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。     

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.     

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.     

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.     

Genetic diversity of mtDNA D-loop sequences in four native Chinese chicken breeds

1. To explore the genetic diversity of Chinese indigenous chicken breeds, a 585 bp fragment of the mitochondrial DNA (mtDNA) region was sequenced in 102 birds from the Xichuan black-bone chicken, Yunyang black-bone chicken and Lushi chicken. In addition, 30 mtDNA D-loop sequences of Silkie fowls were downloaded from NCBI. The mtDNA D-loop sequence polymorphism and maternal origin of 4 chicken breeds were analysed in this study.

2. The results showed that a total of 33 mutation sites and 28 haplotypes were detected in the 4 chicken breeds. The haplotype diversity and nucleotide diversity of these 4 native breeds were 0.916 ± 0.014 and 0.012 ± 0.002, respectively. Three clusters were formed in 4 Chinese native chickens and 12 reference breeds. Both the Xichuan black-bone chicken and Yunyang black-bone chicken were grouped into one cluster. Four haplogroups (A, B, C and E) emerged in the median-joining network in these breeds.

3. It was concluded that these 4 Chinese chicken breeds had high genetic diversity. The phylogenetic tree and median network profiles showed that Chinese native chickens and its neighbouring countries had at least two maternal origins, one from Yunnan, China and another from Southeast Asia or its surrounding area.     

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。     

基于线粒体控制区的鸡不同杂交组合遗传多样性研究

旨在探讨鸡不同杂交组合线粒体控制区（mtDNA D-loop区）的遗传多样性和单倍型特性。选取固始鸡和隐性白羽鸡及其正、反交F1代、藏鸡以及F2代等6个群体共387个个体的mtDNA D-loop区进行测序,分析其遗传规律和单倍型特性,并与不同红色原鸡亚种进行聚类,分析其母系起源。结果显示,6个群体D-loop区全序列大小为1 231 bp,共检测到28个多态位点和1个C碱基缺失,共构成19种单倍型,分为A、B、C和E 4个单倍型群,其中,固始鸡和反交F1代主要为A、C单倍型,固始鸡A、C单倍型比例分别为53.42%和46.58%,反交F1代A、C单倍型比例分别为50.75%和49.25%;隐性白羽鸡、正交F1代和F2代优势单倍型均为E单倍型,占比分别为48.89%、48.84%和50.00%。6个鸡群体单倍型多样度（Hd）在0.496~0.729之间,核苷酸多样度（Pi）在0.003 40~0.005 41之间,Hd值和Pi值最大的均为正交F1代,其次为隐性白羽鸡和F2代,固始鸡和反交F1代群体遗传多样性接近。聚类分析显示,A、B单倍型群与滇南亚种交叉聚为一枝;E单倍型群与印度亚种交叉聚为一枝;C单倍型群与印度亚种、指名亚种、印尼亚种以及滇南亚种聚为一枝。结果提示,mtDNA D-loop区遵循严格的母系遗传,后代的遗传多样性和单倍型比例与其母本基本一致;我国家鸡群体具有多个红色原鸡母系起源,且主要起源于原鸡滇南亚种。     

建昌马mtDNA D-loop区遗传多样性及系统进化分析

试验旨在以线粒体DNA(mitochondrial DNA,mtDNA)为切入点,研究建昌马的母系遗传多样性与系统进化。从建昌马(n=39)血液中提取基因组DNA,用PCR方法扩增mtDNA D-loop区并直接测序,分析其高变区247 bp序列信息,统计mtDNA D-loop区的单倍型及变异位点,计算单倍型多样性(haplotype diversity,Hd)、核苷酸多样性(nucleotide diversity,Pi)和平均核苷酸变异数(average number of nucleotide differences,K)。构建包括建昌马在内的19个品种马的NJ系统进化树,计算各品种间的遗传距离。结果显示,试验获得了清晰的PCR扩增产物,并通过直接测序方法获得了约1200 bp的序列。39匹建昌马mtDNA D-loop区247 bp序列(其中1个样品缺失1 bp)的AT碱基含量为61.45%,属AT碱基对富集区,检测到33个多态性位点,共显示26种单倍型,其中4种为共享单倍型,且Hap7和Hap1为优势单倍型,单倍型多样性为0.947,核苷酸多样性为0.02399,平均核苷酸变异数为5.901,显示丰富的母系遗传多样性;NJ系统进化树显示,建昌马分布在A、C、D、E、F、G共6个支系中,约50%的样品分布在A支系,显示出复杂的母系起源;建昌马与关中马的遗传距离最小(0.021),其次是三河马、文山马、韩国车巨马(0.024),与韩国济州岛马遗传距离最大(0.032)。本研究结果表明,建昌马的mtDNA D-loop高变区遗传多样性丰富,具有多个母系起源,且A支系占有明显优势,与关中马、文山马可能有共同的母系起源。     

Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

ABSTRACT

1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.

2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.

3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.

4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.     

