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本研究旨在分析绿壳蛋鸡与白来航蛋鸡microRNA变异及其靶基因,将已鉴定的microRNA与预测microRNA组成全基因组的microRNA,并通过与GGRS得到的两种鸡群体SNP位点进行映射,挖掘含SNP的microRNA。利用生物信息学的方法,对含SNP的microRNA进行靶基因预测,并对直接含有SNP的mature-microRNA进行聚焦。将这些靶基因进行富集,一共得到22个GO分类和10条KEGG信号通路与3个主要IPA调控网络,发现其在与生长相关的mTOR信号通路、Wnt信号通路、生长激素受体网络、胰岛素样生长因子Ⅰ受体网络得到了富集,与产蛋性状相关的卵母细胞减数分裂信号通路、黄体酮卵母细胞成熟信号通路得到了富集。此研究方法和结果可以给后期研究提供参考。 相似文献
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试验旨在通过对藏鸡和白羽肉鸡垂体转录组测序和生物信息学分析,筛选出与鸡生长发育相关的差异表达基因（differentially expression genes,DEGs）及信号通路。本研究选用42日龄健康藏鸡和白羽肉鸡各3只,分别采集垂体组织利用Illumina HiSeq 2000平台进行转录组mRNA测序,对筛选到的DEGs筛选DEGs,GO和KEGG数据库功能注释和富集分析,实时荧光定量PCR验证随机挑选的DEGs表达水平。结果显示,藏鸡和白羽肉鸡分别获得126 094 302和125 666 442条clean reads。与白羽肉鸡相比,藏鸡垂体组织中共有DEGs 392个,其中196个为上调基因,196个为下调基因（P<0.05）,其中包括生长激素（GH）基因、生长激素释放激素受体（GHRHR）基因和胰岛素样生长因子2 mRNA结合蛋白1（IGF2BP1）基因。GO和KEGG富集分析发现,DEGs显著富集于细胞黏附分子信号通路和神经活性配体-受体相互作用信号通路等细胞通讯相关的信号通路,GH、GHRHR和IGF2BP1基因也显著富集于神经活性配体-受体相互作用信号通路。实时荧光定量PCR结果显示,转录组测序结果准确可靠。综上研究,本研究初步揭示了影响藏鸡和白羽肉鸡生长发育速度差异的关键候选基因和信号通路,为了解鸡垂体组织调节生长发育的分子机制提供了理论依据。 相似文献
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鸡繁殖性能近交衰退是地方鸡遗传资源活体保种过程中面临的重要问题之一,本研究旨在探讨全基因组CpG岛（CpG island,CGI）区DNA甲基化在鸡繁殖性能近交衰退中的作用。分别从狼山鸡高近交组和低近交组中各选取健康母鸡3只,即试验分2个组,每组3个重复,然后采用全基因组重亚硫酸盐测序（WGBS）技术,检测分析两组个体性腺轴组织（包括卵巢和下丘脑）全基因组DNA甲基化差异,筛选差异甲基化区域（DMRs）,并对CpG岛区差异甲基化基因进行功能注释和富集分析。结果表明,狼山鸡高近交组和低近交组比较,其卵巢和下丘脑基因组整体甲基化水平均不存在显著差异（P>0.05）;高、低近交组间差异甲基化区域检测发现,下丘脑和卵巢中分别检测到5 948和4 593个差异甲基化区域,其中1 798和995个差异甲基化区域位于基因组CpG岛区,分别注释到1 020和552个基因;下丘脑中,这些CpG岛区差异甲基化基因显著富集在信号转导、神经系统发育、生殖系统发育和卵母细胞成熟调控等繁殖相关的GO条目,以及转化生长因子β信号通路、乙型肝炎、脂肪酸代谢、胰岛素信号通路等19条KEGG信号通路（P<0.05）;卵巢中,CpG岛区差异甲基化基因显著富集于12条信号通路（P<0.05）,包括慢性骨髓白血病、流感A、精氨酸和脯氨酸代谢、粘着连接等,一些与卵子发育和性激素分泌相关的信号通路也被富集到,如黄体酮介导的卵母细胞成熟、卵母细胞减数分裂、GnRH信号通路、雌激素信号通路等,其中包含CDC27、ADCY8、AKT3等10个差异甲基化基因。因此,本研究在狼山鸡高、低近交组间检测到了大量差异甲基化区域,并发现大量差异甲基化基因与繁殖性状相关,推测这些基因CpG岛区DNA甲基化可能在狼山鸡繁殖性能近交衰退调控中发挥重要作用,研究结果为进一步深入探索鸡繁殖性能近交衰退调控机制奠定了基础,为物种资源保护和家禽育种工作提供了理论参考依据。 相似文献
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【目的】丰富非洲猪瘟病毒（African swine fever virus,ASFV）感染后猪外周血淋巴细胞长链非编码RNA（long non-coding RNA,lncRNA）表达谱,并进一步挖掘影响Toll样受体信号通路的调控网络。【方法】试验动物感染ASFV,于第7天采集外周血并分离得到外周血淋巴细胞,运用Illumina高通量组学测序对外周血淋巴细胞中lncRNA进行测序,原始数据经处理后筛选获得差异表达的lncRNA,并进行靶基因预测,利用生物信息学方法对靶基因进行GO功能和KEGG信号通路富集分析,初步绘制与Toll样受体信号通路相关的lncRNA-mRNA调控网络,并对lncRNA-ENSSSCG00000041959在内的4个lncRNAs进行实时荧光定量RT-PCR验证。【结果】共筛选到73个差异表达的lncRNAs,其中上调表达lncRNAs 38个,下调表达lncRNAs 35个。