中国家驴mtDNA D-loop 遗传多样性与起源研究

对我国12个家驴品种126个个体（包括引用26个个体）的mtDNA D-loop区399 bp进行分析,共检测到36种单倍型37个多态位点,其单倍型多样度为0.466 7-0.977 8,核苷酸多样度为0.001 2-0.028 5,表明我国家驴的遗传多态性丰富。与3条努比亚野驴、3条索马里野驴和6条亚洲野驴的序列构建NJ系统发育树,首次证明我国家驴的母系起源为非洲野驴中的索马里驴和努比亚驴,亚洲野驴不是中国家驴的祖先。本文还讨论了我国家驴可能的迁徙路线。     

中国9个家驴品种mtDNA D-loop部分序列分析与系统进化研究

本研究利用Dnasp4.10软件对中国9个家驴品种162个个体的mtDNA D-loop区385bp进行遗传多样性分析,共检测到32种单倍型35个核苷酸多态位点,其单倍型多样度为0.8137～0.9722,核苷酸多样度为0.0182～0.0270,表明我国家驴的遗传多态性丰富;利用MEGA3.1软件采用邻接法与3个努比亚野驴、3个索马里野驴和6个亚洲野驴的序列构建NJ系统发育树,并进行系统进化分析。结果表明:我国家驴的母系起源是非洲野驴中的努比亚野驴和索马里野驴,亚洲野驴不是中国家驴的母系祖先。     

庆阳驴mtDNA D-loop区遗传多样性及起源分析

【目的】研究庆阳驴养殖群体的遗传多样性与母系起源,了解其遗传信息,为保护庆阳驴种质资源、选育和遗传改良工作提供理论依据。【方法】随机选取133头庆阳驴,对其线粒体DNA(mitochondrial DNA,mtDNA)D-loop区序列进行PCR扩增、测序及比对,并探讨庆阳驴的遗传多样性与母系起源。【结果】在获得的520 bp D-loop碱基序列中,AT含量(57.3%)高于GC含量(42.8%),表现出碱基的偏倚性;检测到38个变异位点,包含8个碱基对的转换;其核苷酸多样性(Pi)、单倍型多样性(Hd)、平均核苷酸差异(K)分别为0.01591、0.895和8.274,与欧洲家驴和中国家驴研究的平均值相比较低,说明该驴品种核苷酸变异较为贫乏。庆阳驴mtDNA D-loop区存在35个单倍型,单倍型之间的遗传距离为0.002～0.042。系统进化结果显示,庆阳驴存在2个线粒体支系,表明其具有2个母系起源,且遗传距离表明,庆阳驴与克罗地亚家驴之间的遗传距离较近。【结论】本研究从分子水平初步揭示庆阳驴核苷酸变异比较贫乏,杂交程度高,mtDNA遗传多态性正逐步丧失,应加强庆阳驴品种的遗传资...     

我国北方部分山羊品种mtDNA遗传多样性

用１２种认别６碱基的限制性内切酶Ａｐａ Ｉ、Ｂａｍ ＨＩ、Ｂｇ１ Ｉ、Ｅｃｏ ＲＩ、Ｅｃｏ ＲＶ、Ｋｐｎ Ｉ、Ｐｖｕ Ⅱ、Ｐｓｔ Ｉ、Ｓａｃ Ｉ、Ｃｌａ Ｉ和Ｘｈｏ Ｉ,研究了我国北方地区９个山羊品种和类群共计１１０个体线粒体ＤＮＡ（ｍｔＮＤＡ）的限制性片段长度多态性（ＲＦＬＰ）,利用Ｎｅｉ氏公式计算了各基因单倍型间的遗传距离Ｐ、群体遗传多态性π值以及各群体间的净遗传距离,并利用ＵＰＧＭＡ方法对各     

