从江香猪基因组中2个拷贝数变异区的多态性研究

为了研究从江香猪生长和繁殖差异与拷贝数变异拷贝数变异(copy number variation,CVN)之间的关系,采用实时荧光定量PCR方法,对从江香猪和大白猪基因组中的CNVR100与CNVR373的拷贝数进行了测定,并分析了从江香猪拷贝数与生长繁育性状之间的相关性。结果表明,从江香猪和大白猪基因组中都检测到CNVR100和CNVR373;与大白猪相比,从江香猪的CNVR100拷贝数较低,CNVR373拷贝数较高;相关性分析结果显示,从江香猪2个CNVRs与其体长和胸围有一定的负相关关系,表明这2个CNVRs的多态性可能对从江香猪的生长有一定的影响。     

皱皮香猪3个基因组拷贝数变异的多态性分布

为探究皱皮香猪个体产生皮肤变异的根本原因,本文基于重测序数据,采用生物信息学分析皱皮香猪基因组中的拷贝数变异(CNV),通过荧光定量 PCR 方法检测皱皮香猪中 3 个 CNVs 的拷贝数变异规律,并与香猪和大白猪进行比较。结果表明:3 个 CNVs 在猪群中的拷贝数变异呈现出多态性变化,皱皮香猪中CNV1以拷贝数缺失型为主,其中的 MPC1和 RSK3基因可能与脂肪沉积有关;皱皮香猪 CNV2和 CNV3以拷贝数增加型占优势,其中的 CCL17和 CX3CL1基因参与皮肤等组织的炎症反应,可能通过剂量效应引起香猪皮肤产生褶皱。     

5个猪品种3个拷贝数变异区的多态性分析

为了探究拷贝数变异(copy number variation,CNV)在不同猪品种间的多态性,本试验根据猪SNP60芯片检测结果,以大白猪、香猪、柯乐猪、糯谷猪、荣昌猪为主要研究对象,采用实时荧光定量PCR方法,对5个猪品种基因组中3个CNV区域(CNVR91、CNVR92和CNVR143)的拷贝数进行测定。结果显示,香猪的CNVR91以拷贝数缺失为主,其他4个猪品种的拷贝数以正常为主;香猪、大白猪、柯乐猪、荣昌猪的CNVR92以拷贝数缺失为主,糯谷猪以拷贝数正常为主;香猪和糯谷猪的CNVR143以拷贝数增加为主,其他3个猪品种以拷贝数正常为主。表明3个拷贝数变异区在5个猪品种之间具有多态性,可能通过剂量效应影响香猪、糯谷猪和柯乐猪等相关基因的表达和生理功能。     

贵州地方猪品种毛色与KIT基因拷贝数之间的关联分析

为了研究KIT基因的拷贝数与贵州地方猪毛色之间的关系,本试验以黔北黑猪、柯乐猪、糯谷猪、香猪4个地方品种为试验材料,采用实时荧光定量PCR方法检测基因组中KIT基因的拷贝数变异,并与荣昌猪和大白猪2个白毛色猪品种相比较.结果显示,4个贵州地方猪种中,全黑/全棕毛色个体的KIT基因拷贝数以缺失为主,黑色带白斑个体的KIT基因拷贝数全部缺失,而棕色带白个体的KIT基因拷贝数增加、正常各半.大白猪的KIT基因拷贝数显著增加,荣昌猪KIT基因拷贝数以正常类型为主.表明大白猪的白毛色由KIT基因拷贝数增加决定,但荣昌猪的白毛色可能与KIT基因的拷贝数变异之间没有直接的联系;4个贵州地方品猪的全黑/全棕色毛色与KIT基因拷贝数的缺失有关,但柯乐猪和香猪中带白斑个体的KIT基因拷贝数并未增加,提示贵州地方猪品种的白斑毛色的形成机制有一定的特殊性.     