GO功能分析结果显示,靶基因显著富集在调节免疫系统过程、防御反应、生物刺激、病毒反应和先天性免疫;KEGG信号通路富集分析显示,大部分靶基因与细胞循环、疾病及免疫应答有关,其中免疫相关信号通路有Toll样受体信号通路、TNF信号通路、产生IgA的肠道免疫网络等。进一步挖掘出lncRNA-ENSSSCG00000041959-RIPK1和lncRNA-ENSSSCG00000041959-IRAK1可能是影响Toll样受体信号通路的重要调控网络,实时荧光定量RT-PCR与测序结果一致。【结论】本研究初步鉴定出lncRNA-ENSSSCG00000041959-RIPK1和lncRNA-ENSSSCG00000041959-IRAK1可能是影响Toll样受体信号通路的lncRNA-mRNA调控网络,为进一步探索lncRNA调控ASFV感染机体免疫反应奠定了理论基础。 相似文献
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Yi ZHENG Yingmin ZHOU Yijie HUANG Haoqi WANG Haixiang GUO Bao YUAN Jiabao ZHANG 《Integrative zoology》2023,18(3):552-568
With the completion of the draft assembly of the giant panda genome sequence, RNA sequencing technology has been widely used in genetic research on giant pandas. We used RNA-seq to examine black and white hair follicle samples from adult pandas. By comparison with the giant panda genome, 75 963 SNP loci were labeled, 2426 differentially expressed genes (DEGs) were identified, and 2029 new genes were discovered, among which 631 were functionally annotated. A cluster analysis of the DEGs showed that they were mainly related to the Wnt signaling pathway, ECM–receptor interaction, the p53 signaling pathway, and ribosome processing. The enrichment results showed that there were significant differences in the regulatory networks of hair follicles with different colors during the transitional stage of hair follicle resting growth, which may play a regulatory role in melanin synthesis during growth. In conclusion, our results provide new insights and more data support for research on the color formation in giant pandas. 相似文献
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【目的】分析产肠毒素大肠杆菌（enterotoxigenic Escherichia coli，ETEC）诱导猪小肠上皮细胞（IPEC-J2）炎症反应的主要宿主调控基因及相关分子通路，为进一步揭示ETEC感染引发炎症反应的作用机制提供理论依据。【方法】用感染复数（multiplicity of infection，MOI）为100的ETEC菌液感染IPEC-J2细胞，18 h后收集细胞上清，通过ELISA方法检测炎性因子白细胞介素1β（interleukin 1 β，IL-1β）的分泌水平。由Illumina PE150测序平台进行高通量转录组测序，通过edgeR v 3.12.1软件对测序结果进行差异表达分析，利用GOseq和KOBAS 2.0软件对得到的差异表达mRNA进行GO功能和KEGG通路富集分析，随机挑选5条差异表达mRNA，利用实时荧光定量PCR对其验证。【结果】试验成功建立了ETEC感染诱导的IPEC-J2细胞炎症模型。与对照组相比，炎症模型组共发现529条差异表达mRNA，其中236条表达上调，293条表达下调，包括HSP90AA1、CGNL1、CADPS2、EHBP1等免疫相关基因。GO功能分析表明，ETEC感染后差异表达mRNA显著富集于细胞组分和生物过程，包括细胞内成分（intracellular part）、细胞质（cytoplasm）、核成分（nuclear part）、胞内膜结合细胞器（intracellular membrance-bounded organelle）、膜结合细胞器（membrance-bounded orgabelle）及细胞进程（cellular process）等。KEGG通路分析表明，炎症模型中差异表达基因大多数被注释到疾病相关通路及Toll样受体信号通路、mTOR信号通路、细胞周期、黏附连接等免疫相关信号通路。利用实时荧光定量PCR验证随机挑选的5条差异表达mRNA，结果与测序报告中差异表达mRNA变化趋势一致，证明测序结果可信。【结论】HSP90AA1、CGNL1、CADPS2和EHBP1等基因可能在ETEC黏附IPEC-J2细胞并诱导炎症反应中发挥关键作用，并通过Toll样受体、mTOR等信号通路进行免疫调控。研究结果为进一步揭示ETEC感染诱导炎症反应的分子机制及相关调控网络提供参考依据。 相似文献
