基于线粒体DNA序列探讨中国紫貂的起源

为了研究中国紫貂的起源,试验利用PCR方法和直接测序技术对中国境内分布的18只野生紫貂线粒体DNA控制区全序列进行了测定和群体分析.结果表明:所获得的7个单倍型序列长度介于1 073～1 134 bp之间,在保守序列区CSB1与CSB2之间存在AC串连重复序列,长度介于198 ～258 bp,这是导致紫貂线粒体控制区序...     

基于线粒体16S rRNA全序列分析我国绵羊痒螨兔亚种的遗传多样性

为了探讨我国绵羊痒螨兔亚种的遗传变异特征和种群结构,利用PCR技术对我国5个地理区域(华北、华东、华中、西南、西北)的83个绵羊痒螨兔亚种株的线粒体16SrRNA全序列进行扩增和遗传多样性分析。结果显示,83个样品的16SrRNA全序列长度均为1 025bp,共存在83个变异位点和52个单倍型;样品所代表的5个地理区域种群间的Fst值为-0.037 59~0.587 63,基因流值为-6.900 7~31.117 62;进一步用NJ树和单倍型网络图分析显示,52个单倍型构成2个大的分支,但却呈现出杂乱的分布格局,即地理区域、温度带和兔的品种特征性种群结构不显著。我国绵羊痒螨兔亚种的遗传多样性较高,遗传分化不明显,尚未形成地理种群结构。     

基于线粒体12S基因全序列分析我国绵羊痒螨(兔亚种)的遗传多样性

为了探讨我国绵羊痒螨(兔亚种)的遗传变异情况及群体遗传结构,采用PCR测序技术测定我国5个地区(华北、华东、华中、西北、西南)绵羊痒螨(兔亚种)线粒体12S基因的全序列,并进行遗传多样性分析。结果共获得89条序列,长度均为657bp,核苷酸变异位点76个,单倍型50个(H1～H50),单倍型多样性(Hd)与核苷酸多样性(π)分别为0.931 05和0.005 59。进一步分析发现5个地理种群遗传分化程度较弱(Fst=0.042 322),基因交流非常频繁(Nm=5.657 372)。中性检验结果均为负值(Tajima’s D=-0.928 31,Fu’s Fs=-7.066 71),并且差异性不显著(P0.05)。构建的NJ树和单倍型网络图均显示绵羊痒螨(兔亚种)5个地理种群的50个单倍型散在分布于不同的支系内,未形成明显的地理分布格局。我国绵羊痒螨(兔亚种)具有较高的遗传多样性,且有一定的遗传分化,基因交流频繁,但未形成以兔品种、温度带和地域来源划分的种群遗传结构。     

基于线粒体12S基因分析四川地区鸡异刺线虫的种群遗传多态性

为探讨四川地区鸡异刺线虫的遗传变异特点和种群遗传结构特征,利用PCR技术扩增了四川7个地区共58株鸡源鸡异刺线虫分离株的线粒体12S基因全序列,经测序后分析其遗传多样性。结果显示,58条鸡异刺线虫12S基因全序列均为699bp,序列中共有38个变异位点和34个单倍型(HS1-HS34);单倍型多样性(Hd)和核苷酸多样性(π)分别为0.822和0.003 95。进一步分析表明,7个地理种群遗传分化不明显(Fst=0.007 87),种群间基因交流较频繁(Nm=31.52);分子方差分析(AMOVA)表明,四川地区鸡异刺线虫的遗传分化主要来自于种群内部(99.21%),种群间遗传变异水平较低(0.79%);单倍型网络图和NJ系统发育树显示,鸡异刺线虫7个地理种群的34个单倍型散在分布于不同种群内,分布格局较为混杂,未形成明显的地理分布格局。结果表明,四川地区的鸡异刺线虫遗传多样性较低,遗传分化不明显,还未形成显著的地理遗传结构。     