固原鸡线粒体DNA控制区全序列测定及分析

固原鸡是宁夏唯一的地方鸡品种资源,具有肉质细嫩、味道鲜美、营养丰富等遗传特性。该试验采用PCR和直接测序的方法测定固原鸡(白羽、麻羽、红羽)线粒体DNA(mtDNA)控制区(D-loop)全序列,结果表明固原鸡3个类群线粒体DNA控制区全序列长度分别为1230bp、1231bp或1232bp。分析种内的遗传变异,3个类群固原鸡共发现6个变异位点,其中4个转换,2个缺失/插入,没有观测到颠换;A、T碱基含量占59.9%~60.0%,G、C碱基含量占40.0%;固原鸡与其它8种禽类的D-loop基因序列同源性的分子进化树聚类结果表明固原鸡不同类群与红色原鸡亲缘关系最近。     

中国家鸡和红色原鸡mtDNA控制区遗传多态性及系统进化分析

通过线粒体DNA控制区的结构和多态性来研究中国家鸡和红色原鸡的遗传多态性与系统进化。测定14个中国地方鸡种和红色原鸡2个亚种的256个个体线粒体DNA控制区部分序列约560bp,结果表明,A、C、G、T这4种核苷酸的平均比例分别为25．∞％、37．40％、4．40％和33．20％。共发现44个变异位点,约占分析位点总数的7．86％,没有观测到插入／缺失,颠换和转换之比为0．13;共具有32种单倍型,9种为共享单倍型;16个群体内单倍型多样度从0到0．964,单倍型变异度总体为0．909±0．014,整体的平均核苷酸差异数为7．276,核苷酸多样度为1．851％。群体间核苷酸分歧度（Dxy）在0．747％～3．125％之间变化,核苷酸净遗传距离（Da）为0．015％～2．633％。16个群体表现出较高水平的遗传多态性,群体间表现出显著的遗传分化。群体遗传多态性和亲缘关系分析表明,一些中国家鸡的群体（如固始鸡和仙居鸡）起源于泰国红色原鸡Gallus gallu sgallus亚种,一些中国家鸡的群体（如茶花鸡和藏鸡等）起源于中国红色原鸡Gallus gallus spadiceus亚种,在一些中国地方鸡种还同时具有这2种红色原鸡的遗传贡献;认为中国家鸡起源于泰国或单纯起源于中国的观点都是不全面的。     

Analyses of Genetic Diversity and Phylogeny of mtDNA D-loop from Yak in Karakoram-Pamir Area

This experiment was conducted to clarify the genetic diversity,genetic differentiation and phylogenetic status of yak in Karakoram-Pamir area.The mtDNA D-loop region sequence was selected as a molecular marker,and the sequence and genetic diversity of the mtDNA D-loop region of yak in Karakoram-Pamir area were analyzed by PCR direct sequencing and bioinformatics methods.The yak sequence in GenBank was used.The maximum likelihood method was used to construct the phylogenetic tree and the intermediary network relationship.The results showed that the mtDNA D-loop sequence of yak in Karakoram-Pamir area was rich in A and T bases,with AT content of 61.2%,and there were 63 polymorphic loci,accounting for 7.04% of the total number of nucleotides.The results indicated that A and T bases were rich in the mtDNA D-loop sequences at 61.2%.There were 63 mutation sites,accounting for 7.04% of all nucleotides,The average haplotype diversity (Hd) was 0.806,the average nucleotide diversity (π) was 0.01528,and the average nucleotide difference (K) was 13.509,indicating that the yak was rich in genetic diversity in Karakoram-Pamir area;Through phylogenetic analysis,there were two branches in yak in China,forming two branches and six small clades.The yak in Karakoram-Pamir area involved in this study had two different maternal origins.Additionally,yak in the Karakoram-Pamir area was less shared with other breeds of yak haplotypes.In the branch C,the yak group in the Karakoram-Pamir area accounts for a large proportion and was shared with wild yak.The yak population in Karakoram-Pamir area had a unique genetic background,which might be the result of early domestication of wild yaks.It was suggested to increase the identification of yak breeds and the formulation of breed standards in this area,and strengthen the protection of yak genetic resources in this area.According to the current situation of the population,wild blood yaks were introduced for purification and rejuvenation to prevent breed degeneration and decrease of genetic diversity.The introduction of foreign yak breeds and disorderly hybridization were reduced to ensure the characteristics of this breed of high-quality yak breed resources.     

