基于线粒体基因的新疆三种野兔分类及遗传多样性

旨在利用分子遗传学方法探讨新疆3种野兔的系统发育关系和遗传多样性,以期明确其亲缘关系和分类地位,并评估其遗传多样性水平,为后续新疆野兔乃至中国野兔的保护遗传学等研究提供基础数据。本研究选用线粒体DNA的COI、ND4、16S rRNA 3个基因为分子标记,通过PCR扩增及测序技术分别测定采自新疆8个地区、4个地理组群共计57例野兔组织样本的3个基因序列,将序列校正拼接后用MEGA 7、DNAsp 6、Arlequin 3.1、MrBayes 3.2等软件进行数据分析。结果表明,将57例野兔样本的3个基因序列合并后共检测到43种单倍型,系统发育和中介网络图将相同及相邻地区的野兔划分为5个支系（Clade A-E）3大枝,且3大枝之间的遗传距离（4.21%~9.09%）均达到种间距离水平;其中,第3大枝中来自中部地区的野兔（Clade D）和新疆北部野兔（Clade E）的亲缘关系较近,二者之间的遗传距离≤2.26%,未达到种间遗传距离水平。新疆3种野兔中塔里木兔、藏兔帕米尔亚种和托氏兔西域亚种的单倍型多样性（h）较高,分别为0.979±0.014、0.972±0.064和0.972±0.064,而托氏兔西域亚种和中亚亚种的核苷酸多样性（π）较高,分别为0.033±0.018和0.023±0.015。基于线粒体3个基因的综合分析结果,结合已报道文献,本研究认为来自新疆西南部帕米尔高原的野兔应属于藏兔帕米尔亚种,支持将来自新疆北部阿勒泰及中部达坂城和托克逊地区的野兔分别划分为托氏兔西域亚种和托氏兔中亚亚种。新疆3种野兔具有丰富的遗传多样性和较明显的系统地理分布格局。     

陕西省本氏针茅自然种群遗传多样性的ISSR分析

利用ISSR分子标记,对采自陕西省不同地区的5个本氏针茅(Stipa bungeana)自然种群进行遗传变异及群体遗传结构分析,旨在探讨本氏针茅遗传变异产生的分子生态机理,为其资源保护提供理论依据。在100个供试单株中,采用15条ISSR引物共扩增出223条可统计条带,其中多态性带182条,多态性位点比率为81.61%,Nei’s基因多样性(H)为0.1887,Shannon 信息指数(I)为0.2975,各种群之间存在较高的多态性。种群间的遗传变异为63.01%,种群内的遗传变异为36.99%,遗传分化系数φ_st 为0.6300,种群间的基因流(N_m)为0.1468,表明本氏针茅遗传分化程度较高,遗传变异主要分布在种群间,而种群内变异相对较小,且各种群间的基因交流非常有限。     

基于ND2基因的崖沙燕遗传多样性和遗传结构初探

利用线粒体DNA中的NADH脱氢酶第二亚基(ND2)对来自齐齐哈尔市50个崖沙燕(Riparia riparia)样本进行扩增和测序,发现了11条新的单倍型序列。结合从GenB ank中下载的104条序列,对崖沙燕3个亚种种群(154只个体)进行序列变异及系统发育分析。结果显示,3个亚种种群中有2个共享单倍型。群体总的单倍型多样性(Hd)为(0. 885±0. 019),群体总的核苷酸多样性(Pi)为(0. 002 92±0. 000 18)。与其近缘物种淡色崖沙燕(Riparia diluta)相比较,崖沙燕种群表现出较低水平的遗传多样性。分子方差分析(AMOVA)显示变异主要来自种群内(72. 82%)。构建的单倍型系统发育树表明,62个单倍型没有形成明显的亚种分化和地理分化。     

5个新疆绵羊群体线粒体DNA的遗传多样性研究

为了探讨5个新疆绵羊群体的群体内和群体间的遗传变异,试验采用PCR-SSCP和克隆测序技术利用3对引物对5个新疆绵羊群体的线粒体DNA做了系统的分析研究.结果表明:5个新疆绵羊品种中都存在A、B、C 3种单倍型,且以A单倍型为主,而欧洲绵羊以B单倍型为主.     