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。     

胎生蜥蜴线粒体Cyt b基因和D-loop区序列多态性分析

为了探讨我国胎生蜥蜴(Zootoca vivipara)种群的遗传多样性,试验采用分子生物学的方法测定我国3个胎生蜥蜴种群(黑龙江呼玛、内蒙古额尔古纳和新疆布尔津)共36只个体的线粒体Cyt b基因全序列和D-loop区部分序列。结果表明:胎生蜥蜴Cyt b基因全序列长度为1 143 bp,A、T、G、C4种核苷酸碱基含量的平均值分别为29.46%、34.15%、11.66%和24.73%,共包括8个单倍型;Dloop区部分序列长度为712 bp,A、T、G、C 4种核苷酸碱基含量的平均值分别为27.48%、39.23%、11.22%和22.04%,共包括4个单倍型。其中内蒙古额尔古纳种群的单倍型数量多,遗传多样性高;而新疆布尔津种群的单倍型数少,遗传多样性低。     

基于SRY基因分析梅花鹿的遗传多样性及父系类型

试验旨在研究梅花鹿SRY基因的遗传多样性及其父系类型。选取东北亚种、北海道亚种、本州亚种、指名亚种、屋久岛亚种5个亚种的144个个体,利用试剂盒和传统酚/仿(1∶1)法进行DNA的提取,采用PCR扩增和直接测序法分析梅花鹿的核苷酸多样性(Pi)、单倍型多样性(Hd)、遗传距离及系统进化关系。结果显示,试验所获序列长度为1 613bp,在第47、62、602、1 148、1 569、1 604bp处共检测到6个SNPs多态位点,占核苷酸总数的0.3%,碱基替换以碱基转换为主。通过6个SNPs多态位点确立了6种单倍型:Hap-1、Hap-2、Hap-3、Hap-4、Hap-5和Hap-6,其中Hap-4、Hap-5和Hap-6为新发现单倍型。遗传多样性由高至低依次为:指名亚种、屋久岛亚种、东北亚种、本州亚种、北海道亚种。各亚种间遗传距离最小为北海道亚种与本州亚种的距离(0.000056),最大为东北亚种与指名亚种的距离(0.001733)。基于单倍型利用邻接法构建系统进化树,结果显示,与日本梅花鹿相比,东北亚种与马鹿关系更近,东北亚种存在两大分支,日本梅花鹿各亚种间无明显分支,其他单倍型均是由Hap-3进化而来,单倍型最小跨度网络图与系统进化树一致。结果表明,东北梅花鹿存在两大父系类型,日本梅花鹿存在一个父系类型,单倍型Hap-3是日本梅花鹿的原始单倍型。     

基于SRY基因分析梅花鹿的遗传多样性及父系类型

试验旨在研究梅花鹿SRY基因的遗传多样性及其父系类型。选取东北亚种、北海道亚种、本州亚种、指名亚种、屋久岛亚种5个亚种的144个个体,利用试剂盒和传统酚/仿(1∶1)法进行DNA的提取,采用PCR扩增和直接测序法分析梅花鹿的核苷酸多样性(Pi)、单倍型多样性(Hd)、遗传距离及系统进化关系。结果显示,试验所获序列长度为1 613bp,在第47、62、602、1 148、1 569、1 604bp处共检测到6个SNPs多态位点,占核苷酸总数的0.3%,碱基替换以碱基转换为主。通过6个SNPs多态位点确立了6种单倍型:Hap-1、Hap-2、Hap-3、Hap-4、Hap-5和Hap-6,其中Hap-4、Hap-5和Hap-6为新发现单倍型。遗传多样性由高至低依次为:指名亚种、屋久岛亚种、东北亚种、本州亚种、北海道亚种。各亚种间遗传距离最小为北海道亚种与本州亚种的距离(0.000056),最大为东北亚种与指名亚种的距离(0.001733)。基于单倍型利用邻接法构建系统进化树,结果显示,与日本梅花鹿相比,东北亚种与马鹿关系更近,东北亚种存在两大分支,日本梅花鹿各亚种间无明显分支,其他单倍型均是由Hap-3进化而来,单倍型最小跨度网络图与系统进化树一致。结果表明,东北梅花鹿存在两大父系类型,日本梅花鹿存在一个父系类型,单倍型Hap-3是日本梅花鹿的原始单倍型。     