泰国红色原鸡和中国红色原鸡mtDNA控制区遗传多态性和分类关系研究

对泰国红色原鸡Gallus gallus gallus亚种和中国红色原鸡Gallus gallus spadiceus亚种各16个个体mtDNAD-loop序列进行系统分析,测定线粒体D-loop部分序列大小约为560bp,A、C、G、T这4种核苷酸的平均比例分别为13.6%、43.2%、4.3%和38.9%,A+T含量高于G+C含量。结果共发现27个变异位点,颠换和转换之比为0.13,没有观测到插入/缺失情况。测定的6种单倍型中,2个红色原鸡亚种没有共享单倍型,单倍型多样度分别为0.250和0.695,平均核苷酸差异数分别为3.750和10.833,核苷酸多样度分别为0.954%和2.757%。泰国红色原鸡中性检验的Tajima'sD值为-1.800(P<0.05),不符合中性突变。2个红色原鸡亚种间核苷酸分歧度(Dxy)为2.847%,核苷酸净遗传距离(Da)为0.991%。序列群体间的方差组分(Va)占总变异的47.31%,Fst=0.473,差异极显著(P<0.01);群体间mtDNAD-loopFst值也差异显著(P=0.035)。红色原鸡2个亚种具有不同的群体遗传结构,群体之间存在明显的遗传分化,本研究支持这2个亚种并非是同一个亚种的观点。     

郏县红牛mtDNA D-loop区遗传多样性与母系起源研究

［目的］探究郏县红牛的mtDNA D-loop遗传多样性与母系起源。［方法］采用生物信息学方法。［结果］在46头郏县红牛mtDNA D-loop区全序列共检测到60个变异位点,定义20种mtDNA D-loop单倍型,平均单倍型多样度(Hd)为0.8530,平均核苷酸多样度(Pi)为0.0254,表明郏县红牛有丰富的母系遗传多样性。构建的IQ系统发育树表明郏县红牛具有瘤牛和普通牛两个母系支系。［结论］郏县红牛具有丰富的母系遗传多样性,有普通牛和瘤牛两个母系起源。     

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.     

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。     

黄河下游同域山羊种群mtDNA D-环多态性及系统发育

对黄河下游7个山羊种群共59个个体的mtDNA D-环533 bp序列进行分析,发现59个多态位点,其中单一多态位点21个,简约信息位点38个,分别占全序列的11.7%、3.94%和7.13%。确定了37种单倍型,崂山奶山羊1个个体还发现了1处5碱基的缺失。各群体单倍型多样度为0.785 7~0.969 7,核苷酸多样度为1.27%~1.73%,遗传多样性较丰富。构建系统发育树将37种单倍型分为2个分支,由此推断黄河下游山羊资源至少具有2个母系起源,角猾羊与A类型聚为1支,7个群体具有角猾羊起源,未发现捻角山羊对7个群体有贡献的证据。错配分析表明,A类型经历过群体扩张,B类型未经历过群体扩张。并通过遗传距离分析了各群体的遗传分化。     

中国荷斯坦牛mtDNA D-Loop全序列分析

本文分析了3头中国荷斯坦牛线粒体DNA D－Loop区910bp核革酸序列的变异情况，结果发现，3头中国荷斯坦牛mtDNA D-Loop区的平均核苷酸变异率为0.59%，其核苷酸变异类型包括转换、颠换和插入3种形式，其中，以转换最为常见。     

藏系绵羊、新疆细毛羊及阿勒泰羊mtDNA D-loop基因序列分析及系统进化研究简

为研究藏系绵羊的贾洛、红原、欧拉3个类群与新疆细毛羊、阿勒泰羊的遗传多样性及系统进化关系,试验对该5个类群89个绵羊个体的mtDNA D-loop区全序列进行测序分析。结果显示,该5个绵羊类群89个个体总共发现有168个多态性位点,单一多态位点（singleton variable sites） 82个,简约信息位点（parsimony informative sites）86个,碱基A+T的平均含量达到了62.5%,明显高于C+G（37.5%）,共检测到70种单倍型,核苷酸多样性（Pi）在0.01040～0.02892之间,单倍型多样性在0.640～1.000之间,平均核苷酸差异数（K）为18.340,Tajima’s D中性检验发现这5个类群均不显著。通过构建NJ进化树结果表明,在藏系绵羊中红原类群与欧拉类群的亲缘关系最近,其次藏系绵羊中贾洛类群才与红原、欧拉类群聚为一类,再依次聚类的为新疆细毛羊、欧洲摩弗伦羊、东方盘羊;盘羊与羱羊单独聚为一类。该5个类群存在明显的3个母系起源。     

关中驴线粒体DNA D-loop多态性分析

本文对 6头关中驴线粒体DNAD loop区 399bp的核苷酸序列进行了分析。结果发现 ,关中驴的D loop区核苷酸变异只有转换 1种形式。 6头关中驴D loop区的核苷酸序列组成 3种单倍型 ,单倍型比例为 5 0 .0 0 % ,说明关中驴mtDNA遗传多样性正逐步丧失 ,需要加强驴种质资源保护。以欧洲驴D loop序列为对照 ,关中驴 3种单倍型的核苷酸变异率分别为 4 .2 1%、4 .5 1%和 0 .2 5 %。在获得的 399bpD loop碱基序列中 ,共检测出核苷酸多态位点18个 ,多态位点比例为 4 .5 1%。从D loop区核苷酸序列的 3种单倍型分析 ,发现关中驴可能有 2种不同的母系起源