隆林牛与郏县红牛线粒体DNA全基因组遗传多样性比较研究

摘　要：［目的］本研究旨在从基因组水平探究隆林牛和郏县红牛的线粒体DNA（mtDNA）全基因组遗传多样性与母系起源,并对2个黄牛品种的mtDNA全基因组遗传多样性进行比较分析。［方法］采用全基因组重测序及生物信息学方法。［结果］在15头隆林牛和28头郏县红牛mtDNA全基因组序列中,共检测到36种单倍型,其中郏县红牛有26种单倍型,隆林牛仅有8种单倍型,2个黄牛品种共享2种单倍型。郏县红牛和隆林牛的平均单倍型多样度（Hd）分别为1.000和0.943,平均核苷酸多样度（Pi）分别为0.0080和0.0053,表明其遗传多样性丰富。构建的系统发育树表明,隆林牛和郏县红牛具有瘤牛和普通牛两个母系支系。［结论］隆林牛以瘤牛起源为主,郏县红牛为普通牛与瘤牛的混合起源,这2个地方黄牛品种具有独特的母系遗传信息,表现出明显的母系遗传差异。     

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。     

黄陂牛mtDNA D-loop区遗传多样性研究

【目的】探究黄陂牛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】在21头黄陂牛mtDNA D-loop区共检测到55个变异位点,定义了10个mtDNA单倍型,平均单倍型多样度为0.7760,平均核苷酸多样度为0.0234,表明黄陂牛具有丰富的遗传多样性。构建的NJ系统发育树表明黄陂牛具有瘤牛和普通牛两个母系起源。【结论】黄陂牛有丰富的遗传多样性,有瘤牛和普通牛两个母系起源,且受瘤牛的影响较大。     

温岭高峰牛线粒体DNA全基因组遗传多样性分析

[目的]通过测定温岭高峰牛线粒体DNA全基因组序列以分析温岭高峰牛的母系起源及遗传多样性。[方法]采用DNA提取、测序及生物信息学方法。[结果]通过对19头温岭高峰牛线粒体DNA全基因组序列分析,共发现263个变异位点,定义9种单倍型,单倍型多样度(Hd±SD)为0.778±0.096,核苷酸多样度(Pi±SD)为0.0017±0.0014,表明温岭高峰牛的遗传多样性较低。构建的NJ系统发育树和单倍型进化网络图表明温岭高峰牛有普通牛和瘤牛2种母系起源。[结论]温岭高峰牛线粒体DNA基因组的遗传多样性较低,有瘤牛和普通牛两个母系起源,但主要受瘤牛的影响。     

甘孜藏牛mtDNA 基因组遗传多样性分析

［目的］探究甘孜藏牛的mtDNA基因组遗传多样性与母系起源。［方法］采用mtDNA全基因组序列比对及生物信息学方法。［结果］结果显示：在28头甘孜藏牛mtDNA 基因组中,共检测到1232个变异位点,确定了22种单倍型,其单倍型多样度（Hd）为0.98820±0.00010,核苷酸多样度（Pi）为0.02420±0.00003,表明甘孜藏牛具有丰富的母系遗传多样性。系统发育树和网络分布图表明,28头甘孜藏牛mtDNA基因组包括4种母系支系,分别为普通牛的T2、T3与T4支系,还有牦牛支系,其中T2支系占7.14%,T3支系占64.29%,T4支系占3.57%,牦牛支系占25 %。［结论］甘孜藏牛具有较丰富的母系遗传多样性,为普通牛母系起源,但与牦牛有杂交。     

秦川牛mtDNA全基因组遗传多样性与母系起源研究

[目的]从32头秦川牛全基因组中提取其mtDNA全基因组序列进行分析,以揭示秦川牛mtDNA基因组的遗传多样性与母系起源。[方法]采用mtDNA全基因组序列比对及生物信息学方法。[结果]在32头秦川牛mtDNA全基因组序列中,共检测到30种不同的单倍型,其平均单倍型多样度（Hd±SD）为0.996±0.009,其平均核苷酸多样度（π±SD）为0.0067±0.0010,表明秦川牛具有丰富的母系遗传多样性。构建的mtDNA全基因组系统发育树与单倍型网络图表明,32头秦川牛的mtDNA全基因组序列包括T2、T3、T4、I1共4个不同的支系,其中T2支系占21.88%,T3支系占40.625%,T4支系占9.375%,I1支系占28.125%。说明秦川牛具有普通牛和瘤牛两个支系,其中普通牛支系占71.88%,瘤牛支系占28.12%。[结论]秦川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,但以普通牛起源为主。     

