检索结果-南通市图书馆

Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken population

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Journal of animal Science and Biotechnology 2018年第2期9卷 294-305页

作者： Shaopan Ye Xiaolong Yuan Xiran Lin Ning Gao Yuanyu Luo Zanmou Chen Jiaqi Li Xiquan Zhang Zhe Zhang Guangdong Provincial Key Lab of Agro-animal genomics and Molecular breeding National Engineering Research Centre for Breeding Swine IndustryCollege of Animal Science South China Agricultural University

Background: Genome-wide association studies and genomic predictions are thought to be optimized by using whole-genome sequence(WGS) data. However, sequencing thousands of individuals of interest is *** from SNP panels to WGS data is an attractive and less expensive approach to obtain WGS data. The aims of this study were to investigate the accuracy of imputation and to provide insight into the design and execution of genotype ***: We genotyped 450 chickens with a 600 K SNP array, and sequenced 24 key individuals by whole genome re-sequencing. Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. By increasing the sequencing cost from 24 X to 144 X, the imputation accuracy increased from 0.525 to 0.698 for Beagle and from 0.654 to 0.823 for FImpute. With fixed sequence depth(12 X), increasing the number of sequenced animals from 1 to 24, improved accuracy from 0.421 to0.897 for FImpute and from 0.396 to 0.777 for Beagle. Using optimally selected key individuals resulted in a higher imputation accuracy compared with using randomly selected individuals as a reference population for resequencing. With fixed reference population size(24), imputation accuracy increased from 0.654 to 0.875 for FImpute and from 0.512 to 0.762 for Beagle as the sequencing depth increased from 1 X to 12 X. With a given total cost of genotyping, accuracy increased with the size of the reference population for FImpute, but the pattern was not valid for Beagle, which showed the highest accuracy at six fold coverage for the scenarios used in this ***: In conclusion, we comprehensively investigated the impacts of several key factors on genotype imputation. Generally, increasing sequencing cost gave a higher imputation accuracy. But with a fixed sequencing cost, the optimal imputation enhance the performance of WGP and GWAS. An optimal imputation strategy

关键词： Chickens Imputation Re-sequencing SNP

Bombyx mori nucleopolyhedrovirus induces BmFABP1 downregulation to promote viral proliferation

在线全文

学校读者我要写书评

暂无评论

Insect Science 2023年第6期30卷 1595-1606页

作者： Xiong Wang Guangyu Ma Feifei Ren Mian Muhammad Awais Jingchen Sun College of animal Science Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular BreedingSouth China Agricultural UniversityGuangzhouChina

Fatty acid binding proteins (FABPs) play an important role as endogenous cytoprotectants. However, studies on FABPs in invertebrates are scarce. Previously, we discovered Bombyx mori fatty acid binding protein 1 (BmFABP1) through co-immunoprecipitation. Here, we cloned and identified BmFABP1 from BmN cells. The results of immunofluorescence indicated that BmFABP1 was localized in the cytoplasm. The tissue expression profile of silkworms showed that BmFABP1 was expressed in all tissues except hemocytes. The expression level of BmFABP1 gradually decreases in BmN cells and B. mori larvae after infection with B. mori nucleopolyhedrovirus (BmNPV). Upregulation of BmFABP1 expression through overexpression or WY14643 treatment significantly inhibited the replication of BmNPV, while downregulation of BmFABP1 expression by RNA interference promoted the replication of BmNPV. The same results were obtained in experiments on silkworm larvae. These results suggest that BmNPV induces BmFABP1 downregulation to promote its proliferation and that BmFABP1 has a potential anti-BmNPV role. This is the first report on the antiviral effect of BmFABP1 in silkworms and provides new insights into the study of the FABP protein family. Also, it is important to study BmNPV resistance in silkworms to breed transgenic silkworms with BmNPV resistance.

关键词： antiviral BmFABP1 BmNPV Bombyx mori

Efficient production of chimeric mice from embryonic stem cells injected into 4-to 8-cell and blastocyst embryos

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Journal of animal Science and Biotechnology 2013年第4期4卷 264-270页

作者： Minhua Hu Hengxi Wei Jingfeng Zhang Yinshan Bai Fenglei Gao Li Li Shouquan Zhang Agricultural animal genomics and Molecular breeding Key Lab of Guangdong Province College of Animal Science South China Agricultural University

Background： Production of chimeric mice is a useful tool for the elucidation of gene function. After successful isolation of embryonic stem （ES） cell lines, there are many methods for producing chimeras, including co-culture with the embryos, microinjection of the ES ceils into pre-implantation embryos, and use of tetraploid embryos to generate the full ES-derived transgenic mice. Here, we aimed to generate the transgenic ES cell line, compare the production efficiency of chimeric mice and its proportion to yield the male chimeric mice by microinjected ES cells into 4- to 8-cell and blastocysts embryos with the application of Piezo-Micromanipulator （PMM）, and trace the fate of the injected ES cells. Results： We successfully generated a transgenic ES cell line and proved that this cell line still maintained pluripotency. Although we achieved a satisfactory chimeric mice rate, there was no significant difference in the production of chimeric mice using the two different methods, but the proportion of the male chimeric mice in the 4- to 8-cell group was higher than in the blastocyst group. We also found that there was no tendency for ES cells to aggregate into the inner cell mass using in vitro culture of the chimeric embryos, indicating that they aggregated randomly. Conclusions： These results showed that the PMM method is a convenient way to generate chimeric mice and microinjection of ES cells into 4- to 8-cell embryos can increase the chance of yielding male chimeras compared to the blastocyst injection. These results provide useful data in transgenic research mediated by ES cells.