基于线粒体CO2和ND4基因对四川省豆状带绦虫种群遗传多样性的分析

利用PCR扩增了中国四川省7个不同地理区域(雅安、攀枝花、乐山、广元、泸州、广安和阿坝)23株家兔体内豆状囊尾蚴的CO2(Cytochrome oxidase subunit 2,468 bp)和ND4(NADH dehydrogenase subunit 4,1 077 bp)基因的部分序列,并进行分析.结果显示,7个种群23个分离株中CO2和ND4基因序列中分别有21个和32个变异位点,分别检测出了5个和7个单倍型,2个基因的种群分析结果显示乐山种群最为保守;CO2分析结果显示攀枝花和雅安种群内变异最大,且高于种群间变异.2个线粒体基因构建的NJ/MP树显示7个种群的系统发生与他们分布的地理区域没有直接的相关性,还未形成显著的地理种群结构.结果表明,四川省7个地理种群间和种群内豆状囊尾蚴均存在一定的遗传变异和遗传多样性,为豆状带绦虫的分子流行病学调查和群体遗传研究奠定了基础.     

基于线粒体Cyt b基因和CR序列的养殖貉(Nyctereutes procyonoides)种群遗传多样性和结构分析

貉(Nyctereutes procyonoides)是一种重要的经济动物。经过50年的人工驯养繁育,国内养殖种群不断扩大,但对其遗传多样性和结构了解很少,难以开展有效的遗传管理。本研究分析了东北、华北地区养殖貉种群(N=160)的线粒体细胞色素b(Cyt b)基因和控制区(CR)序列,并与已经发表的同源序列进行比较。结果定义了5个Cyt b基因和6个CR序列单倍型,其中与俄罗斯产乌苏里亚种共享单倍型分别是3个和4个。种群遗传多样性分析表明,养殖貉种群单倍型多样性处于临界点(Hd=0.50)、核苷酸多样性处于较高水平(Pi>0.5%),但二者均明显低于俄罗斯野生乌苏里貉种群。这种遗传多样性模式可能主要是由奠基者效应(founder effect)导致的。此外,红褐色型貉遗传多样性水平显著低于野生型和白色型貉。系统发育分析表明国内养殖貉种群分为3个世系,主要是乌苏里亚种、与同亚种的俄罗斯野生种群亲缘关系密切。研究还发现有1个单倍型(CH5-DH5)与越南产指名亚种共享同一个单倍型世系。这说明建群引种中可能偶然引入了华南地区分布的指名亚种。综上分析,我国养殖貉种群已经出现遗传多样性下降的迹象,需要监控种群遗传多样性的变化,引入具有新基因型的野生貉种,制定科学的交配模式,避免近交衰退。     

利用微卫星和线粒体D-loop区联合分析大尾寒羊的遗传多样性

本研究对42只大尾寒羊的10个微卫星标记进行了遗传多样性分析,并对其中38只个体的线粒体DNAD-loop区的进行了测序和多态性分析。结果表明,10个微卫星位点共发现38个等位基因,平均观察杂合度为0.3631,平均PIC值为0.416,FST、FIS和FIT平均值分别为0.0842、0.1784和0.2466,且该群体的HO相似文献   