中国四个地方驴品种mtDNA D-Loop部分序列分析与系统进化研究

对中国4个家驴品种95个个体的mtDNAD—loop部分序列进行测序。用clustalX软件进行同源序列比对。Dnasp4-10软件用于遗传多样性分析，计算单倍型多样度、核苷酸多样度、平均核苷酸差异。MEGA3．1软件采用邻接法构建系统进化树并进行系统发生分析。以欧洲驴线粒体基因组为对照（Genbank登录号为X97337），中国家驴4个品种95个个体385bp序列共检测到核苷酸多态位点33个，其中31个位点为转换，1个位点为颠换，1个位点有插入现象。95个序列由31个单倍型组成，单倍型比例为32．6％。德州驴单倍型比例最高为100％，凉州驴单倍型比例最低为42．42％。31个单倍型与引用Genbank已登录的13条序列构建系统发育树，发现31个单倍型聚为两支，说明中国家驴可能有两个母系起源。以欧洲野驴线粒体D—loop为对照（登录号为AF403063、AF403063、AF403065），揭示本研究涉及的中国家驴品种与非洲野驴的进化亲缘关系较亚洲野驴近，并且从分子水平证明中国家驴可能起源于非洲野驴中的索马里野驴分支。     

阿坝藏族羌族自治州若尔盖地区藏猪mtDNA D-Loop的遗传多样性分析

旨在通过获得和对比若尔盖地区藏猪mtDNA D-Loop高变区的部分序列,为该地区藏猪遗传资源的保护与利用提供参考。本试验收集了若尔盖地区9个乡镇共80头藏猪耳组织,以甘南州藏猪mtDNA D-Loop基因序列为模板设计引物,采用PCR扩增测序技术获得了80条核苷酸序列,并采用生物信息学的数据处理方法进行分析。结果表明,若尔盖地区藏猪mtDNA D-Loop高变区（435 bp）的A+T含量（56.46%）明显高于G+C含量（43.54%）,存在碱基偏倚性现象;在80条长度为435 bp的序列中,共检测到14个变异位点,鉴定了17个单倍型,单倍型多样度（Hd）、核苷酸多样度（Pi）和平均核苷酸差异数（k）分别为0.881、0.004 66和2.028,其中Hd、Pi和k在降扎乡藏猪群体中最高,Pi和k在占哇乡藏猪中最低;共享单倍型8个,特有单倍型9个,且若尔盖地区不同藏猪群体间特有单倍型数差异较大,其中,降扎乡藏猪的特有单倍型数量最多,占单倍型总数的17.65%（3/17）;Hap_1和Hap_15单倍型是4个乡镇（降扎乡、益哇乡、热尔乡和冻列乡）群体的共享单倍型,表明这4个乡镇藏猪群体存在两个共同的母系祖先单倍型。若尔盖地区藏猪的平均遗传距离为0.004 66,其中降扎乡和冻列乡藏猪间的遗传距离最大为0.006 90,包座乡和益哇乡藏猪间的遗传距离最小为0.002 16;构建的NJ分子系统进化树将若尔盖地区藏猪分为2支,而加入中国地方家猪、野猪和引种猪后,若尔盖地区藏猪在进化树中比较分散,说明该地区藏猪母源血统遗传复杂,彼此之间基因交流多。本研究进一步证实了若尔盖地区藏猪比西藏林芝、山南、日喀则、甘孜州、阿坝州藏猪的遗传多样性程度高,受到人工选择强度低,应强化对若尔盖地区藏猪遗传资源的保护与利用。     

中国部分地方水牛品种mtDNA D-loop区遗传多样性与起源研究

对我国10个地方水牛品种110个个体的mtDNA D-loop区序列(930 bp左右)进行分析,共检测到50种单倍型,107个核苷酸多态位点,其单倍型多样度(Haplotype diversity,Hd)为0.895 2±0.024 0,核苷酸多样度(Nucleotide diversity,π)为0.020 0±0.005 6,平均核苷酸差异(Average number of nucleotide differences,k)为18.445 0,表明我国水牛的遗传多态性丰富。构建的NJ进化树显示这10个品种的水牛主要有两个母系起源。     