贵州地方猪品种HSL基因多态性与屠宰性状的关联性研究

本研究旨在分析HSL基因多态性与地方猪品种瘦肉率之间的相关性。采用RFLP方法,以二元杂交猪（长白猪×大约克猪）为对照,对贵州地方猪品种糯谷猪和萝卜猪的HSL基因进行多态性分析。结果表明,贵州地方猪品种HSL基因外显子1中存在BsaH I酶切片段长度多态性,从3个猪群体中都检测到AA、AB和BB基因型,克隆测序后证实,A等位基因于第442 bp处发生了单碱基突变（G→A）,导致氨基酸Val→Ile替换。地方猪品种以A等位基因占优势,杂交猪以B等位基因占优势。将猪胴体性状与HSL基因型之间进行关联分析,结果显示大部分年龄段的猪品种中,BB、AB和AA 3种基因型的瘦肉率和眼肌面积均表现出从高到低的变化趋势,而背膘厚则完全相反。结果提示,HSL外显子1的B等位基因具有增加胴体瘦肉率和眼肌面积、降低背膘厚的遗传效应,可作为贵州地方猪品种瘦肉率的分子标记。     

3个地方猪品种BOLL和STRA8基因结构变异位点的群体分布研究

为了探讨BOLL-I6-sv285（15号染色体BOLL基因第6内含子）和STRA8-I4-sv447（18号染色体STRA8基因第4内含子）这两个结构变异在地方猪与欧洲猪品种中的群体分布差异,试验采用PCR方法对从江香猪、江口萝卜猪、荣昌猪和大白猪4个猪品种进行基因分型,并通过在线软件miRBase、UCSC、RegRNA 2.0对结构变异序列所含的功能元件进行分析。结果显示,BOLL-I6-sv285为一段285 bp的插入,经群体验证,3个地方猪品种以DI和DD基因型为主,I等位基因的频率高于大白猪,插入基因型（Ⅱ）对应较高的产仔数,基因型与从江香猪产仔数之间呈显著相关（P<0.05）;STRA8-I4-sv447为一段447 bp的插入突变,群体中DD基因型占优势,从江香猪、江口萝卜猪和大白猪的I等位基因频率高于荣昌猪,插入基因型（Ⅱ）对应较低的产仔数,基因型与从江香猪产仔数之间呈显著相关（P<0.05）。本试验鉴定的BOLL-I6-sv285和STRA8-I4-sv447两个结构变异可作为从江香猪产仔数的候选分子标记。     

从江香猪CD53基因的组织表达和结构变异多态性研究

基于比较基因组学,在猪源白细胞表面抗原CD53基因中发现一段265 bp的结构变异(Structure Variant,SV).为了研究该结构变异在不同猪种中的多态性变化,本研究采用RT-qPCR检测从江香猪各组织中CD53基因mRNA的表达差异,并建立了结构变异CD53-I4-SV265的PCR检测方法,应用建立的检...     

贵州白香猪BF基因多态性研究

贵州白香猪为贵州特有的地方品种猪,本研究采用直接测序法对贵州白香猪BF基因外显子15、16、17的733bp进行多态性分析。结果显示,在第16外显子41bp处存在A→C的碱基突变,导致编码的氨基酸由谷氨酸（Glu）突变为天冬氨酸（Asp）。在贵州白香猪群体内检测到AA、AC和CC3种基因型,等位基因A和C频率分别为0.88和0.12。     

贵州从江香猪基因组中CNVR36的多态性与产仔数和体尺相关分析

为了研究拷贝数变异与香猪生长及产仔数之间的关系,采用荧光定量PCR方法,测定香猪高、低产群体基因组中CNVR36的拷贝数变化,并与柯乐猪、荣昌猪、大白猪和糯谷猪4个猪品种相比较,进而分析拷贝数变异与香猪生长及产仔数性状之间的关系。结果显示,从香猪基因组中检测到CNVR36的拷贝数存在多态性变化:高产群体中以拷贝数增加为主,低产群体中以拷贝数缺失为主,经卡方检验,两个群体间的拷贝数变异频率差异极显著(P0.01)。柯乐猪、荣昌猪、大白猪和糯谷猪4个猪品种的CNVR36拷贝数以增加为主,相关性分析结果表明,香猪CNVR36拷贝数与胸围之间存在弱的负相关关系,糯谷猪CNVR36的拷贝数与其体宽和胸围有一定的相关关系,荣昌猪的CNVR36拷贝数与体高有一定的负相关关系。推测香猪CNVR36的拷贝数变异可能与生长发育有一定的联系。     

