysis using q RT-PCR revealed that MSRB3 was expressed in the heart, liver, lung, kidney, spleen, ear, muscle, fat, lymph, skeletal, and hypothalamic tissues. Three single nucleotide polymorphisms（SNPs） were identified in MSRB3： c.-735 C 〉 T in the 5＇ flanking region,c.2571 T 〉 C in the 3＇-UTR, and a synonymous mutation of c.484 T 〉 C in the coding region. The SNPs c.-735 C 〉 T and c.2571 T 〉 C were significantly associated with ear size in a Large White × Minzhu F2 population other than in Beijing Black pigs. Subsequently, at SNP c.-735 C 〉 T, the m RNA of MSRB3 was significantly higher expressed in ears of individuals with the TT genotype（Minzhu） than those with CC（Large White）.Conclusions： The porcine MSRB3 owned a 3,765-bp full-length c DNA sequence and was detected to express in ear tissue. Two SNPs of this gene were shown to be significantly associated with ear size in a Large White × Minzhu intercross population instead of Beijing Black pig population. What＇s more, the individuals with higher m RNA expression of MSRB3 have larger ear sizes. These results provide useful information for further functional analyses of MSRB3 influencing ear

关键词： Association study Ear size Expression MSRB3 cloning Pig

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Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing

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Journal of Animal Science and Biotechnology 2019年第2期10卷 339-352页

作者： Yuebo zhang longchao zhang Jingwei Yue Xia Wei Ligang Wang Xin Liu Hongmei Gao Xinhua Hou Fuping Zhao Hua Yan Lixian Wang Key Laboratory of Animal(Poultry)Genetics Breeding and Reproduction Ministry of Agriculture Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China

Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still ***: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue ***, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the ***: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.

关键词： ADAR A-to-G High-throughput sequencing RNA editing Swine

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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 ***(≥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 *** 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 *** high-quality SVs were used to recover the population genetic structure,confirming the accuracy of *** functional SV loci were then identified based on positional effects and breed ***,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic *** 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 *** addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,*** 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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Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population

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Journal of Animal Science and Biotechnology 2020年第4期11卷 965-974页

作者： Liangyu Shi Ligang Wang Jiaxin Liu Tianyu Deng Hua Yan longchao zhang Xin Liu Hongmei Gao Xinhua Hou Lixian Wang Fuping Zhao Key Laboratory of Animal Genetics Breeding and Reproduction(poultry)of Ministry of AgricutureInstitute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China

Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate ***: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and ***: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding *** findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an

关键词： Candidate genes Inbreeding coefficients Runs of homozygosity Sus scrofa

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The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

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Journal of Animal Science and Biotechnology 2021年第4期12卷 1281-1295页

作者： Jingwei Yue Xinhua Hou Xin Liu Ligang Wang Hongmei Gao Fuping Zhao Lijun Shi Liangyu Shi Hua Yan Tianyu Deng Jianfei Gong Lixian Wang longchao zhang Key Laboratory of Animal(Poultry)Genetics Breeding and Reproduction Ministry of AgricultureInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China

Background:The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms,which depend on chromatin ***,how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been *** gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development,we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45,70 and 100 days post coitus(dpc).Results:In total,21,638,35,447 and 60,181 unique regions(or peaks)were found across the embryos at 45 dpc(LW45),70 dpc(LW70)and 100 dpc(LW100),*** than 91%of the peaks were annotated within−1 kb to 100 bp of transcription start sites(TSSs).First,widespread increases in specific accessible chromatin regions(ACRs)from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic ***,the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated ***,the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle developmentrelated genes,such as MyoG,Mef2c,and *** potential transcriptional repressors,including E2F6,OTX2 and CTCF,were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq ***:This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription *** results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

关键词： Chromatin accessibility Embryo Pig Skeletal muscle Transcriptome

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Single-cell RNA Sequencing Reveals Thoracolumbar Vertebra Heterogeneity and Rib-genesis in Pigs