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JIN Meilin LU Jian FEI Xiaojuan LU Zengkui QUAN Kai CHU Mingxing DI Ran WANG Huihua WEI Caihong 《畜牧兽医学报》1956,51(12):2991-3000
The purpose of this study was to screen the genome-wide selection signals of Liaoning cashmere goat and Inner Mongolia cashmere goat. Based on the Illumina Caprine 50K SNP chip, Liaoning cashmere goat, Inner Mongolia cashmere goat and Huanghuai goat were genotyped, and the common 50 010 SNPs were obtained after quality control. Using population differentiation coefficients Fst and XP-EHH, Huanghuai goats were used as reference populations to detect selection signals for Inner Mongolia cashmere goats and Liaoning cashmere goats. The top 5% of Fst and XP-EHH values was used as the threshold. The result showed that 501 candidate genes were selected by Fst and 145 candidate genes were selected by XP-EHH in cashmere goats. Based on these SNPs, we detected 12 SNPs under strong selection by Fst and XP-EHH. After gene annotation, 21 candidate genes were identified, such as EXOC4, ASIC2, PCDH9, RHBDD1, IRS1 and PDE10A. These genes were found to be mainly enriched in PI3K-Akt signaling pathway, protein digestion and absorption and relaxin signaling pathways. The study indicated that genes associated with cashmere traits were subjected to strong artificial selection pressure during domestication of the cashmere goats. These findings also help us better understand the selection progress of cashmere goats and provide a new theoretical basis for the protection and utilization of germplasm resources of Chinese cashmere goat breeds. 相似文献
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旨在对辽宁绒山羊和内蒙古绒山羊的基因组选择信号进行筛选。本研究利用Illumina 50K的山羊芯片，对内蒙古绒山羊、辽宁绒山羊和黄淮山羊进行基因型检测，质控后获得50 010个共同SNPs位点。通过群体分化系数Fst和XP-EHH，以黄淮山羊为参考群体分别对内蒙古绒山羊和辽宁绒山羊进行选择信号检测，Fst和XP-EHH值的top 5%作为阈值。结果，利用Fst在绒山羊基因组中筛选到501个候选基因，利用XP-EHH在绒山羊基因组中筛选到145个候选基因。其中有12个SNPs在绒山羊基因组中受到较强选择。通过基因注释筛选到21个候选基因，包括EXOC4、ASIC2、PCDH9、RHBDD1、IRS1和PDE10A等。这些基因主要富集在PI3K-Akt信号通路、蛋白质消化吸收和松弛素信号通路等。研究结果发现，绒山羊在驯化过程中其基因组很多与毛囊相关的基因受到了强烈的选择。这些发现也有助于更好地了解绒山羊的选择进展，为中国绒山羊品种的种质资源保护和利用提供重要参考。 相似文献