从mtDNA的控制区序列变异分析松鼠(S.vulgaris)和日本松鼠(S.lis)的分子系统关系

为了进一步明确松鼠和日本松鼠系统分化关系,研究利用线粒体控制区的251 bp或252 bp序列,对松鼠10个亚种和日本松鼠共43个样本进行研究。结果表明:具有38个单倍型,分化指数和遗传距离的结果均表现出日本松鼠和松鼠10个亚种存在明显分化,分化指数范围为0.663 9~0.827 7,遗传距离范围为0.083 8~0.107 2;分布于意大利南部卡拉布里亚的亚种(S.v.meridionalis)与其他松鼠亚种存在较明显的分化,分化指数范围为0.533 5~0.753 2,遗传距离范围为0.063 3~0.079 6,其他9个松鼠亚种并无显著分化。聚类分析和单倍型网络图分析结果基本相同,产生两个明显分化,一个是日本松鼠,另一个是意大利南部卡拉布里亚的亚种;日本松鼠与松鼠存在一定分化,大于意大利南部卡拉布里亚的亚种分化,无法定性说明日本松鼠与松鼠是种间分类关系还是亚种间分类关系。     

云南省不同蚕区桑园中桑粉虱种群的遗传分化初步研究

桑粉虱(Pealius mori)是云南蚕区主要的桑树害虫之一。对滇南至滇西沿线3个蚕桑区7个采样点的桑粉虱种群进行线粒体细胞色素C氧化酶亚基Ⅰ基因(mt DNA COⅠ)序列分析,应用Dna SP5.0、Arlequin3.1.1.1、Network4.6软件进行桑粉虱样本的单倍型、遗传多样性、遗传分化分析。在35个样本的mt DNA COⅠ序列中,检测到23种单倍型,其中20种单倍型分别为7个种群独有;总群体的mt DNA COⅠ序列单倍型多样度(Hd)为0.966,各种群单倍型Hd介于0.700~1.000间;总群体遗传分化指数(FST)为0.747 98,基因流(Nm)为0.17。AMOVA分子变异分析表明桑粉虱的遗传变异主要来自种群间,种群内变异小于种群间变异;总群体及各种群间Tajima's D中性检验差异不显著,表明桑粉虱群体在近历史时期无群体扩张。构建的单倍型UPGMA聚类树与单倍型网络图显示,桑粉虱单倍型呈明显种群分布格局。依据研究结果初步认为:滇南至滇西沿线7个采样点的桑粉虱种群因遗传漂变产生了较大遗传分化;桑粉虱mt DNA COⅠ序列单倍型呈现明显的地理区域种群分布格局。     

Identification of mitochondrial DNA substitutions related to meat quality in Japanese Black cattle

Complete sequences of mitochondrial (mt) genomes of eight Japanese Black cattle were determined to investigate the relationships between mt deoxyribonucleic acid (DNA) displacement loop (D-loop) types and other mtDNA regions and to identify the variation in the coding region that may influence the economic traits. The survey of mitochondrial sequences in the encoding region revealed 14 substitutions including six antonymous substitutions and one in 16S ribosomal ribonucleic acid (rRNA). Three methods of polymorphic DNA analyses (polymerase chain reaction [PCR]-restriction fragment length polymorphism [RFLP], mismatch PCR-RFLP, PCR-single-strand conformation polymorphism [SSCP]) were performed on these seven candidate substitutions (base pair [bp] 2,232, 12,158, 12,908, 13,310, 14,122, 14,140, and 14,565) for 202 Japanese Black cattle. The substitution of bp 13,310 was observed in all samples, but not in the reference sequence, indicating that this is a minor substitution or a sequencing mistake in the reference sequence. The substitutions at bp 14,122, 14,140, and 14,565 were observed in only a few samples, suggesting that these were also minor substitutions. The substitutions at bp 2,232 (16S rRNA), 12,158, and 12,908 (reduced nicotinamide adenine dinucleotide-ubiquinone oxidoreductase chain-5) were closely related to mitochondrial D-loop types that have previously been related to differences in the carcass traits of Japanese Black cattle. Evaluation of the effects on six carcass traits with mixed model procedures suggests that the bp 2,232 substitution affects longissimus muscle area and beef marbling score. The substitution at bp 2,232 is a strong candidate for the mitochondrial effect on meat quality.     

