Genetic Diversity and Phylogenetic Relationship of Introduced Alpaca in Xinjiang

In order to understand the genetic diversity and phylogenetic relationship of the alpacas,39 blood samples of alpaca were collected in 3 places of Xinjiang (Qinghe county of Aletai city,Tacheng city and Tianshan wildlife park) and mitochondrial D-loop gene was amplified and sequenced. The results showed that 733 bp fragment was obtained. The population haplotype diversity (Hd),nucleotide diversity (Pi) and gene flow (Nm) was 0.954,0.0091 and 1.97,respectively. 25 haplotypes were defined among the 39 gene sequences,and H7 was the most shared haplotype by groups. The genetic distance of three alpaca groups was small (0.002 to 0.003). The genetic distance between alpaca and Lama glama,Lama guanicoe and Vicugna was 0.002,0.004 and 0.017,respectively. The genetic distance between alpaca and Camelus bactrianus was the highest (0.050 to 0.051).The results of cluster analysis showed that three alpaca groups were gathered first,and then gathered with Lama glama,Lama guanicoe and Vicugna, Camelus bactrianus belonged to another branch along. In conlusion,the genetic diversity and gene flow level of alpacas in Xinjiang was high and the genetic differentiation was relatively small. The genetic relationships between alpaca and Lama glama,Lama guanicoe and Vicugna were close, that with Camelus bactrianus was relatively far.     

囊谦青牦牛母系遗传多样性及遗传背景探析

为从分子水平上揭示青海省囊谦青牦牛的母系遗传多样性、群体结构及遗传背景,对31头囊谦青牦牛mtDNA D-loop区序列进行PCR扩增、测序和序列比对分析,确定序列变异位点和单倍型数目,计算单倍型多样度和核苷酸多样度大小,并进行系统发育分析。结果表明,在囊谦青牦牛618 bp D-loop区序列分析中,共检测到34个多态位点,包括8个单一多态位点和26个简约信息位点。根据序列间核苷酸变异共确定了12种单倍型,单倍型多样度和核苷酸多样度分别为0.846±0.055和0.011±0.005。与野牦牛及我国其他18个家牦牛品种相比,囊谦青牦牛群体核苷酸多样度和单倍型多样度值均较低,表明囊谦青牦牛母系遗传多样性水平较低。以美洲野牛为外群构建的系统发育树结果显示,囊谦青牦牛群体的12种单倍型分布在3种单倍型组A、C、D中,且聚为2个大的分支,提示囊谦青牦牛由2个母系支系组成,拥有2个母系起源。综上,囊谦青牦牛群体母系遗传多样性较低,由2个母系支系组成,推测其有2个母系起源。     

新疆马鹿群体遗传多样性及起源进化研究

为了科学评价、保护和利用新疆马鹿遗传资源,检测新疆马鹿群体遗传多样性和确定新疆马鹿起源进化的系统地位。对新疆塔里木马鹿、阿尔泰马鹿、天山马鹿3个群体,及与其距离相近的阿拉善马鹿、甘肃马鹿2个群体共108个个体的D-loop全序列扩增、测序,分析其碱基组成及变异。结果:共检测到40个单倍型,单倍型多样度(Hd)0.998±0.006,核苷酸多样度(Pi)0.041±0.005,平均核苷酸差异数K=36.08。构建NJ和MP分子系统发育树发现,塔里木马鹿与其他马鹿遗传距离较远,分属于不同的类群;阿尔泰马鹿、天山马鹿及甘肃马鹿之间都存在基因交流情况,可能是群体间引种杂交所致。结论:新疆马鹿遗传多样性丰富,新疆塔里木马鹿可能起源于欧洲,其他马鹿起源于亚洲。部分群体间存在基因交流情况。     

甘肃地方绵羊品种微卫星遗传多样性与系统发育分析

通过对甘肃省6个地方绵羊品种(240只个体)15个微卫星座位的等位基因的研究,结果共发现了179个等位基因。其中在藏羊中发现的等位基因数最多(136个),兰州大尾羊最少(94个)。多态信息含量、期望杂合度和观察杂合度的数据表明:在研究的6个绵羊品种中藏羊和甘肃高山细毛羊的遗传多样性较丰富,而兰州大尾羊和岷县黑裘皮羊的遗传多样性较低。DA遗传距离和D s遗传距离构建的NJ系统发育树均表明:兰州大尾羊、蒙古羊和滩羊具有较近的亲缘关系,预示这3个品种可能具有相同的原始祖先。而甘肃高山细毛羊与其他5个甘肃地方品种的遗传距离较远,另为一类。     