甘肃地方绵羊品种mtDNA D-环序列遗传多样性与起源分析

为了研究甘肃地方绵羊品种mtDNA D-环序列遗传多样性与起源,利用设计的1对引物对绵羊mtDNA D-环序列进行PCR扩增和纯化测序.对序列数据进行单倍型、遗传多样性、系统发育树和网络关系分析.分析结果显示:120只绵羊mtDNA D-环序列(部分)表现出2种长度变异,其中3个序列长度为573 bp,117个序列长度为648 bp.对117个长度为648 bp的序列进行分析,发现77个单倍型.单倍型比例、单倍型多样度、核苷酸多样度和平均核苷酸差异数在蒙古羊都较高,而在兰州大尾羊和岷县黑裘皮羊都较低.系统发育树和网络关系分析均将77个单倍型明显的分为3个分支.研究认为:含有4个重复单元(75 bp)是甘肃地方绵羊品种mtDNA D-环的序列特征,在甘肃6个地方绵羊品种中,蒙占羊的遗传多样性最丰富,兰州大尾羊和岷县黑裘皮羊遗传多样性最低.系统发育和网络关系分析认为甘肃6个地方绵羊品种有3个母系起源.     

广东3个地方鸡种mtDNA D-loop全序列的遗传多样性分析

基于mtDNA D-loop全序列分析广东3个地方鸡种的遗传多样性.利用PCR和测序技术获得清远麻鸡、阳山鸡和惠阳胡须鸡共98个个体mtDNA D-loop全序列,结合NCBI已收录的地方鸡种、红色原鸡和绿头鸭共33条序列综合分析.结果表明:广东3个地方鸡种mtDNA D-loop区全长1231～1232 bp,其A、...     

中国西南地区5个地方绵羊群体mtDNA遗传多样性及系统进化研究

采用PCR—SSCP技术及mtDNA D-loop序列分析相结合的方法，对我国云南昭通绵羊、腾冲绵羊、宁蒗绵羊及西藏的多玛绵羊、江孜绵羊5个地方绵羊群体共232个个体进行遗传多样性及系统进化分析。PCR-SSCP分析显示，在西藏的多玛绵羊和江孜绵羊中均检测到线粒体编码区的Cytb和ND2基因的3种单倍型A、B和C，且在西藏的多玛绵羊、江孜绵羊中C单倍型比例高于B型；而在云南的昭通绵羊、腾冲绵羊和宁蒗绵羊中只检测到单倍型A和B。根据不同的单倍型从5个群体中筛选出39个样品进行mtDNAD-loop区克隆测序，经过系统进化分析揭示西藏绵羊存在A、B、C3种mtDNA单倍型；而云南绵羊只存在A、B2种mtDNA单倍型。以上基于PCR-SSCP和D-loop区序列的分析结果一致提示西藏绵羊有3个母系来源，云南绵羊有2个母系来源。基于mtDNAD-loop序列的多态性分析结果显示西藏多玛绵羊和江孜绵羊的单倍型多样度（Hd）、核苷酸多样度（Pi）及平均核苷酸差异数（k）均高于云南3个地方绵羊品种，提示西藏绵羊遗传多样性较丰富，云南绵羊遗传多样性相对贫乏。     

中国部分山羊品种线粒体DNA D-loop序列遗传多样性分析

分析了中国部分本地山羊品种(18个品种200个体)以及在中国饲养的引入品种(4个品种25个体)线粒体DNA控制区(D-loop)的全序列,结合已报道的世界其它地方的山羊(15个品种77个体)以及2只野山羊的线粒体DNA控制区(D-loop)全序列共304个体,研究结果表明:山羊线粒体DNA控制区约为1 212 bp,检测到228个变异位点,203种单倍型,单倍型多样度为0.993±0.001;核苷酸多样度0.018±0.001。中国部分山羊的变异类型主要为类型A和B,而在巴基斯坦山羊中还检测到类型C和D。比较分析结果表明中国山羊遗传多样性和基因交流比中国黄牛品种要高。     