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禽致病性大肠杆菌Hcp2b对雏鸡气管黏膜细胞因子-细胞因子受体相互作用通路的影响 总被引：1，自引：0，他引：1
T6SS （type VI secretion system）是革兰阴性菌中常见的一种分泌系统,其效应蛋白Hcp2b作用机制迄今仍未明晰。本研究以禽致病性大肠杆菌（avian pathogenic Escherichia coli,APEC） Hcp2b蛋白为研究主体,旨在探究Hcp2b蛋白在APEC感染鸡气管黏膜过程中发挥的作用及机制。采用Red重组方法以质粒pKD3为模板构建hcp2b缺失株,pSTV-28质粒连接hcp2b目的片段构建重组载体,导入感受态Δhcp2b菌株构建回复株,并对Δhcp2b菌株的生长曲线进行测定。7日龄雏鸡气管感染hcp2b缺失株及野生株,感染后12、24 h收集鸡气管黏膜细胞进行转录组学测序及生物信息学分析。结果表明,hcp2b缺失株及回复株构建成功,hcp2b基因缺失对菌株的生长性能无影响。hcp2b基因缺失株感染气管黏膜后,mRNA的表达谱发生变化,感染后12 h,有144个基因表达量发生变化（上调差异基因87个,下调57个）;感染后24 h,有135个基因表达量发生变化（上调差异基因79个,下调56个）。生物信息学分析发现差异基因富集在Cytokine-cytokine receptor interaction、Protein processing in endoplasmic reticulum等信号通路。hcp2b基因缺失未影响APEC的生长特性,hcp2b基因缺失后影响雏鸡气管黏膜Cytokine-cytokine receptor interaction通路基因mRNA转录水平的变化,IL-1β、IL-12b的表达均上调。该结果为APEC的致病机制研究提供了理论依据。 相似文献
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本研究旨在探讨TAFA趋化素样家族成员1（TAFA1）基因多态性与郏县红牛生长的关联性。试验共采集了79头郏县红牛成年母牛的血样并提取基因组DNA,利用直接测序法对TAFA1基因上的错义突变SNP rs137516577进行基因型分型,并与郏县红牛体高、体长、胸围、腰角宽、坐骨端宽、尻长、十字部高、荐高、胸深、胸宽、体重等11个生长和体尺性状进行关联分析。同时根据“Animal Omics Datebase”数据库对TAFA1基因的组织表达情况进行分析。结果发现该SNP与体长、腰角宽、坐骨端宽、尻长和体重等性状显著相关（P<0.05）,且GC型个体体长、腰角宽、坐骨端宽、尻长和体重均显著高于GG型（P<0.05）。TAFA1基因在牛大脑组织中表达量最高。结果表明,TAFA1基因上错义突变SNP rs137516577与郏县红牛生长性状相关,可作为郏县红牛生长性状的分子标记。 相似文献
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Assessment of positional candidate genes myf5 and igf1 for growth on bovine chromosome 5 in commercial lines of Bos taurus 总被引：1，自引：0，他引：1
Li C Basarab J Snelling WM Benkel B Murdoch B Hansen C Moore SS 《Journal of animal science》2004,82(1):1-7
Quantitative trait loci for growth traits in beef cattle have been previously reported and fine-mapped in three chromosomal regions of 0 to 30 cM, 55 to 70 cM, and 70 to 80 cM of bovine chromosome 5. In this study, we further examined the association between gene-specific single nucleotide polymorphisms (SNP) of two positional candidate genes, bovine myogenic factor 5 (myf5) and insulin-like growth factor-1 (igf1), in the QTL regions and the birth weight (BWT), preweaning average daily gain (PWADG), and average daily gain on feed (ADGF) in commercial lines of Bos taurus. The QTL regions for the growth traits identified using a haplotype association analysis, which included the gene-specific SNP markers for both genes in this study, were in agreement with previous studies. The gene-specific SNP marker association analysis indicated that