基于线粒体cox1和Cyt b基因对四川地区多头带绦虫的种群遗传多样性研究

为研究四川地区多头带绦虫的种群遗传多样性和系统发生关系,用线粒体cox1基因和Cyt b基因全序列分析了20株四川山羊源多头蚴(11株寄生于脑,9株寄生于肌间)的遗传变异,并构建了系统发育树。结果显示:20株多头蚴cox1和Cyt b基因全序列长度分别为1 623和1 068bp,分别有59个和9个变异位点,其碱基变异率分别为0.1%~2.5%和0.1%~0.7%;分别检测到17个和6个单倍型,总的单倍型多样性分别为0.968±0.033和0.737±0.068,核苷酸多样性分别为0.005 98±0.001 33和0.003 06±0.000 79,平均遗传距离分别为0.006和0.003。构建的系统进化树均显示来源于脑部和肌间的20株四川山羊源多头蚴与多头带绦虫同在一个支系,均为多头带绦虫,且多头带绦虫四川分离株与伊朗、土耳其分离株亲缘关系较近,而与中国甘肃、中国广州、意大利分离株亲缘关系较远。研究结果表明线粒体cox1和Cyt b基因均可作为检测多头带绦虫种群遗传多样性的有效分子标记,且Cyt b基因的多样性水平低于cox1基因。     

基于小尺度高原鼢鼠种群遗传结构研究

高原鼢鼠是青藏高原特有的地下啮齿动物,研究其种群遗传结构对于了解扩散、基因交流等方面具有重要意义。本研究利用微卫星分子标记技术,分析祁连山东段高寒草甸区小尺度下4个高原鼢鼠种群的遗传多样性和遗传结构特点。结果表明:1)4个种群有效等位基因(Ne)为83.6,种群平均观测杂合度(Ho)最高为0.32,平均期望杂合度(He)最高为0.50,平均多态信息含量(PIC)为0.40,遗传多态性处于中等水平。2)种群遗传结构推导分析结果为 4 个种群被分成 2 组,MYT(马营滩种群)为一组,XNG(下南泥沟种群)、MYR(马营河东边种群)、MYL(马营河西边种群)为一组。3)试验区高原鼢鼠种群间近交系数(F_ST)都大于0.05,种群间的基因流值(N_m)都小于1,特殊岛状栖息地限制了高原鼢鼠种群基因流,河流和公路可能对种群内和种群间个体交流有阻碍作用。     

3个品种兔微卫星标记的遗传多样性研究

为分析福建黄兔、新西兰兔、日本大耳白兔群体内的遗传变异情况和群体间的遗传相关性,本试验选取3个品种兔各25只,分别耳静脉采血并采用试剂盒抽提全血基因组,运用15个微卫星标记,结合荧光PCR技术和毛细管电泳方法获得目的片段,通过计算等位基因数、有效等位基因数、杂合度、多态信息含量和遗传距离,分析3个品种兔的遗传多样性。结果显示,3个品种兔在15个座位共检测到110个等位基因,平均等位基因数为7.3个,其中福建黄兔、新西兰兔和日本大耳白兔分别检测到95、95和88个等位基因,且分别在11、12和11个微卫星座位表现为高度多态,表明3个品种兔在筛选的15个微卫星座位均呈现较丰富的遗传多态信息。Hardy-Weinberg遗传平衡检验结果表明,福建黄兔、新西兰兔和日本大耳白兔分别有8、8和6个座位处于Hardy-Weinberg不平衡状态。Nei氏遗传距离分析显示,福建黄兔与新西兰兔、福建黄兔与日本大耳白兔、新西兰兔与日本大耳白兔的Nei氏遗传距离分别为0.1761、0.2347和0.0432。遗传距离越小时,相似度越高,亲缘关系越近,因此,新西兰兔与日本大耳白兔间的亲缘关系最近,福建黄兔与日本大耳白兔间的亲缘关系最远。     

Classification and Genetic Diversity of Three Hare Species in Xinjiang Based on Mitochondrial DNA