A Genetic Diversity Analysis of Mitochondrial DNA D-loop Region in Four High Quality Chicken Breeds

This study was conducted to elucidate the genetic diversity of mitochondrial DNA (mtDNA) D-loop region in Qingyuan partridge chicken group 1,Qingyuan partridge chicken group 2,Yangshan chicken and Qingyuan Yellow feather black-bone chicken.The specific primers were designed according to mtDNA D-loop region of Gullus gullus spadiceus (accession No.:NC_007235.1) in GenBank.The sequence was analyzed after PCR amplification and sequencing,and the haplotype number,polymorphism number,haplotype diversity,nucleotide diversity and nucleotide mean difference were counted.The evolution divergence among breeds was calculated by Mega 5.10 software,and the phylogenetic tree was constructed.The results showed that the length of mtDNA D-loop region in four high quality chicken breeds was 591 bp,and 549 bp were used for subsequent analysis.The content of A,T,C and G were 27.2% to 27.3%,30.1% to 30.4%,29.5% to 29.8% and 12.8% to 12.9%,respectively,and the average content of G+C was 42.5%.There were 92 polymorphic sites which contained 14 singleton variable sites and 78 parsimony informative sites,and the percentage of transitions and transversions were 89.13% (82/92) and 10.87% (10/92),respectively.The haplotype diversity ranged from 0.682 to 0.835,and the nucleotide diversity ranged from 0.00849 to 0.01167.There were 32 haplotypes in all sequences,which could be divided into clades A,B,C and E,however,most of the individuals belonged to clades B (51.2%) and E (37.6%).The phylogenetic tree results showed that four high quality chicken breeds could be classified as 4 branches which were consistent with the haplotypes classification results.The results indicated that the four high quality chicken populations from Qingyuan had relatively high haplotype and nucleotide diversity and likely shared two or more common maternal lineages.     

陆川猪mtDNA D-loop序列遗传多样性分析

本研究测定了陆川猪17个个体mtDNA D-loop高变区序列,共检测到5个单倍型,单倍型多样度和核苷酸多样度分别为0.640和0.0074,表明陆川猪有较高的遗传多样性。结合已报道的中国地方猪种的mtDNA D-loop序列进行分析,结果发现,陆川猪和属于华中型的宁乡猪、大花白猪有很近的遗传关系,但与传统上同属华南型的香猪和滇南小耳猪的遗传关系较远,这与传统的分类方法不一致。     

The Genetic Diversity and Phylogenetic Relationships of Five Guangxi Pig Breeds and Three Exotic Pig Breeds by Analysis of mtDNA D-loop Sequences

In order to compare the genetic diversity and phylogenetic relationships between Guangxi pig breeds and three exotic pig breeds,one pair of primers was used to amplify 85 mtDNA D-loop sequences of five Guangxi pig breeds (Bama Xiang pig,Dongshan pig,Guizhong spotted pig,Luchuan pig,Huanjiang Xiang pig),and we downloaded 45 mtDNA D-loop sequences of three exotic pig breeds (Duroc,Yorkshire,Landrace) from GenBank.Then the haplotype,genetic diversity and phylogenetics analysis were carried out.The results showed that 38 haplotypes were identified in 130 sequences,and the mean distances among Guangxi pig breeds were smaller than that among Duroc,Landrace and Guangxi pig breeds.The NJ phylogenetic tree classified all samples into two clusters.One contained all of Guangxi pig breeds and partial Yorkshire,the other was composed wholly of exotic pig breeds,which mean there were two distinct maternal origins.In the cluster of Guangxi pig breeds,Luchuan pig were clustered,and the others were rather dispersive.It indicated that Luchuan pig had simple maternal bloods,and the other breeds had complex maternal bloods,and they had gene flow with each other.The maternal pig resources in Guangxi were not affected by the introduction of exotic pig breeds,and they were still suitable for use as a female parent in their development and utilization.     

