Mitochondrial DNA diversity of Anatolian indigenous domestic goats

Anatolia has been an important region for civilizations and agricultural revolution as a major domestication centre for livestock species. Goats (Capra hircus) were among the earliest domesticated animals in this region. In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phylogeographical structure. The nucleotide diversity values were found to be higher than those in previously studied goat breeds. The fact that Anatolia is a domestication centre and its geographical position as a junction of trade routes may have caused the higher genetic diversity of Anatolian goat breeds.     

Human and animal fasciolosis: Coprological survey in Narok,Baringo and Kisumu counties,Kenya

Fasciolosis is caused by digenean trematodes of the genus Fasciola. The principal definitive hosts are cattle, sheep and goats. Humans are infected as accidental hosts. Fasciolosis is one of the major neglected tropical diseases and is considered an emerging zoonotic infection. This study was aimed at determining the prevalence of human and domestic animal fasciolosis in selected counties in Kenya. Stool samples for Fasciola diagnosis were collected from humans and domestic animals and transported to the laboratory at Egerton University and processed using sedimentation technique and examined for the presence of eggs. A total of 272 human samples collected were all negative for Fasciola eggs. A total of 582 domestic animals (cattle [46.0%], sheep [29.9%] and goats [24.1%]) samples collected had overall prevalence of 30.9% for Fasciola infection. There was no significant differences (p > 0.05) between the prevalence of fasciolosis and origin of the animals, sex and season. There was a significant difference (p < 0.05) between the prevalence of fasciolosis and domestic animals, age and body condition. The prevalence of fasciolosis was high in two irrigation schemes which favour the breeding of intermediate host snail and grazing of animals along the irrigation canals where metacercaria of Fasciola parasites could be present on the vegetation. Although human fasciolosis was not detected in this study, the presence of animal fasciolosis can pose public health risk because of its zoonotic nature. Therefore, it is important to introduce measures which would help to reduce the exposure of animals to Fasciola infection.     

四川7个地方山羊品种(类群)mtDNA遗传多样性研究

测定了四川7个地方山羊品种（类群）43个个体的mtDNA控制区全序列，结果表明：山羊mtDNA控制区全序列长度为1212bp或1213bp，A＋T含量（59．9％）明显高于G＋c含量（40．1％）。共检测到74个变异位点，序列均为中性突变，核苷酸多样度为1．686％，这些差异共定义了27种单倍型，单倍型多样度为0．966，遗传多样性较为丰富，品种（类群）间存在不同程度的遗传分化。7个地方山羊品种（类群）间的遗传距离变异范围为0．0017～0．0306。用MEGA软件的NJ法构建单倍型序列的系统发育无根树，结果表明四川地方山羊品种（类群）有两个母系来源，但是否就对应于角笋骨羊（Capra aegagrus）和捻角山羊（Capra falconeri）两个野生祖先，还有待于进一步研究。     

Risk factors for symptoms of gastrointestinal illness in rural town Isiolo, Kenya

This study assesses risk factors for food-borne gastrointestinal illness indicated by diarrhoea and/or vomiting using 14-day recalls among children and young adults. The study was set in Isiolo, a rural town of Kenya, inhabited mainly by pastoralists of different ethnic groups. The preparation methods of milk at the household level were also investigated. The study was cross-sectional and involved 900 participants from randomly selected households. They were interviewed using a structured questionnaire. An unmatched nested case-control study was constructed by randomly selecting three controls for each case. Potential risk factors for gastrointestinal illness were analysed using both univariate and multivariate logistic regression models with random effect on ethnic groups. The study results showed that consumption of mutton, carrots, Irish potatoes, raw camel milk, boiled camel milk and fermented camel milk were important risk factors for diarrhoea and/or vomiting, whereas the consumption of boiled goat milk, boiled cow milk, spinach, washing of hands with soap and the presence of proper drainage system had protective effects (odds ratio < 1). We conclude that in this setting, primarily vegetables and the camel milk market chain pose the greatest risks for symptoms of food-borne gastrointestinal illness.     