The study aimed to explore the phylogeny and genetic diversity of 3 hare species in Xinjiang by molecular genetics methods, define the relationship and taxonomy status, assess diversity level of Lepus in Xinjiang, and provide the basic data for conservation genetics of hares in Xinjiang and even in China. Three mitochondrial DNA genes, COI, ND4 and 16S rRNA, were used as molecular markers, and the sequences of 3 genes of 57 samples collected from 8 different regions (4 geographic groups) in Xinjiang were determined by PCR amplification and sequencing technology. After the sequences of COI, ND4 and 16S rRNA of each sample were revised and pooled together, data were analyzed with softwares such as MEGA 7, DNAsp 6, Arlequin 3.1 and MrBayes 3.2. A total of 43 haplotypes were detected from the combined sequences of 3 genes of 57 hare samples. Five distinct clades (A-E) and 3 clusters were clearly showed in phylogenetic tree and median-joining network (MJN). Furthermore, the genetic distance between 3 clusters reached the level of species (4.21%-9.09%). However, the genetic distance between hares from northern Xinjiang (Clade E) and those from central Xinjiang (Clade D) were not up to the level of species (≤2.26%) in the third cluster. The haplotype diversity (h) of Lepus yarkandensis, Lepus tibetanus pamirensis and Lepus tolai lehmanni were higher(0.979±0.014, 0.972±0.064 and 0.972±0.064, respectively), while the nucleotide diversity (π) of the L. t. lehmanni and L. t. centrasiaticus were higher (0.033±0.018 and 0.023±0.015, respectively). Based on comprehensive analysis of 3 genes of mitochondrion and reference with published research, it is suggested that hares from southwestern Pamir Plateau of Xinjiang should belong to L. t. pamirensis. Meanwhile,hares distributed in northern and central Xinjiang might be considered as L. t. lehmanni and L. t. centrasiaticus. Moreover, there is abundant genetic diversity in the 3 hare species in Xinjiang, and the obvious phylogeographic pattern is showed.     

SNP芯片评估柯尔克孜羊群体遗传多样性和遗传结构

旨在了解柯尔克孜羊群体的遗传多样性和遗传结构,有效地保护和利用其遗传资源。本研究利用绵羊SNP 50K v3芯片检测61只柯尔克孜种羊(31只公羊、30只母羊)个体的单核苷酸多态性(single nucleotide polymorphism, SNP);Plink(V1.90)软件对数据进行质控,计算群体有效含量、多态标记的比例、观测杂合度、期望杂合度、多态信息含量、有效等位基因数、最小等位基因频率,分析群体的遗传多样性;Plink计算连续性纯合片段(runs of homozygosity, ROH)和近交系数F_ROH;构建状态同源距离矩阵(identical by state, IBS),并采用Gmatrix软件构建G矩阵,解析柯尔克孜羊群的遗传距离和亲缘关系;使用Mega X软件构建种公羊进化树,分析群体家系结构。结果显示,61只柯尔克孜羊共得到64 734个SNPs标记,通过质检的SNPs为56 763个;平均多态信息含量为0.273±0.112,平均观察杂合度和平均期望杂合度分别为0.368±0.140和0.368±0.130,平均最小等位基因频率为0...     

Genetic Diversity of Gazella subgutturosa Based on Mitochondrial DNA D-Loop Sequence in Xinjiang Ebinur Lake

To investigate the genetic diversity and genetic data of Gazella subgutturosa from Xinjiang Ebinur lake National Wetland Nature Reserves, the Ebinur lake goose antelope 35 feces samples were analyzed.Using noninvasive DNA technology, the mitochondrial DNA D-Loop 878 bp fragment was successfully amplified.Sequences results for GenBank database BLAST comparison and Clustal W and DNASP software analysis.The results showed that the sequences of the above fragments were successfully amplified, total 55 polymorphic loci were detected, which were not found insert and deficiency.This study found 15 variable sites, including 14 transversion sites and 1 top transposition.The average A, T, C and G contents in D-Loop were 28.03%, 31.57%, 24.84% and 15.56%, respectively.The contents of A+T (59.6%) were higher than G+C (40.4%).In addition, a total of 16 mtDNA haploid type were detected, haploid type polymorphism (h) was 0.886 ±0.037, nucleotide diversity degree (π) was 0.037±0.01528.The results showed that Ebinur lake Gazelle subgutturosa maintained high variation in mitochondrial D-Loop sequences.     