The complete mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken

ABSTRACT

1. The objectives of the current study were to investigate the mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken, and provide molecule base to preserve and explore the specific chicken strain.

2. Based on sequencing and clustering, the complete mitochondrial DNA map and sequences of Lueyang black-bone chicken were revealed, and two phylogenetic trees of Lueyang black-bone chickens based on D-loop sequences and the mitochondrial genome were constructed.

3. The results showed that the complete mitochondrial genome of Lueyang black-bone chickens is 16,784bp in size, consisting of 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and one non-coding control region. The base composition of the complete mtDNA sequence is 30.28% for A, 23.78% for T, 32.42% for C, 13.52% for G. Additionally, 10 haplotypes of D-loop sequences in 32 Lueyang black-bone chickens were detected, which were distributed into 4 clades (A, B, C and E).

4. It was concluded that genetic diversity is wide in Lueyang black-bone chickens, and this strain has multiple maternal origins from different regions in China and neighbouring regions.     

4个引进山羊品种mtDNA控制区序列变异和系统发生关系研究

本研究测定了四川4个引进山羊品种24个个体的线粒体控制区全序列,并从GenBank获得山羊属2个野山羊种的2每控制区序列。利用MEGA2．0软件构建分子系统发育无根树。序列分析表明:山羊控制区线粒体控制全序列长度为1 212bp或1 213 bp,A+T含量占59．9％,其中64个核苷酸位点存在变异(约占5．28％),核苷酸多样度为 1．731％,这些差异共定义了16种单倍型,单倍型多样性为0．913±0．048。安哥拉山羊、波尔山羊都有自己独特的单倍型,与其他品种间都没有共享类型。使用NJ法构建了系统发育树,结果表明:2个野山羊种中,角(?)羊与家养山羊的关系相对较近,4个家养山羊品种有2个母系来源,在4个家养山羊品种内部,安哥拉山羊的分化要比其他3个品种早。     

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.     

原鸡线粒体DNA部分序列多态性分析

测定了分布于中国的红原鸡两个亚种(Gallus gallus spadiceus亚种、Gallus gallus jabouillei亚种)5个个体的线粒体细胞色素B(cytb)部分序列(289bp)和控制区(D环)的部分序列(539bp)，并结合GENBANK中已有的原鸡的相应片段进行分析，结果显示分布在中国的两个红原鸡亚种与在泰国等地分布的红原鸡亚种可归为一类，而与爪哇岛上分布的红原鸡亚种差异较大。我们的结果支持红原鸡可以分为陆地型和海岛型亚种，家鸡可能来源于陆地型红原鸡，并经受了多次独立驯化。     

贵州下司犬线粒体DNA控制区核苷酸序列分析

采用聚合酶链式反应和直接测序的方法,分析了贵州下司犬线粒体D-loop区序列。结果显示,该犬的线粒体D-loop全长1260bp,碱基序列中A、T含量明显高于G、C含量。其中有一段以串连方式排列、重复29次的序列,重复单元为TACACGT(A/G)CG。对该串连重复序列上游673bp的碱基序列进行分析,比较已知犬种相应碱基序列之间的差异,聚类分析结果显示下司犬与亚洲犬种的亲缘关系较近。     