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。     

Anthelmintic resistance amongst sheep and goats in Kenya

Faecal egg count reduction tests (FECRT) and larval cultures were used to assess the prevalence of anthelmintic resistance amongst sheep and goats on farms served by Kenya's five regional Veterinary Investigation Laboratories. Twenty-four out of 42 farms tested (57%) showed resistance to at least one anthelmintic group. Resistance to levamisole was found in nine out of 35 sheep farms tested (26%) and 12 out of 24 goat farms (50%). Resistance to benzimidazole drugs was found in 10 out of 28 sheep farms (36%) and six out of 20 goat farms (30%). Larval cultures of post-treatment faecal samples showed resistance to be predominantly due to Haemonchus contortus. Twelve farms were routinely using substandard products which appeared to have no anthelmintic activity.     

东方蜜蜂线粒体DNA应用进展

【研究目的】为掌握线粒体DNA（mtDNA）在东方蜜蜂研究中的取得的进展。【方法】本文总结了蜜蜂mtDNA结构特征、mtDNA标记研究技术和东方蜜蜂非编码区和编码区标记的应用情况。【结果】RNA^leu-COⅡ区和部分COⅡ区的酶切和测序均发现了丰富的多态性。RNA^leu-COⅡ区和部分编码区标记能较好地解决泰国、菲律宾东方蜜蜂的种群遗传分化问题。根据RNA^leu-COⅡ区的系统发育关系将东方蜜蜂分成5个类型,并推测了他们的地理发育关系。【结论]mtDNA标记是解决东方蜜蜂遗传学和进化学问题较好的标记,增加样本量和研究的区段能解决mtDNA存在的不足。     

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。     

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.     

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。     

利用线粒体D-loop区分析家鸭品种遗传多态性与系统进化

通过线粒体DNA控制区的结构和多态性来研究我国家鸭的遗传多态性与系统进化。利用DNA测序技术测定了我国9个家鸭品种106个个体线粒体DNA控制区多变序列。序列分析结果显示:A、C、T、G碱基的平均含量分别为25.6%、33.3%、15.2%和25.9%。检测到34个变异位点,约占分析位点总数的5.1%,有转换、颠换、插入/缺失4种类型的变异。确定了31种单倍型,其中单倍型A7为家鸭的主体单倍型,品种之间有9种共享单倍型。9个家鸭品种单倍型多样度(Hd)平均为0.798,核苷酸多样度(Pi)平均为0.28%,单倍型多样度在荆江麻鸭中最高,其次是攸县麻鸭和恩施麻鸭,在文登黑鸭中最低。9个品种家鸭之间双参数距离范围为0.001 3~0.004 4。31个家鸭单倍型序列的系统发生分析表明,9个家鸭品种只有1个母系起源,没有发现东亚斑嘴鸭对9个家鸭品种起源有贡献的证据。     

Complete Mitochondrial DNA D-Loop Sequence and Genetic Diversity of Wuzhishan Pig

In order to research the genetic diversity and phylogenies of Wuzhishan pig, 56 complete mtDNA D-Loop were analyzed.55 sequences were amplified by polymerase chain reaction (PCR) and 1 sequence was downloaded from GenBank.The results showed that repetitive sequence "TTATAAAACAC" appeared in the conservative regions of 21 mtDNA D-Loop sequences.13 haplotypes and 14 variable sites were observed in 56 sequences.Haplotype diversity and nucleotide diversity (Hd =0.838 and Pi=0.00334) indicated that Wuzhishan pig had high genetic diversity.Two branches in the phylogenetic tree and Network analysis diagram indicated that there were two maternal origins in Wuzhishan pig.The phylogenetic tree of Wuzhishan pig and other 23 species showed that Wuzhishan pig had close genetic relationship with the pig breeds in the south region of the Yangtze river.     