the SNP in myf5 had a significant additive effect on PWADG in the M1 line of Beefbooster Inc. (P < 0.10), and a significant additive effect (P < 0.05) and a significant dominance effect (P < 0.10) on ADGF in the M3 line of Beefbooster Inc. When the data from the two commercial lines were pooled, the SNP in myf5 showed a significant association with PWADG (P < 0.10) and with ADGF (P < 0.05). The association between the SNP and BWT, however, did not reach a significance level in the M1 line, the M3 line, or across the lines. For igf1, no significant association between the SNP and the growth traits was detected in either the M1 line or the M3 line, whereas there was only a significant dominance effect (P < 0.10) on BWT detected for the SNP in igfl when the data from the two commercial lines were pooled. These results suggest that myf5 is a strong candidate gene that influences PWADG and ADGF in beef cattle. The SNP of igf1 may not be a causative or close to the causative mutation that affects the three growth traits in the populations of beef cattle examined in this study. Other SNP of igf1 and myf5 or other genes in their respective chromosomal regions, however, should also be studied. 相似文献
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APAP急性肝损伤小鼠肝脏组织转录组RNA-seq及相关信号通路分析 《畜牧与饲料科学》2021,42(4):1-6
[目的]筛选与对乙酰氨基酚（acetaminophen,APAP）诱导的急性肝损伤发生发展相关的基因和关键信号通路。[方法]建立C57BL/6J小鼠APAP急性肝损伤模型。构建正常小鼠肝脏组织样本和APAP急性肝损伤小鼠损伤后第2天肝脏组织样本的2个cDNA文库,进行转录组测序。对获得的转录组测序数据进行组装及功能注释。使用DESeq R包（1.10.0）分析具有生物学重复的差异基因的表达,利用KOBAS软件确定KEGG信号通路中差异表达基因的静态富集。[结果]APAP急性肝损伤小鼠损伤后第2天与正常小鼠肝脏组织转录组相比,共有7 270个DEGs,包括3 707个显著（P<0.05）上调表达基因和3 563个显著（P<0.05）下调表达基因。在所有显著上调表达基因中,表达量变化幅度较大的是Col1a1、Gsta1、S100a6基因;在所有显著下调表达基因中,差异表达量位于前3位的基因是Slc1a2、Glul、Acaa1b。共有2 515个DEGs在316个不同的KEGG通路中富集,显著上调表达基因富集的信号通路主要是趋化因子信号通路、B细胞受体信号通路、NOD样受体信号通路、ECM受体相互作用信号通路等免疫和炎症相关信号通路,显著下调表达基因富集的信号通路主要是氧化磷酸化、脂肪酸降解、脂肪酸代谢、碳代谢等合成代谢信号通路。[结论]在APAP急性肝损伤过程中涉及多个信号通路的参与,趋化因子信号通路和ECM受体交互作用信号通路可能是急性损伤期中发挥主要作用的信号通路。 相似文献
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羊绒细度是评价羊绒品质和衡量羊绒价格的关键数量性状,近年来,随着羊绒细度功能标记基因的深入研究,通过高通量数据解析及全基因组关联分析,逐步筛选出羊绒细度性状的候选基因,但是羊绒细度关键调控基因、表达量及分子调节机制尚未明了。基因表达受多种调节因子调控,其中非编码RNA的调节作用比较活跃,主要包括microRNA、lncRNA和circRNA等。经高通量测序和生物信息分析发现,非编码RNA在绒山羊品种间和品种内的不同羊绒细度个体皮肤、次级毛囊及次级毛囊周期性生长发育中差异表达并调节羊绒细度相关靶基因,但多种非编码RNA共同调节同一靶基因的信号通路甚少。目前通过对羊绒细度差异基因进行SNP标记辅助选择、转录组筛选、高通量解析非编码RNA调节及全基因组关联分析等相关研究发现,两两通路聚焦相同的羊绒细度靶基因较多,两条通路以上共同聚焦到某个或某几个羊绒细度的关键靶基因较少。作者主要讨论了羊绒细度候选基因及转录水平上microRNA、lncRNA和circRNA对羊绒细度相关靶基因分子调控机制的研究进展。 相似文献