贵州白香猪BF基因多态性研究

贵州白香猪为贵州特有的地方品种猪,本研究采用直接测序法对贵州白香猪BF基因外显子15、16、17的733 bp进行多态性分析。结果显示,在第16外显子41 bp处存在A→C的碱基突变,导致编码的氨基酸由谷氨酸(Glu)突变为天冬氨酸(Asp)。在贵州白香猪群体内检测到AA、AC和CC 3种基因型,等位基因A和C 频率分别为0.88和0.12。     

江西地方猪种SLA-DRB基因外显子2的多态性研究

采用PCR-RFLP法对3个江西地方猪种(乐平花猪、修水杭猪和万安花猪)的SLA-DRB基因外显子2的PCR产物进行多态性分析。通过限制型内切酶RsaⅠ酶切后,共产生9种组合带型。通过检测发现:乐平花猪有8种组合带型,即AA、AB、AC、BB、BC、BD、CD和DD;修水杭猪有3种组合带型,即AA、AB和AC;万安花猪有4种组合带型,即AA、AC、BC和CC,且3个猪种中均以A为优势带型,在猪种中频率相差不大。χ2检测表明,乐平花猪和修水杭猪SLA-DRB基因外显子2在RsaⅠ酶切位点达到了Hardy-Weinberg平衡状态,而万安花猪未达到Hardy-Weinberg平衡状态。     

Porcine endogenous retrovirus copy number in different pig breeds is not related to genetic diversity

The risk of zoonoses is a major obstacle to xenotransplantation. Porcine endogenous retrovirus (PERV) poses a potential risk of zoonotic infection, and its control is a prerequisite for the development of clinical xenotransplantation. The copy number of PERV varies among different breeds, and it has been suggested that the PERV integrations number is increased by inbreeding. The purpose of this study was (i) to examine the copy number of PERV in different Spanish pig breeds, Spanish wild boar and commercial cross-bred pigs from five different farms and genetic background (CCP1-CCP5) and (ii) to investigate the correlation between PERV copy number and the genetic background of the pigs in order to improve the selection of pigs for xenotransplantation. PERV copy number was determined by quantitative, real-time polymerase chain reactions. Thirty-four microsatellite markers were genotyped to describe the genetic diversity within populations (observed and expected heterozygosities, Ho and He, respectively) and the inbreeding coefficient (F). Pearson's correlation coefficient was used to determine the relationship between PERV copy number and Ho, He and F. The copy number of PERV among different pig breeds was estimated to range between three (CCP1) and 43 copies (Iberian Pig). Statistical differences were found among the studied populations concerning PERV copy number. No correlation was found between the PERV copy number and the heterozygosity (calculated at an individual level or at a population level) or the inbreeding coefficient of each population. Our data suggest that pigs inbreeding does not increase PERV copy number and support the idea that careful selection of pigs for organ donation with reduced PERV copy number will minimize the risk of retrovirus transmission to the human receptor.     

7个猪品种IBSP基因结构变异SV13的群体分析

应用Hiseq 2000平台测定了香猪的全基因组序列,从中发现整合素结合涎蛋白(IBSP)基因内含子4中存在结构变异,命名为SV13,为了进一步探究SV13在猪群体中的分布,采用PCR技术检测了7个猪品种的SV13基因型。7个猪品种群体中均存在DD、DA和AA三种基因型,对纯合的DD和AA基因型测序,明确D等位基因缺失了227 bp。香猪、可乐猪和糯谷猪群体以DD为优势基因型,大白猪以AA基因型为主,6个地方猪品种群体中D的基因频率明显高于大白猪品种(P0.01),香猪和大白猪群体基因型频率处于Hardy-Weinberg不平衡状态(P0.05)。SV13可以作为辅助鉴别6个地方猪品种和大白猪的分子标记。     