五指山猪线粒体控制区序列分析及遗传多样性研究

为了研究五指山猪遗传多样性和系统地位,本研究采用PCR产物直接测序法得到55条五指山猪线粒体控制区(mtDNA D-Loop)全序列,并结合GenBank中发表的1条五指山猪mtDNA D-Loop全序列进行结构分析、遗传多样性研究及系统发育分析。结果发现,56条序列中出现21次保守区变异,即"TTATAAAACAC"序列重复,共定义13个单倍型,发现14个变异位点,单倍型多样度(Hd)和核苷酸多样度(Pi)分别为0.838和0.00334,表明五指山猪遗传多样性较丰富。五指山猪线粒体控制区序列构建的系统发育树和Network网络分析呈现两大分支,推测有两个母系起源,且与GenBank中其他23个猪种的聚类结果表明,五指山猪与长江流域以南地区的猪种有着较近的亲缘关系。     

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。     

猪核线粒体假基因的分布特征研究

核线粒体假基因(NUMT)是线粒体DNA插入到核基因组中的DNA片段。目前,已经发现越来越多的真核生物基因组存在线粒体假基因现象。猪线粒体假基因在核基因组中的分布尚未见报道。研究通过猪线粒体基因组全序列与核基因组全序列进行比对,由BLAST程序鉴别出132个NUMT。结果表明:这些NUMT的大小在37～4 453bp,其中90%的NUMT长度处于40～1 000 bp的范围内,NUMT与相应的线粒体DNA片段之间的同源性数值范围为66%～100%。此外,鉴定出的NUMT序列几乎涵盖了包括线粒体DNA控制区在内的全部线粒体基因组,包括30个完整的线粒体基因,分布于猪的1、4、5、7、11、13、14、15、17号染色体上,近50%的NUMT定位在14号染色体上。     

Mitochondrial DNA sequence variation in Hippopotamus amphibius from Kruger National Park,Republic of South Africa

Populations of Hippopotamus amphibius have declined throughout Africa in recent years, and are expected to decline further. An understanding of the population genetics of individual populations of hippos is necessary for effective management. To that end, we sequenced a portion of the mitochondrial DNA (mtDNA) control region or D-loop from 37 H. amphibius, from six herds in the central region of Kruger National Park (KNP), Republic of South Africa. We amplified a 453 bp segment by PCR, and identified 21 polymorphic sites and seven haplotypes. All of these haplotypes are private alleles, not found in other populations of hippos from southern Africa. Overall nucleotide diversity (π) was 0.01739, and haplotype diversity (hd) was 0.8273, within the range observed in other parts of Africa. Mismatch analysis conformed more closely to a model of constant population size than either rapid demographic or spatial expansion. An analysis of molecular variance demonstrated no significant differentiation among herds, and Mantel tests showed no significant relationship between geographic and genetic distance among herds separated by up to 47 km (measured as Euclidean [x,y] distance) or 77 km (measured along rivers). Over this range, the population appears to be a single panmictic unit. A test of the hypothesis that calves are more likely to share a mtDNA haplotype with an adult female in the same herd than an adult female from a different herd was not significant.     

新疆野生盘羊mtDNA D-loop序列的多态性

根据GenBank中3条羊亚科动物线粒体DNA全序列设计并合成1对引物,成功扩增了新疆天山亚种野生盘羊线粒体(mtDNA)控制区(D-loop)全长序列片段,并进行序列分析。结果显示,1号和2号盘羊mtDNA D-loop序列全长分别为1 070,1 169 bp;在检测的2个个体上共发现73个突变位点,其中有7个插入,50个转换,11个颠换,5个缺失,表明碱基的替换有明显偏倚;1号和2号新疆天山亚种野生盘羊mtDNA D-loop区核苷酸突变位点分别为35个和38个,核苷酸变异率分别为3.27%和3.25%。这一结果表明,新疆天山亚种野生盘羊群体线粒体D-loop区存在着丰富的多态性,同时进一步说明了我国新疆野生盘羊遗传资源比较丰富。     

Mitochondrial DNA variation of the dog hookworm Ancylostoma caninum in Brazilian populations

The mitochondrial cytochrome oxidase I gene was partially sequenced for 164 Ancylostoma caninum individuals, originating from five different localities in Brazil, with the aim of describing the genetic diversity and genetic structure of Brazilian hookworm populations. Allelic and nucleotide diversity were moderate (overall h=0.88 and pi=0.016) and were similar among cities. There was moderate genetic differentiation among the populations sampled (approximately Phi(ST)=0.12) and a weak but nonsignificant correlation between geographical and genetic distance. This genetic structure was similar to that observed among populations of the human hookworm, Necator americanus, but distinct from that typically found in trichostrongylid nematode parasites of livestock. Thus, a pattern of different genetic structures among different groups of nematodes is emerging. We also observed a few individuals that had a highly divergent mtDNA sequence (almost 7% sequence divergence from the other sequences). These results in combination with data from other studies suggest that A. caninum populations worldwide consist of a mix of previously differentiated populations, or perhaps even cryptic species. This study contributes to the knowledge of genetic structure and diversity of hookworms, which in turn will be useful in developing methods for their control.     