四川白三叶根瘤菌遗传多样性及系统发育研究

为阐明四川部分地区野生白三叶根瘤菌的遗传多样性及系统发育地位,对分离自四川雅安、康定、泸定、西昌、成都和乐山6个地区白三叶根瘤的69株菌进行系统研究。采用16S rDNA限制性片段长度多态性分析(restriction fragment length polymorphism, RFLP)和16S rDNA基因、持家基因(recA、atpD、glnII)、结瘤基因(nodC)、固氮基因(nifH)系统发育分析的方法进行了研究。结果表明,16S rDNA PCR-RFLP中所有供试菌株产生了4种酶切图谱类型,表现出较为丰富的遗传多样性。持家基因与16S rDNA基因系统发育分析结果基本一致,9株代表菌株主要分布在α-变形菌纲(Alpha-Proteobacteria)的根瘤菌属(Rhizobium),并与豌豆根瘤菌三叶草生物型(R. leguminosarum bv. trifolii) ATCC 14480^T的亲缘关系较近。PCR可扩增出nodC和nifH基因片段,但从属于土壤杆菌属(Agrobacterium)的菌株LS1105中则扩增不出这两个基因。所有供试菌株被鉴定到了种的水平,证实了68株为白三叶根瘤菌,并通过不同采样地点菌株之间的比较,发现白三叶与根瘤菌的共生关系因地理分布不同而具有多样性,对于丰富白三叶根瘤菌资源及其开发利用具有重要意义。     

陇东地方牛种遗传多样性研究

对陇东地方牛种及其与秦川牛和南德温牛杂交群体共计113个个体线粒体D-loop区461 bp序列进行多态性分析,结果表明,3个群体该区域A+T含量(64.2%)明显高于G+C含量(35.8%),表现出明显的碱基偏倚;3个群体核苷酸变异率介于0.42%和3.27%之间,陇东牛和南德温牛杂交群体核苷酸变异率最高;核苷酸变异类型以转换为主,转换占核苷酸多态位点的90.94%,其次为颠换,占4.59%,同样表现出明显的碱基替换偏倚;3个群体核苷酸岐异度介于0.008 95和0.029 06之间,遗传距离介于0.000 15和0.008 36之间,陇东地方牛及其与秦川牛的杂交群体核苷酸歧异度和遗传距离最小。     

唐古拉山牦牛群体的母系遗传多样性及遗传结构分析

[目的]从分子水平上探究青海省唐古拉山牦牛群体的母系遗传多样性、群体遗传结构及其遗传背景。[方法] 对52头唐古拉山牦牛个体mtDNA D-loop区序列进行测定后,使用生物信息学软件分析确定其核苷酸变异位点和单倍型数目,计算单倍型多样度和核苷酸多样度大小,并进行系统发育分析。[结果] 在619 bp唐古拉山牦牛D-loop区序列分析中,排除2处插入（缺失）后共检测到31处多态位点,包括单一多态位点5处和简约信息位点26处。根据序列间核苷酸变异共确定了13种单倍型,单倍型多样度和核苷酸多样度分别为0.821±0.043和0.007±0.004。与我国其他18个家牦牛品种和野牦牛相比,唐古拉山牦牛群体单倍型多样度和核苷酸多样度值均较低,表明该群体遗传变异较为贫乏,母系遗传多样性水平较低。以美洲野牛为外群,邻接法（即NJ法）构建的系统发育树结果显示：唐古拉山牦牛群体13种单倍型分布在A、B、C、D和E五种单倍型组中,且聚为2个大的母系分支（即I和II）,支系Ⅰ占比为77%,提示唐古拉山牦牛由2个母系支系组成,拥有2个母系起源且以支系Ⅰ为主。 [结论] 唐古拉山牦牛母系遗传多样性水平较低,由2个母系支系组成,以支系Ⅰ为主,推测其有2个母系起源。     

张掖肉牛线粒体DNA D-loop区遗传多样性研究

为研究张掖肉牛的遗传多样性及母系起源,利用特异性引物扩增mtDNA D-loop区全序列,采用最大似然法构建了张掖肉牛mtDNA D-loop区分子系统树,对核苷酸多态性和遗传距离进行了分析。结果表明,构建的166头张掖肉牛mtDNA D-loop区全序列分子系统树分为3组（普通牛、瘤牛、牦牛）,其中,普通牛血统基因型组占比80.7%,有93种单倍型（Hd=0.988),核苷酸变异度π=0.005 79;瘤牛血统基因型组占比13.2%,有6种单倍型（Hd=0.476）,核苷酸变异度π=0.001 19;牦牛血统基因型组占比6.1%,有5种单倍型（Hd=0.867）,核苷酸变异度π=0.009 65。张掖肉牛与中国北方牛的遗传距离比较近（Fst=0.01）。综上所述,张掖肉牛具有混合母系起源的特点,但受普通牛的影响较大,亲缘关系明显表现出了中国北方黄牛的地理生态分布特征,该研究结果可为张掖肉牛生态区的分布提供理论依据,也可为遗传育种提供参考。     