中国地方猪保种与利用工作的思考

简述了我国地方猪保种与利用工作的成效,提出了我国地方猪品种资源危机带有全局性,亟待采取应急措施;当前紧迫的任务是保持其遗传多样性,维持公猪现有的血统数;活体保种应立足于保种场,兼顾保种区;资源评估工作有待加强;有计划地开展有利于保种的优质商品猪生产。     

贵州地方猪品种与欧洲猪品种MUC13基因的多态性比较

产肠毒素大肠杆菌(Enterotoxigenic Escherichia coli,ETEC)是导致仔猪腹泻的主要病原,MUC13基因被认为是控制仔猪ETEC易感或抗性的候选基因。本文通过等位基因特异性PCR(Allele-specific PCR)方法对4个贵州地方猪种MUC13基因的多态性进行研究,并与两个欧洲猪群相比较。结果显示:贵州地方猪群中MUC13基因的G等位基因频率较高,特别是香猪和黔北黑猪群体分别达到了95.21%和96.43%,与贵州地方猪品种优良的抗腹泻表现相符。提示贵州地方猪品种MUC13基因的G119A位点可以作为抗腹泻筛选的SNP分子标记。     

The physiological effects of natural variation in growth hormone gene copy number in ram lambs

The effects of natural variation in the number of copies of the growth hormone (GH) gene on growth parameters, plasma GH profiles, and the response to GHRH challenge were compared in Coopworth ram lambs from selection lines differing in body composition and GH levels. Different genotypes at the GH locus carried two, three, or four copies of the GH gene and GH secretion was studied under ad libitum feeding conditions and in the fasted state. There were no significant effects of GH genotype on any parameters of growth or body composition. Basal serum GH concentration, GH pulse frequency, and GH pulse amplitude differed significantly with selection line and fasting, but did not differ significantly between the GH genotypes. Significant differences of subtle nature were found between the GH genotypes in their responsiveness to GHRH. For the ad libitum-fed Lean selection line animals, the first GHRH challenge resulted in a higher mean maximum response for GH1/GH1 than GH2/GH2 (P < 0.05). Between the first and the second challenges there was a decrease in maximum response for the GH1/GH1 genotype and an increase for the GH2/GH2 genotype (P < 0.05 for GH genotype main effect). The differences between GH genotypes in response to GHRH challenge suggest that polymorphism in the number of GH gene copies in sheep may have physiological implications for the function of the GH axis, which may be manifested in growing lambs only under specific genotype-environment combinations.     

微卫星标记ILSTS011在3个绵羊品种中的遗传多样性分析

为了分析微卫星标记ILSTS011的遗传多态性,研究以河南省地方绵羊品种大尾寒羊、小尾寒羊和豫西脂尾羊为研究对象,采用聚丙烯酰胺凝胶电泳技术分离微卫星标记的带型.结果表明:在3个绵羊品种中均检测到微卫星标记ILSTS011有3个等位基因,微卫星标记ILSTS011的平均杂合度为0.614 1,平均有效等位基因数为2.614 0,平均多态信息含量为0.551 3.说明ILSTS011为高度多态基因座,可作为有效的遗传标记用于大尾寒羊、小尾寒羊和豫西脂尾羊的遗传多样性分析.     

Comparison of production systems for efficient use of indigenous pig breeds in developing countries

Conserving pig genetic resources and improving their productivity is important to increase returns over investment in developing countries. The purebred, first‐cross, rotational cross and backcross matings representing production systems based on pig breeds indigenous to the country and exotic pig breeds were investigated. The number of pigs in the nucleus and commercial herds necessary to produce a defined quantity of pork was considered. The amount of heterosis between the indigenous and exotic breeds, superiority in meat production, and degree of inferiority in reproductive performance of the exotic breed compared with that of the indigenous breed were investigated. The number of breeding pigs in the whole system was in the following order: pure breeding (PB) > first‐cross (F1) > rotational cross (RC) > backcross (BC) systems. The number of breeding pigs in the nucleus herds of the RC and BC systems was smaller than that in the nucleus herds of the PB and F1 systems. The degree of inferiority in reproductive performance of the exotic breed compared with that of the indigenous breed affected the efficiency of the production system.     

Detection and analysis of genome-wide copy number variation in the pig genome using an 80 K SNP Beadchip

Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome-wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.