基于线粒体DNA控制区(mtDNA D-loop)序列分析贵妃鸡的遗传多样性

采用PCR产物直接测序技术对30只贵妃鸡样品的线粒体DNA控制区(mtDNA D-loop)第Ⅰ高变区序列进行了分析。结果表明,在所分析的D-loop区部分序列中(520 bp),A、G、C、T平均含量分别为26.8%、13.0%、31.1%和29.1%;共发现13个核苷酸多态位点,均为转换位点,未检测到插入/缺失和颠换,核苷酸多样度(Pi)为0.0059,单倍型变异度(Hd)为0.538,中性检验Tajima’s D值为-0.67065。通过群体构建的NJ聚类图分子系统树发现,贵妃鸡起源于红原鸡。     

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.     

云南水牛mtDNA D-loop遗传多样性研究

[目的] 探究云南3个水牛品种(德宏水牛、滇东南水牛、盐津水牛)的mtDNA D-loop区的遗传多样性与母系起源。[方法]采用PCR扩增、测序及生物信息学方法。[结果] 本研究共分析了215条云南水牛mtDNA D-loop全序列,检测到107个多态位点,定义了86种单倍型。结果表明,云南3个水牛品种的mtDNA遗传多样性非常丰富,其中,滇东南水牛的遗传多样性最高(Hd: 0.946±0.017,Pi: 0.0162±0.0018),盐津水牛的遗传多样性最低(Hd: 0.805±0.063,Pi: 0.0141±0.0031)。系统发育分析结果表明,在3个云南水牛品种中检测到2个主要支系(A和B支系及其亚支系)及一个稀有支系C,其中A支系为主要支系(79.07%),且经历了强烈的群体扩张。[结论] 云南3个水牛品种具有丰富的mtDNA遗传多样性,主要有A与B两个母系起源。     

Study on Genetic Diversity and System Evolution of mtDNA D-Loop Region in Xianglushan Chicken

This study was aimed to analyze the genetic diversity and phylogenetic evolution in Xianglushan chicken.The full-length sequences of mitochondrial DNA D-Loop (mtDNA D-Loop) region of 121 Xianglushan chickens were analyzed by PCR amplification combined with bidirectional sequencing,and the composition,variation and maternal origin of mtDNA D-Loop region were discussed.The results showed that the total length of mtDNA D-Loop region in Xianglushan chicken was 1 231-1 233 bp.The contents of A,T,C and G were 26.62%,33.55%,26.49% and 13.34%,respectively.The content of T was the highest,the content of G was the lowest,and the content of A+T was significantly higher than that of G+C,it indicated that region might have certain base hobbies.Analysis of 121 full-length sequences were found to coexist in 11 haplotypes and 26 mutation sites,of which 2 were single polymorphic information sites,24 were simple information sites,4 bases were inserted and 2 bases were missing.The genetic diversity analysis results showed that the haplotype diversity was 0.814,the nucleotide diversity was 0.00447,the average nucleic acid difference was 5.494,which indicated that the genetic diversity of Xianglushan chicken was relatively rich,the effect of preservation was better,which had a certain breeding space.Tajima's D was 0.39378 and the test results were not significant (P>0.10),in line with neutral mutations.The cluster analysis results showed that Xianglushan chicken and Gallus gallus gathered as one,indicating that Xianglushan chicken originated from Gallus gallus, and there were 4 branches inside the branch,indicating that Xianglushan chicken had many matrilineal origins.The results could provide some reference data for the protection and exploitation of pheasant germplasm resources in Xianglushan chicken.