利用微卫星分析康西草原马匹种群的遗传多样性和群体结构

旨在揭示康西草原马匹的品种来源以及群体遗传结构。本研究采集了当地60匹健康状况良好、体重适中、3～6岁之间不区分公母马的血液样品,试验分为6个种群并以纯血马等4个国外马品种、1个我国地方马品种作为对照, 通过设计引物并提取基因组DNA结合微卫星扩增法对染色体上12个微卫星位点的等位基因进行检测,并对各种群遗传多样性参数、群体分化指数、瓶颈效应以及群体结构进行分析。试验按照群体个数为依据分为6组,每组1个重复,每个重复以该组样本量为标准。分析6个种群马的遗传参数结果表明,其中共检测到221个等位基因,平均Shannon指数为1.691;有效等位基因数(Ne)为3.649～5.397;期望杂合度(He)为0.681～0.798;观测杂合度(Ho)为0.632～0.780;平均多态信息含量(PIC)为0.643～0.772。这些结果表明,6个群体都具有很高的遗传多样性。通过微卫星DNA位点的连锁不平衡及哈迪-温伯格平衡分析发现, 大多数位点的P值都大于校正值(P=0.006 5),表示较多位点都处于哈迪-温伯格及连锁平衡状态。各群体间群体分化系数(Fst)表明,群体间分化程度较低(Fst<0.15)。基于Nei’s遗传距离与地理距离之间Mantel相关性检验显示二者之间呈现正相关性(R=0.502),但未达到显著水平(P=0.310);各马匹种群瓶颈效应分析表明,P值极显著(P_(IAM)<0.01)说明该地区的马群体受到过瓶颈效应的影响且该马群体历史上数量有大规模的减少。通过 FCA因子分析、基于Nei’s标准遗传距离UPGMA树状图以及Structure贝叶斯聚类分析发现,该地区马种群与纯血马和温血马聚为一类,说明该种群最有可能主要来源于温血马和纯血马。这些结果揭示,康西草原地区马匹具有较高的遗传多样性,该地马群体的血统与纯血马和温血马相近,这为当地马遗传资源评估以及开发利用打下了坚实的基础。     

基于线粒体Cytb基因的贵州野猪(Sus scrofa)群体遗传多样性分析

【目的】评估贵州地区野猪(Sus scrofa)的遗传多样性和遗传结构,为进一步开展保护遗传学研究和种群生态管理提供理论依据,进而为研究野猪的保护生物学及其对环境的适应奠定基础。【方法】对野猪线粒体Cytb基因进行PCR扩增及测序,结合从GenBank中下载的国内其他9个地区的55条野猪线粒体Cytb基因序列,利用Mega 7.0软件进行碱基组成和遗传距离分析,并使用DnaSP 6.0软件进行遗传多样性分析。【结果】贵州野猪Cytb基因(1 140 bp)碱基组成与其他地区野猪种群相似,AT含量高于GC含量;贵州采集的11头野猪的Cytb基因共有6个变异位点,4种单倍型,单倍型多样性为0.600,核苷酸多样性为0.00118;单倍型多样性与核苷酸多样性仅高于江西和东北地区的野猪种群;种内遗传距离较小,亲缘关系较近;中性检验Tajima’s D值和Fu’s Fs值均为负值且差异不显著,错配分布分析呈单峰分布,表明贵州野猪种群在历史上较为稳定。使用Network构建单倍型网络图,结合Mega 7.0软件构建的单倍型系统发育树分析结果表明,贵州野猪单倍型与其他地区种群存在共享单倍型(Hap＿...     