关键词： Chimeric mice Embryonic stem cell Microinjection

Functional verification of the diphtheria toxin A gene in a recombinant system

在线全文

学校读者我要写书评

暂无评论

Journal of animal Science and Biotechnology 2013年第1期4卷 34-40页

作者： Jingfeng Zhang Hengxi Wei Xinzheng Guo Minghua Hu Fenglei Gao Li Li Shouquan Zhang Agricultural animal genomics and Molecular breeding Key Lab of Guangdong Province College of Animal Science South China Agricultural University

Diphtheria toxin A （DTA）, a segment of the diphtheria toxin （tox）, inhibits protein synthesis in cells. When released from a cell, DTA is nontoxic and cannot enter other cells independently without the help of diphtheria toxin B. In this study, we artificially synthesized the DTA gene sequence and cloned it into pEGFP-N1 to generate the recombinant vector pEGFP-N1-DTA. This recombinant vector was then transfected into 293T cells to observe the effect of DTA protein expression on enhanced green fluorescent protein （EGFP） protein expression and the proliferation of 293T cells. After 48 h, high levels of EGFP expression were seen in control pEGFP-Nl-transfected cells, whereas very low levels were seen in cells transfected with pEGFP-N1-DTA. Reverse transcription polymerase chain reaction confirmed the expression of the DTA gene in cells transfected with pEGFP-N^-DTA. Further, the 3-（4,5-dimethylthiazol-2-yl）-2,5-diphenyltetrazolium bromide （M-I-I-） assay revealed a significant difference in cell proliferation between the control group and the pEGFP-N1-DTA-transfected group. Using the expression of EGFP expression as an indicator, this study revealed that DTA expression can inhibit intracellular protein synthesis and cell proliferation.

关键词： Diptheria toxin A Cell proliferation Protein synthesis

Multi-omics-data-assisted genomic feature markers preselection improves the accuracy of genomic prediction

在线全文

学校读者我要写书评

暂无评论

Journal of animal Science and Biotechnology 2021年第2期12卷 508-519页

作者： Shaopan Ye Jiaqi Li Zhe Zhang Guangdong Provincial Key Lab of Agro-animal genomics and Molecular breeding National Engineering Research Centre for Breeding Swine IndustryCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina

Background:Presently,multi-omics data(e.g.,genomics,transcriptomics,proteomics,and metabolomics)are available to improve genomic *** data not only offers new data layers for genomic prediction but also provides a bridge between organismal phenotypes and genome variation that cannot be readily captured at the genome sequence ***,using multi-omics data to select feature markers is a feasible strategy to improve the accuracy of genomic *** this study,simultaneously using whole-genome sequencing(WGS)and gene expression level data,four strategies for single-nucleotide polymorphism(SNP)preselection were investigated for genomic predictions in the Drosophila Genetic Reference ***:Using genomic best linear unbiased prediction(GBLUP)with complete WGS data,the prediction accuracies were 0.208±0.020(0.181±0.022)for the startle response and 0.272±0.017(0.307±0.015)for starvation resistance in the female(male)*** with GBLUP using complete WGS data,both GBLUP and the genomic feature BLUP(GFBLUP)did not improve the prediction accuracy using SNPs preselected from complete WGS data based on the results of genome-wide association studies(GWASs)or transcriptome-wide association studies(TWASs).Furthermore,by using SNPs preselected from the WGS data based on the results of the expression quantitative trait locus(eQTL)mapping of all genes,only the startle response had greater accuracy than GBLUP with the complete WGS *** best accuracy values in the female and male lines were 0.243±0.020 and 0.220±0.022,***,by using SNPs preselected based on the results of the eQTL mapping of significant genes from TWAS,both GBLUP and GFBLUP resulted in great accuracy and small bias of genomic *** with the GBLUP using complete WGS data,the best accuracy values represented increases of 60.66%and 39.09%for the starvation resistance and 27.40%and 35.36%for startle response in the female and male lines,respective

关键词： Accuracy Drosophila melanogaster Genomic prediction Multi-omics data SNP preselection

MicroRNAs Involved in Skeletal Muscle Differentiation

在线全文

学校读者我要写书评

暂无评论

Journal of Genetics and genomics 2013年第3期40卷 107-116页

作者： Wen Luo Qinghua Nie Xiquan Zhang Guangdong Provincial Key Lab of Agro-animal genomics and Molecular breeding and Key Lab of Chicken Genetics Breeding and Reproduction Ministry ofAgriculture South China Agricultural University