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Lawrence R. Schaeffer Keng Pee Ang Jake A. K. Elliott Marine Herlin Frank Powell Elizabeth Grace Boulding 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2018,135(5):349-356
Genetic evaluations of individual fish were calculated for growth traits in North American Atlantic salmon with and without inclusion of genetic markers. The number of SNP markers was reduced to 6,000 and further to 270 in order to reduce the problem of overparameterization. SNP genotypes were predicted for all ungenotyped animals in the pedigree. Analysis of traits used a model with polygenic effects and SNP markers together. Polygenic effects refer to the additive genetic effects that remain after accounting for SNP genotypes. SNP marker genotypes were included as covariates to evaluate fish for growth traits (weight and length) in different environments (freshwater and seawater) with genders separated. Including regressions on SNP marker genotypes reduced the sum of squares of residuals by 2.7%–12.5% and increased the variability of Mendelian sampling effects (i.e., within‐family variation) compared to traditional animal model evaluations. Genetic evaluations may be carried out with a few hundred markers which may be more affordable for genotyping large numbers of fish. 相似文献
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Sherman EL Nkrumah JD Murdoch BM Li C Wang Z Fu A Moore SS 《Journal of animal science》2008,86(1):1-16
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[目的] 检测隆林猪的全基因组拷贝数变异。[方法] 采集33头隆林猪的耳组织样本,通过酚-氯仿法提取DNA后,使用猪中芯一号50K SNP芯片进行基因分型,得到的原始数据通过Genomestudio软件和Linux系统进行处理,使用CNVPartition和PennCNV软件分别检测拷贝数变异（copy number variation,CNV）,并利用Bedtools软件将CNV合并为拷贝数变异区域（copy number variation region,CNVR）,使用Biomart对CNVR进行基因定位,利用David网站对定位到的基因进行GO和KEGG富集分析,使用猪QTL数据库对共同CNVR进行QTL注释。[结果] CNVPartition软件共检测到260个CNVs,合并为47个CNVRs,其中缺失型40个、获得型5个、混合型2个,共定位到84个基因,显著富集到13条信号通路;PennCNV软件共检测到96个CNVs,合并为15个CNVRs,其中缺失型9个、获得型1个、混合型5个,共定位到8个基因,显著富集到8条信号通路;2个软件检测结果定位到的基因主要富集在嗅觉相关通路和G-蛋白偶联相关通路中,其中INPP5B、NEURL1和GAPDHS基因显著富集到精子活力通路;2个软件获得了3个共同CNVRs,其中缺失型、获得型和混合型均为1个,共定位到8个基因,显著富集到涉及嗅觉感官知觉的化学刺激检测通路、嗅觉受体活性通路、嗅觉转导通路、G-蛋白偶联受体活性通路、G-蛋白偶联受体信号通路、膜整体组件通路和质膜通路共7条信号通路;共有130个QTLs与3个共同CNVRs重叠,其中与背膘厚、肉质和乳头数相关的QTLs分别有11、9和6个。[结论] 隆林猪CNV可能与嗅觉功能、繁殖性能、背膘厚、肉质和乳头数性状相关。 相似文献