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 423-436页

作者： Jianbo Li Ligang Wang Dawei Yu Junfeng Hao longchao zhang Adeniyi C.Adeola Bingyu Mao Yun Gao Shifang Wu Chunling Zhu Yongqing zhang Jilong Ren Changgai Mu David M.Irwin Lixian Wang Tang Hai Haibing Xie Yaping zhang State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223China Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Core Facility for Protein Research Institute of BiophysicsChinese Academy of SciencesBeijing 100101China State Key Laboratory for Molecular and Developmental Biology CAS Center for Excellence in Brain Science and Intelligence TechnologyInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650223China Department of Laboratory Medicine and Pathobiology University of TorontoTorontoOntario M5S1A8Canada Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Development of thoracolumbar vertebra(TLV)and rib primordium(RP)is a common evolutionary feature across vertebrates,although whole-organism analysis of the expression dynamics of TLV-and RP-related genes has been ***,we investigated the single-cell transcriptome landscape of thoracic vertebra(TV),lumbar vertebra(LV),and RP cells from a pig embryo at 27 days post-fertilization(dpf)and identified six cell types with distinct gene expression ***-depth dissection of the gene expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and RP *** analysis of cell type-specific and strand-specific expression uncovered the extremely high level of HOXA103′-UTR sequence specific to osteoblasts of LV cells,which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV ***,this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell type-specific resolution,which serves as a comprehensive view on the transcriptional profile of animal embryo development.

关键词： scRNA-seq Thoracolumbar vertebra transition Rib-genesis Osteogenesis Angiogenesis

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Genome-wide search for candidate genes determining vertebrae number in pigs

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Frontiers of Agricultural Science and Engineering 2017年第3期4卷 327-334页

作者： longchao zhang Jingwei YUE Xin LIU Jing LIANG Kebin ZHAO Hua YAN Na LI Lei PU Yuebo zhang Huibi SHI Ligang WANG Lixian WANG Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China Institute of Animal ScienceChinese Academy of Agricultural Sciences

Longer porcine carcasses may be expected to have more vertebrae. Therefore, vertebrae number in pigs is an economically important trait. To examine the genetic basis of this trait, we genotyped 578 F-2 Large White x Minzhu pigs using the Porcine SNP60K BeadChip. A genome-wide association study (GWAS) identified 36 significant single nucleotide polymorphisms (SNPs) on the chromosomes SSC1 (294.28-300.32 Mb) and SSC7 (102.22-109.39 Mb). A 6.04-Mb region that contained all 13 significant SNPs on SSC1 also contained the gene NR6A1, previously reported to influence the number of vertebrae in pigs. However, the reported putative casual mutation of NR6A1 c. 748C > T showed no genome-wide significant association with the trait, suggesting it was not a causal mutation in our population. The remaining 23 significant SNPs on SSC7 were concentrated in a 7.17-Mb region, which was within a quantitative trait locus interval for number of vertebrae. TMED10 was the closest gene to the most significant SNP and might be a candidate. Haplotype sharing and block analysis refined the QTL to an interval of about 3 Mb containing 29 candidate genes. Of these 29 genes, the previously reported possible casual mutation of VRTN g. 19034A > C was not found to be a causal mutation in our population. Exploration of these genes via additional genetic and functional studies in mammals revealed that TGF beta 3 could be a good candidate on SSC7. A mutation of TGF beta 3 c. 1749G > A was detected by GWAS and could be proposed as a candidate causal mutation, or as closely linked to a causal mutation, for the number of vertebrae in pigs.

关键词： genome-wide association study number of vertebrae pig SSC7 TGF beta 3

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畜禽肉中代谢物质对肉品质的影响及相关基因研究进展

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畜牧兽医学报 2022年第8期53卷 2444-2452页

作者：张润杨曼王立贤张龙超中国农业科学院北京畜牧兽医研究所北京100193

肉质风味是味觉和嗅觉感知的感官印象,其根本是由肉中的代谢物质的含量及复杂的化学过程所决定。随着代谢物质测定技术的不断进步,肉中代谢物质的含量对肉品质的影响也越来越受到关注,肉中代谢物质含量也逐渐成为研究及育种工作的热点,... 详细信息