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。     

崇仁麻鸡mtDNA D-loop区遗传结构与遗传多样性分析

为研究崇仁麻鸡线粒体DNA(mitochondrial DNA,mtDNA)D-loop区遗传多样性和遗传结构,试验采用PCR产物直接测序的方法,测定崇仁麻mtDNA D-loop区的全序列,并与其他5个红色原鸡亚种进行系统进化关系分析。结果显示：30个样本的mtDNA D-loop区序列长度范围为1 231～1 232 bp,共发现27个多态位点,单倍型多样性（Hd）、核苷酸多样性（Pi）和平均核苷酸差异（K）数值分别为0.947、0.006 89和8.476。群体中16种单倍型划分为A、B、C和E单倍型类群。研究表明,崇仁麻鸡具有较高的线粒体遗传多样性,可能来源于不同的母系。     

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。     

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。     

基于线粒体DNA D-loop区全序列分析儋州鸡遗传多样性及其起源进化关系

为了研究儋州鸡的遗传多样性及其起源进化关系,本研究对36只儋州鸡样品的线粒体DNA(mtDNA) D-loop区全序列进行PCR扩增和测序,结合GenBank中公布的部分品种鸡的mtDNA D-loop区全序列,利用生物信息学方法进行数据处理,分析儋州鸡的遗传多样性及其起源进化关系。结果显示,儋州鸡mtDNA D-loop区扩增片段长度为1 210 bp,A+T含量为59.9%,C+G含量为40.1%,变异区在167～1 215 bp之间,高变区主要集中在167～367 bp之间,存在6种单倍型,共有20个变异位点,单倍型变异度(Hd)为0.571,平均核苷酸差异(k)为6.449,核苷酸多样度(Pi)为0.00537,中性检验的Tajima’s D值为1.61643,6种单倍型可分为A、B、C 3个世系,以B世系为主。研究结果表明,儋州鸡群体遗传多样性和单倍型多样性相对偏低,结合群体构建的系统进化树发现,儋州鸡的遗传组成来自3个母系祖先,缅甸红原鸡、爪哇红原鸡及红原鸡海南亚种均是其潜在的祖先,受外来鸡种影响较小,是一个较为封闭的原始鸡种。     

青海省格尔木牦牛的母系遗传多样性及支系组成

[目的]从分子水平上探究青海省格尔木牦牛的母系遗传多样性、群体遗传结构及其遗传背景。[方法]对49头格尔木牦牛mtDNA D-loop区部分序列进行了测定,后使用DnaSP 5.10.01、Arlequin 3.11和MEGA 5.05等生物信息学软件确定其多态位点和单倍型数目,计算核苷酸多样度和单倍型多样度大小,并进行系统发育分析。[结果]在截取的618 bp格尔木牦牛D-loop区分析序列中,排除1处插入(缺失)后共检测到45处多态位点,包括10处单一多态位点和35处简约信息位点;根据序列间核苷酸变异共确定了18种单倍型,其中单倍型H4为优势单倍型,核苷酸多样度为0.015±0.008,单倍型多样度为0.911±0.022。与野牦牛及大通、天祝、金川等其他家牦牛品种相比,格尔木牦牛群体单倍型多样度和核苷酸多样度值均较高,表明该群体具有丰富的母系遗传多样性。以美洲野牛为外群,邻接法(即NJ法)构建的系统发育树结果显示：格尔木牦牛群体18种单倍型分布在A、B、C、D和G 5种单倍型组中,且聚为3个大的分支,提示格尔木牦牛由3个母系支系组成,拥有3个母系起源。[结论]格尔木牦牛群体具有丰...     