岭南牛mtDNA D-loop区遗传多样性研究

[目的]通过测定岭南牛线粒体D-loop全序列来了解岭南牛的母系起源及遗传多样性。[方法]采用PCR扩增、测序及生物信息学方法。[结果]通过对30头岭南牛mtDNA D-loop序列分析,共发现62个变异位点和19种单倍型,核苷酸多样度(Pi)为0.0260,单倍型多样度(Hd)为0.8920,表明岭南牛遗传多样性丰富。构建的NJ系统进化树表明岭南牛有普通牛和瘤牛2种母系起源。[结论]岭南牛属于南方牛类型,受瘤牛的影响较大,具有瘤牛和普通牛的种质特征。     

湘西黄牛mtDNA D-loop区遗传多样性研究

[目的]为了探究湘西黄牛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]在33头湘西黄牛mtDNA D-loop区共检测到55个变异位点,界定了15个mtDNA单倍型,单倍型多样度为0.8750,核苷酸多样度为0.0144,表明湘西黄牛的遗传多样性较低。构建的系统发育树表明湘西黄牛具有普通牛和瘤牛两大母系起源。[结论]湘西黄牛的遗传多样性较低,属于中国南方黄牛,有瘤牛和普通牛两个母系起源,受瘤牛的影响更大。     

夷陵黄牛mtDNAD-loop区遗传多样性研究

【目的】为了探究夷陵黄牛的母系起源与遗传多样性。【方法】采用PCR扩增、测序及生物信息学方法。【结果】在27头夷陵黄牛mtDNA D-loop区共检测到54个变异位点,界定了13个mtDNA单倍型,单倍型多样度为0.7720,平均核苷酸多样度为0.0228,表明夷陵黄牛具有比较丰富的遗传多样性。构建的系统发育树显示夷陵黄牛具有普通牛和瘤牛两大母系起源。【结论】夷陵黄牛受瘤牛的影响大,属于中国南方黄牛,具有普通牛与瘤牛的种质特征。     

吉安牛mtDNA D-loop区遗传多样性研究

[目的]探究吉安牛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]在26头吉安牛mtDNA D-loop区共检测到52个变异位点,定义了7种mtDNA单倍型。构建的NJ系统发育树表明吉安牛具有瘤牛和普通牛两个母系起源。[结论]吉安牛具有丰富的遗传多样性,有瘤牛和普通牛两个母系起源,且受瘤牛的影响较大。     

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。     

蒙古家马和蒙古野马线粒体细胞色素b基因遗传多样性及系统进化分析

通过对马的线粒体细胞色素b（Cytb）基因序列的遗传变异分析,来探讨蒙古家马、蒙古野马和驴之间的亲缘关系和遗传多样性。对各类马和驴样本 mtDNA Cytb 基因进行PCR扩增和测序,运用现代分子生物学软件进行数据处理。结果共检测到15个单倍型,90个突变位点,单倍型多样性（Hd）为0.9356,核苷酸多样性（Pi）为0.01022,平均核苷酸差异数（K）为8.966,各群体间的遗传多样性相差不大。系统发育树和NETwork图中每一分支都至少包含2个群体的信息。4个类型蒙古家马总体上具有较高的遗传多态性,蒙古家马与蒙古野马之间的亲缘关系较近, 且出现数个分支,蒙古家马分布在各独立的进化支中,说明蒙古家马母系来源非常广泛或经过多次驯化。     

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.     

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 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.     

利用基因组重测序技术鉴定黑安格斯牛的纯度

【目的】基于10头黑安格斯牛和60头对照组牛的全基因组重测序数据,分析黑安格斯牛的纯度、遗传多样性及群体结构。【方法】全基因组重测序技术和生物信息学方法。【结果】通过对10头黑安格斯牛全基因组数据进行分析,共检测到15,064,459个SNP位点,其核苷酸多样性（pi）为0.0015,观测杂合度（Ho）为0.2381,期望杂合度（He）为0.2430,表明黑安格斯牛的遗传多样性较低;主成分分析和群体遗传结构分析发现,黑安格斯牛与欧洲普通牛聚为一类,其中有4头黑安格斯牛存在偏离情况,表明这4头牛主要与中国瘤牛与东亚普通牛韩牛之间存在杂交。【结论】10头黑安格斯牛中,6头为纯种黑安格斯牛,4头为杂种牛。