肉质风味是味觉和嗅觉感知的感官印象,其根本是由肉中的代谢物质的含量及复杂的化学过程所决定。随着代谢物质测定技术的不断进步,肉中代谢物质的含量对肉品质的影响也越来越受到关注,肉中代谢物质含量也逐渐成为研究及育种工作的热点,进而挖掘出了很多调控代谢物质的候选基因。本文综述了畜禽肉中代谢物质的种类、形成风味的代谢物质化学反应、代谢物质对肉品质的影响以及代谢物质遗传调控。旨在阐明肉中代谢物质对肉质风味形成的调控机制,为畜禽肉质风味的改良提供理论基础和研究思路。

关键词：风味前体物质亲水性物质肉品质遗传调控脂质

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北京黑猪肌内脂肪含量高、低组间脂质组差异分析

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畜牧兽医学报 2022年第9期53卷 3262-3271页

作者：张润刘海杨曼张龙超王源青岛农业大学动物科技学院青岛266109 中国农业科学院北京畜牧兽医研究所北京100193 北京黑六牧业科技有限公司北京102211

旨在揭示北京黑猪肌内脂肪含量与脂质组学间的关系。本试验主要是从400头210日龄的北京黑猪中按肌内脂肪含量高低筛选出高肌内脂肪组11个样品,其肌内脂肪含量的平均值为3.89%,低肌内脂肪组19个样品,其肌内脂肪含量的平均值为0.81%;对挑... 详细信息

旨在揭示北京黑猪肌内脂肪含量与脂质组学间的关系。本试验主要是从400头210日龄的北京黑猪中按肌内脂肪含量高低筛选出高肌内脂肪组11个样品,其肌内脂肪含量的平均值为3.89%,低肌内脂肪组19个样品,其肌内脂肪含量的平均值为0.81%;对挑选出的高、低两组的个体取60 mg的肌肉样品进行脂质提取,最后进行非靶向脂质组学的检测;针对检测结果,对两组进行多元化分析,利用T检验、差异倍数和偏最小二乘判别分析进行标记物的筛选。结果,共检测出组成9类脂质的104种脂肪酸,其中酰基肉碱(AcCa)3个、甘油二酯(DG)4个、甘油三酯(TG)23个、心磷脂(CL)8个、磷脂酰胆碱(PC)21个、磷脂酰乙醇胺(PE)29个、磷脂酰甘油(PG)3个、磷脂酰肌醇(PI)6个、磷脂酰丝氨酸(PS)7个,通过进行T检验初步筛选(P1)和FC值(FC>2或FC<0.5)进行筛选,最终筛选出22个脂质,其中TG有21个,DG有1个。结果表明,脂质组学可以作为区分北京黑猪肌内脂肪含量高低的方法,构成肌内脂肪含量高低猪肉样品的脂质组差异物质主要集中在TG和DG上。

关键词：北京黑猪脂质组学甘油三酯肌内脂肪

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E355钢焊管裂纹失效分析及改进措施

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焊管 2020年第4期43卷 44-47,51页

作者：张龙超西昌钢钒有限公司科技质量部四川西昌615032

针对汽车转向轴用E355钢焊管裂纹问题,通过金相组织分析和扫描电镜分析等试验方法对钢管进行了失效分析。分析结果显示,裂纹为沿钢管轴向裂纹,位于钢管外壁母材处,焊缝位置无开裂;焊管基体带状组织严重;原始裂纹处主要以铁氧化物为主,且... 详细信息

针对汽车转向轴用E355钢焊管裂纹问题,通过金相组织分析和扫描电镜分析等试验方法对钢管进行了失效分析。分析结果显示,裂纹为沿钢管轴向裂纹,位于钢管外壁母材处,焊缝位置无开裂;焊管基体带状组织严重;原始裂纹处主要以铁氧化物为主,且O含量最高为14.42%,氧化程度较轻。研究表明,焊管基体带状组织严重是导致钢管裂纹的重要原因,建议从控制热轧酸洗板原料连铸板坯偏析缺陷着手,优化冶炼工艺,有效降低焊管裂纹缺陷。

关键词： E355钢焊管裂纹带状组织中心偏析

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