Genetic Diversity and Evolution of Danzhou Chicken Assessed with Mitochondrial Complete DNA D-loop Region Sequencing

The objective of this study was to determine the genetic diversity and evolution of Danzhou chicken.The complete mitochondrial DNA (mtDNA) D-loop regions of 36 Danzhou chickens were amplified,sequenced and analyzed.The sequencing reads were compared with the complete mtDNA D-loop sequence of several relative strains of chicken annotated in GenBank,and analyzed by bioinformatics methods.The genetic diversity and its evolutionary relationship in Danzhou chicken were analyzed.The results showed that the lengths of PCR products at the D-loop region were 1 210 bp,with 59.9% being A+T and 40.1% as C+G.The variable regions were 167-1 215 bp,and the high variable regions were mainly 167-367 bp.A total of 20 variable sites that defined 6 haplotypes were identified.The average haplotype diversity (Hd) and average number of nucleotide difference (k) were 0.571 and 6.449,respectively,the nucleotide diversity (Pi) was 0.00537,and the Tajima's D value of neutrality test was 1.61643.6 haplotypes could be grouped to 3 haplogroups (A,B and C) as determined by phylogenic analysis,with B clade,as the most abundant population.It concluded that the genetic diversity and haplotype diversity of Danzhou chicken were relatively low.Phylogenetic tree showed that the genetic composition of Danzhou chicken came from 3 maternal ancestors,Gallus gallus spadiceus,Gallus gallus bankiva and Gallus gallus jabouillei were potential ancestors.There was few influence of exotic lineage detected,which indicated that Danzhou chicken was a relatively conserved breed.     

青海省同德牦牛的母系遗传多样性及群体遗传结构分析

[目的]从分子水平上揭示青海省同德牦牛的母系遗传多样性、群体遗传结构和遗传背景.[方法]本研究采用PCR方法和扩增产物双向测序技术,对60头(32♂,28♀)同德牦牛mtDNA D-loop区序列进行了测定.经人工核实校对序列后,使用BioEdit、DnaSP、Ar-lequin和Network等生物信息学软件综合分析...     

Genetic Diversity Analysis of Shaanxi Moschus berezovskii Based on mtDNA Cytb Gene and D-loop Region Sequence

【Objective】 This study was aimed to explore the genetic diversity of Shaanxi Moschus berezovskii population,and understand the genetic information of Moschus berezovskii.【Method】 The hair of Moschus berezovskii was collected to extract DNA,the mitochondrial DNA(mtDNA) cytochrome b(Cytb) gene and D-loop sequences of 43 Moschus berezovskii individuals were determined,and the base composition was counted.All sequences were integrated and compared using ClustalX 2.0 software to obtain nucleotide polymorphic sites (SNPs) in the population.The nucleotide diversity (Pi),number of haplotype (H),haplotype diversity (Hd) and average number of nucleotide differences (K) were calculated by DNASP 5.10 software.The genetic distance among different haplotypes of Cytb gene and D-loop sequences was calculated by Mega 7.0 software,and Neighbor-Joining (NJ) phylogenetic tree was constructed.【Result】 The AT content of Cytb gene and D-loop region were higher than GC content,indicating there was bias in base composition.There were 241 and 383 SNPs of Cytb gene and D-loop region,respectively.The nucleotide diversity of Cytb gene and D-loop region were 0.28343 and 0.07707,and the haplotype diversity was 0.983 and 0.975,respectively,indicating that the population genetic diversity was rich.The genetic distances of 35 haplotypes of Cytb gene ranged from 0.002 to 0.831,and 29 haplotypes of D-loop region ranged from 0.006 to 1.342.The phylogenetic tree showed that there were two mitochondrial lineages,indicating that there were two mitochondrial maternal origins.The evolutionary analysis of D-loop region also supported this conclusion.【Conclusion】 The nucleotide diversity and haplotype diversity of Moschus berezovskii population were high,and the genetic diversity was rich.At the same time further supported the view of Moschus berezovskii and Moshus moschiferus belonged to a branch of the view.     

云南肉山羊黑色品系内不同家系遗传多样性分析

应用QIAxcel全自动遗传分析仪进行毛细管电泳,对云南肉山羊黑色品系5只公羊134只后代的基因组DNA进行了11个微卫星位点多态性分析,以期为这一品系的选育提高和合理选配提供科学依据。结果表明,在11个微卫星位点共检测到101个等位基因,片段大小在115～249 bp之间,全群平均期望杂合度和平均多态信息含量均在0.5以上,表明云南肉山羊黑色品系遗传多样性丰富。对5只公羊UPGMA聚类分析表明:5只公羊间遗传一致度较高,说明云南肉山羊黑色品系具备了相对统一的遗传基础;系统聚类图直观地显示出公羊N7379和N7373存在较近的亲缘关系,被聚为一支,而公羊N5043、N7303、N5049间也存在较近的亲缘关系,被聚为另一支,分属于不同分支的公羊间亲缘关系相对较远。     

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.