家鸭、媒鸭和野鸭mtDNA D-loop区的遗传变异

旨在从mtDNA水平探讨我国家鸭的遗传多样性及家鸭与野鸭间的亲缘关系.运用DNA测序方法,测定了不同地域、水域和表型性状的9种家鸭(北京鸭、高邮鸭、巢湖鸭、绍兴鸭、连城白鸭、吉安红毛鸭、文登黑鸭、云南麻鸭、建昌鸭)80个个体、4种媒鸭(西湖野鸭、钱江野鸭、枞阳媒鸭、媒头鸭)26个个体和斑嘴鸭8个个体,共计114个个体的mtDNA D-loop区667 bp序列.9种家鸭单倍型多样度和核苷酸多样度分别为0.250 00～0.607 14和0.000 38～0.001 18;9种家鸭、媒鸭、绿头鸭和斑嘴鸭之间的遗传距离为0.001～0.015;39种单倍型系统发生树和单倍型网络关系图表明,9种家鸭主要属于A1亚簇(绿头鸭单倍型簇).我国家鸭遗传多样性中等丰富,母系起源主要是绿头鸭,极少量个体含有斑嘴鸭血统.     

鸳鸯mtDNA D-loop序列分析

采用PCR和直接测序方法测定鸳鸯线粒体DNA(mtDNA)控制区全序列,与GenBank上已知序列相比较分析mtDNA D-loop 3个区的序列变异。结果发现,鸳鸯mtDNA控制区序列长1035 bp;与欧洲鸳鸯相比,鸳鸯(样品采集来自贵州省石阡县)mtDNA控制区共存在25处转换、12处颠换、2处插入和12处缺失;两种鸳鸯之间mtDNA控制区Ⅰ、Ⅱ和Ⅲ区的序列变异率分别为14.5%、0.64%和0.8%,Ⅰ区的变异速率最快;mtDNA控制区的A、C、T、G碱基含量分别是26.6%、16.0%、26.6%和30.8%,A+T含量稍高于C+G含量,G含量最高,符合序列组成的碱基偏倚性。与其他鸭科物种进行了mtDNA控制区序列一致性的比较,结果均高于80%。     

西北部分地区猪蛔虫rDNAITS基因序列测定及遗传变异分析

为了摸清西北部分地区猪蛔虫内转录间隔区(ITS)的遗传变异特点,扩增了猪蛔虫ITS基因,进行测序,依据GenBank公布的ITS序列将测序结果截为ITS1、5.8S及ITS2三段,分析比对各段序列的差异性。结果显示,所有样品ITS序列长约1 000bp,其中ITS1、5.8S和ITS2的长度分别为450bp~453bp、159bp、272bp,种内差异分别为0~0.2%、0、0。基于ITS1的种系发育分析表明,23个猪蛔虫样品均位于同一分支,而与贝蛔属蛔虫分属两个不同分支。ITS1序列不能作为区分西北不同地区猪蛔虫的种内分子标记,但可以作为区分蛔属蛔虫与贝蛔属蛔虫的种间分子标记,研究结果为猪蛔虫的鉴定和分子流行病学调查提供了基础资料。     

Mitochondrial DNA variation in the Japanese marten Martes melampus and Japanese sable, Martes zibellina

Genetic relationship among Japanese sables, Martes zibellina and the introduced Japanese martens, Martes melampus in northern Japan was revealed by analyzing a 521-524bp DNA sequence from the cytochrome b (112bp)/transfer RNA-threonine (67bp)/tRNA-proline (65bp) and control region (277-280bp) of the mitochondrial genome. Intraspecific differences in sequences of M. zibellina and M. melampus (3.8-15.0% and 1.9-16.4%, respectively) were similar to interspecific differences between these two species (5.8-16.6%). Comparison of sequence data exhibited five haplotypes of M. melampus and four haplotypes of M. zibellina, which clustered into two groups (clusters-A and-B). Cluster-A included two haplotypes of M. melampus and two haplotypes of M. zibellina, whereas cluster-B included three haplotypes of M. melampus and two haplotypes of M. zibellina. Results of this study lead three possible explanations. Firstly, past hybridization between M. zibellina and M. melampus might have occurred. Secondary, these two species might have similar heteroplasmy of mtDNA. Thirdly, these haplotypes might have come from nuclear genome. Although further intensive studies are needed to make a conclusion, detection of hybridization with the Japanese marten are occurred or not is quite important to conserve the Japanese sable.