猪卵母细胞线粒体分布及线粒体DNA拷贝数变化

本研究旨在观察猪卵母细胞线粒体分布及线粒体DNA拷贝数变化,以期作为判定哺乳动物卵母细胞胞质成熟的指标,同时也为今后克隆技术的发展和相关基因表达调控的研究提供基础.运用线粒体分子探针标记技术检测体外成熟不同时期卵母细胞中线粒体的分布变化,运用实时荧光定量PCR技术检测其线粒体DNA拷贝数的变化趋势,揭示线粒体分布、线粒体DNA拷贝数变化与卵母细胞发育潜能的关系.结果表明,猪卵母细胞成熟前后,线粒体分布由未成熟的周边分布变为成熟后的均匀分布,并且线粒体簇变大,着色变深.卵母细胞成熟0、11、22 h的mtDNA拷贝数分别为(2 519.52士940.39)、(3 421.47士345.71)和(9 747.58士1 928.24),他们之间无显著性差异(P＞0.05).卵母细胞成熟33 h的mtDNA拷贝数为(39 913.61±1 180.26),显著高于成熟0、11和22 h的mtDNA拷贝数(P＜0.05).卵母细胞成熟44 h的mtDNA拷贝数为(130 074.30±78 119.45),显著高于成熟33 h的mtDNA拷贝数(P＜0.05).由此可见,随着卵母细胞成熟进程的推进,线粒体活性增强,线粒体DNA拷贝数明显增加.     

基于线粒体DNA D-loop区序列分析中国及新西兰奶山羊遗传进化关系

[目的]分析我国地方培育奶山羊品种与国外引进品种的遗传进化关系。[方法]以4个国内奶山羊品种（文登奶山羊、关中奶山羊、崂山奶山羊、雅安奶山羊）和3个新西兰引进奶山羊品种（阿尔卑斯奶山羊、吐根堡奶山羊、萨能奶山羊）为研究对象,采集33只个体的外周血样本,提取血液基因组DNA,利用PCR法扩增线粒体DNA（mitochondrial DNA,mtDNA）D-loop区全长序列,对测序获得的序列进行生物信息学分析,探究不同奶山羊品种的遗传多样性及进化关系。[结果]7个品种奶山羊的mtDNA D-loop区中A、T碱基含量高于G、C碱基含量。共检测到82个多态位点,25个单一多态位点,55个简约信息位点。各品种单倍型多样度（Hd）范围为0.905~1.000,核苷酸多样度（Pi）范围为0.001 51~0.013 32;共存在26种单倍型,文登奶山羊和萨能奶山羊各有5个单倍型,阿尔卑斯奶山羊有4个单倍型,崂山奶山羊、吐根堡奶山羊、关中奶山羊、雅安奶山羊各有3个单倍型;各品种核苷酸平均差异数（K_XY）范围为6.400 00~38.450 00,核苷酸歧异度（D_XY）范围为0.005 79~0.034 76,遗传分化系数（G_ST）范围为0.000 00~0.186 05,遗传分化指数（F_ST）范围为0.231 56~0.971 52。品种间系统发育树表明,文登奶山羊和崂山奶山羊聚为一支;关中奶山羊与3种新西兰奶山羊遗传距离较近,从遗传学角度证实了关中奶山羊由国外奶山羊与地方品种经杂交选育而成;雅安奶山羊与其他品种遗传距离最远。[结论]中国奶山羊存在2个支系起源且未发现群体扩张;中国培育奶山羊品种含有较多的国外奶山羊血统;文登奶山羊与崂山奶山羊亲缘关系较近,雅安奶山羊在遗传进化中可能存在地域隔离。