MicroRNAs （miRNAs） negatively regulate gene expression by promoting degradation of target mRNAs or inhibiting their translation. Previous studies have expanded our understanding that miRNAs play an important role in myogenesis and have a big impact on muscle mass, muscle fiber type and muscle-related diseases. The muscle-specific miRNAs, miR-206, miR-1 and miR-133, are among the most studied and best characterized miRNAs in skeletal muscle differentiation. They have a profound influence on multiple muscle differ- entiation processes, such as alternative splicing, DNA synthesis, and cell apoptosis. Many non-muscle-specific miRNAs are also required for the differentiation of muscle through interaction with myogenic factors. Studying the regulatory mechanisms of these miRNAs in muscle differentiation will extend our knowledge of miRNAs in muscle biology and will improve our understanding of the myogenesis regulation.

关键词： MicroRNAs Skeletal muscle Differentiation Regulation

m^(6)A demethylase FTO regulate CTNNB1 to promote adipogenesis of chicken preadipocyte

在线全文

学校读者我要写书评

暂无评论

Journal of animal Science and Biotechnology 2023年第2期14卷 578-592页

作者： Kan Li Weichen Huang Zhijun Wang Qinghua Nie Department of animal Genetics Breeding and ReproductionCollege of Animal ScienceSouth China Agricultural UniversityGuangzhou 510642China National‑Local Joint Engineering Research Center for Livestock breeding Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breedingand Key Laboratory of Chicken GeneticsBreeding and ReproductionMinistry of AgricultureGuangzhou 510642China

Background:N6-methyladenosine(m^(6)A)is an abundant post-transcriptional RNA modification that affects various biological *** fat mass and obesity-associated(FTO)protein,a demethylase encoded by the FTO gene,has been found to regulate adipocyte development in an m^(6)A-dependent manner in multiple ***,the effects of the m^(6)A methylation and FTO demethylation functions on chicken adipogenesis remain *** study aims to explore the association between m^(6)A modification and chicken adipogenesis and the underlying mechanism by which FTO affects chicken preadipocyte ***:The association between m^(6)A modification and chicken lipogenesis was assessed by treating chicken pread-ipocytes with different doses of methyl donor betaine and methylation inhibitor *** results showed that betaine significantly increased methylation levels and inhibited lipogenesis,and the inverse effect was found in preadipocytes after cycloleucine *** of FTO significantly inhibited m^(6)A levels and promoted proliferation and differentiation of chicken *** FTO showed opposite ***,FTO overexpression increased the expression of catenin beta 1(CTNNB1)by improving RNA stability in an m^(6)A-dependent manner,and we proved that FTO could directly target ***,CTNNB1 may be a positive regulator of adipogenesis in chicken ***:m^(6)A methylation of RNA was negatively associated with adipogenesis of chicken *** could regulate CTNNB1 expression in a demethylation manner to promote lipogenesis.

关键词： Adipogenesis Chicken CTNNB1 FTO m^(6)A

Genetic parameters and trends for production and reproduction traits of a Landrace herd in China

在线全文

学校读者我要写书评

暂无评论

Journal of Integrative Agriculture 2016年第5期15卷 1069-1075页

作者： ZHANG Zhe ZHANG Hao PAN Rong-yang WU Long LI Ya-lan CHEN Zan-mou CAI Geng-yuan LI Jia-qi WU Zhen-fang College of animal Science National Engineering Research Center for Breeding Swine Industry/Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding South China Agricultural University Guangzhou 510642 P.R. China

The objectives of this study were to estimate the genetic parameters and the breeding progress in a Landrace herd in China, and to predict the potential benefits by applying new breeding technology. Hereby, the performance records from a Landrace swine herd in China, composing over 33 000 pigs born between 2001 and 2013, were collected on six economically important traits, i.e., average daily gain between 30-100 kg（ADG）, adjusted backfat thickness at 100 kg（BF）, adjusted days to 30 kg（D30）, adjusted days to 100 kg（D100）, number born alive（NBA）, and total number born（TNB）. The genetic parameters were estimated by restricted maximum likelihood via DMU, and realized genetic trends were analyzed. Based on the real population structure and genetic parameters obtained from this herd, the potential genetic trends by applying genomic selection（GS） were predicted via a computer simulation study. Results showed that the heritability estimates in this Landrace herd were 0.55（0.02）, 0.42（0.01）, and 0.12（0.01）, for BF, D100, and TNB, respectively. Favorable genetic trends were obtained for D100, BF, and TNB due to direct selection, for ADG and NBA due to indirect selection. Long-term selection against D100 did not improve D30, though they are highly genetically correlated（0.64）. Appling GS in such a swine herd, the genetic gain can be increased by 25%, or even larger for traits with low heritability or individuals without phenotypes before selection. It can be concluded that conventional breeding strategy was effective in the herd studied, while applying GS is promising and hence the road ahead in swine breeding.

关键词： genetic parameter genomic selection swine genetic trend

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

在线全文

学校读者我要写书评

暂无评论

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