略阳乌鸡线粒体DNA控制区(D-loop)的遗传多样性分析

为了研究略阳乌鸡线粒体DNA控制区（mtDNA D-loop）的遗传多样性和起源,本研究对30只略阳乌鸡样品的mtDNA D-loop全序列进行了PCR扩增和测序,结合GenBank中公布的其他鸡的D-loop区序列,分析略阳乌鸡线粒体多态性及其起源。结果表明,略阳乌鸡mtDNA D-loop区全序列中,A、C、G、T平均含量分别为26.6%、26.6%、13.4%和33.4%,26个核苷酸多态位点均为转换位点,核苷酸多样度（Pi）为0.00705,单倍型变异度（Hd）为1.000,中性检验Tajima's D值为-0.47272。通过群体构建的系统进化树发现,略阳乌鸡样品在系统进化树上聚为4大分支。研究结果表明,略阳乌鸡群体内个体序列变异程度较大,遗传多样性丰富,揭示略阳乌鸡在遗传组成上具有4个母系来源。     

Genetic Diversity of Lueyang Black-bone Chicken Based on Mitochondrial DNA D-loop Region Sequence

This study was aimed to assess mitochondrial DNA D-loop sequence diversity and origin of Lueyang Black-bone chicken.The mtDNA D-loop sequence of 30 individuals from Lueyang Black-bone chicken were amplified by PCR and subsequently sequenced.The mtDNA D-loop sequence of other chicken were collected from GenBank and used as reference sequences to analyze the diversity and origin of Lueyang Black-bone chicken.The results revealed that the average values of base composition of A,C,G and T in mtDNA D-loop the sequence of Lueyang Black-bone chicken were 26.6%,26.6%,13.4% and 33.4%,respectively.26 nucleotide polymorphic sites were transition.The average nucleotide diversity (Pi) of the sites and haplotype diversity (Hd) were 0.00705 and 1.000,and the value of Tajima's D was -0.47272.Phylogenetic tree showed that samples were clusted in 4 clades. In the research, it could be concluded that the genetic diversity was relatively rich and wealthy and there were 4 maternal origins to Lueyang Black-bone chicken population.     

中国9个地方山羊品种的遗传多样性和群体结构分析

采用联合国粮农组织(FAO)和国际动物遗传学会(ISAG)联合推荐的数据库中选取的16对微卫星引物对中国9个地方山羊品种和1个引进品种(波尔山羊)的遗传多样性及群体结构进行分析。结果表明,在15个微卫星位点上共检测到159个等位基因;9个地方山羊品种的Fst值为89.5%,说明89.5%的遗传变异存在于品种内,而10.5%的遗传变异存在于品种间;依据Da遗传距离构建UPGMA系统发生树,表明波尔山羊分开独自聚为一类,9个地方山羊品种分为两类;采用Structure软件对10个山羊品种的群体结构进行分析,可以将其分为4组。所得到的群体关系同聚类图得到的结果基本一致。     

Population Structure and Genetic Diversity of Seven Chinese Indigenous Chicken Populations in Guizhou Province

To investigate the population structure and genetic diversity of indigenous chicken breeds in Guizhou, a total of 150 individual samples were collected from 12 breeds, including seven local chicken breeds in Guizhou Province, three Chinese native breeds found in other provinces, and two commercial breeds. The genotype datasets were obtained using a 50K single nucleotide polymorphism array method, and then a series of population analyses were performed. The obtained population parameters and linkage disequilibrium decay indicated a higher degree of genetic diversity in Guizhou chickens than in commercial breeds. Two Guizhou local breeds, Wumeng black-bone and Weining, were clustered with a breed from a neighboring province, Xinwen black-bone, which exhibited similar ancestral composition patterns. A newly found breed, Wumeng crested, had high genetic diversity and displayed genetic differences from other Guizhou breeds. These findings provide insight into the establishment of efficient conservation and utilization programs for Guizhou chicken breeds.