我国水牛地方品种线粒体D-loop区遗传变异与起源分化

测定了我国24个地方水牛品种和2个引进水牛品种共311个个体的线粒体DNA D-Loop区序列.结果表明我国水牛遗传多样性非常丰富,共检测到256个突变位点,132种单倍型,单倍型多样度Hd为0.9288.构建的NJ系统树表明中国水牛都属于沼泽型,并且主要为2个母系起源,分别命名为SA支系和SB支系,所研究的每个地方水牛群体中2个支系都存在.SB支系中还存在两个分化也比较明显的小分支,称为SBI和SBII.所有单倍型中,H2单倍型出现频率最高,且只在24个地方品种中存在,说明H2单倍型是我国地方水牛特有的标志单倍型,也是一种古老的单倍型.中国水牛应是在本土独立驯化的.     

中国山羊mtDNA D-loop遗传多样性及其起源研究

采用DNA测序技术分析了中国9个山羊品种（板角山羊、成都麻羊、贵州黑山羊、贵州白山羊、黔北麻羊、马头山羊、陕南白山羊、黄淮山羊和雷州山羊）共计128个个体的mtDNA D-loop全序列。结果表明：山羊mtDNA D-loop全序列长度为1212-1213bp,检测到102个变异位点,约占分析位点总数的8．42％,可变位点中转换占99个,颠换2个,1个转换/颠换共存;界定了92种单倍型,有78种为各品种独享单倍型,另外14种为群体内或群体间共享单倍型。9个山羊品种单倍型多样度为0．9333-1．0000,核苷酸多样度为0．7062％-1．8265％,表明中国山羊品种遗传多样性丰富。根据92种mtDNA单倍型构建了中国山羊的NJ分子系统树,聚类表明,中国山羊mtDNA D-loop序列单倍型分为支系A和支系B两大类。支系A包括75种单倍型,代表95个样本,占总数的74．22％;支系B包括17种单倍型,代表33个样本,占总数的25．78％,说明中国山羊存在支系A和支系B两大母系起源。对中国山羊mtDNA D-loop的支系A和支系B进行核苷酸不配对分布曲线分析和Fu的Fs中性检验,分析表明,支系A的分布曲线呈单峰形,Fs值为-24．6491,P值为0．0000,显著偏离中性,表明山羊支系A曾经历群体扩张;支系B呈近似双峰分布,Fs值为-3．3947,P值为0．0980,中性检验差异不显著,表明山羊支系B没有经历群体扩张,群体大小保持相对稳定。山羊支系B可能起源于中国。     

The Genetic Diversity of mtDNA D-loop and the Origin of Chinese Goats

The complete sequences of mitochondrial DNA D-loop of 128 individuals in nine Chinese goat (Capra hircu) breeds were analyzed by DNA sequencing technology. The results show that the length of mtDNA D-loop in Chinese goats is 1 212-1 213 bp. There are 102 polymorphic sites, accounting for 8.42% of 1 212 bp sequence. Ninety-two mtDNA haplotypes were determined. The haplotype diversity and nucleotide diversity are 0.9333-1 .0000 and 0.7062%-1.8265%, respectively. The results indicate that the genetic diversity of Chinese goats is very abundant. The NJ tree indicates that Chinese goats have two types of maternal origins from lineage A and lineage B. The possibility of lineage B originating from China is also discussed.     

Origin of Chinese Goldfish and Sequential Loss of Genetic Diversity Accompanies New Breeds

Background

Goldfish, Carassius auratus, have experienced strong anthropogenic selection during their evolutionary history, generating a tremendous extent of morphological variation relative to that in native Carassius. To locate the geographic origin of goldfish, we analyzed nucleotide sequences from part of the control region (CR) and the entire cytochrome b (Cytb) mitochondrial DNA genes for 234 goldfish and a large series of native specimens. Four important morphological characteristics used in goldfish taxonomy–body shape, dorsal fin, eye shape, and tailfin–were selected for hypothesis-testing to identify those that better correspond to evolutionary history.

Principal Finding

Haplotypes of goldfish rooted in two sublineages (C5 and C6), which contained the haplotypes of native C. a. auratus from southern China. Values of F _ST and N_m revealed a close relationship between goldfish and native C. a. auratus from the lower Yangtze River. An extraordinary, stepwise loss of genetic diversity was detected from native fish to goldfish and from Grass-goldfish relative to other breeds. Significantly negative results for the tests of Tajima’s D and Fu and Li’s D* and F* were identified in goldfish, including the Grass breed. The results identified eye-shape as being the least informative character for grouping goldfish with respect to their evolutionary history. Fisher’s exact test identified matrilineal constraints on domestication.

Conclusions

Chinese goldfish have a matrilineal origin from native southern Chinese C. a. auratus, especially the lineages from the lower Yangtze River. Anthropogenic selection of the native Carassius eliminated aesthetically unappealing goldfish and this action appeared to be responsible for the stepwise decrease in genetic diversity of domesticated goldfish, a process similar to that reported for the domestication of pigs, rice, and maize. The three-breed taxonomy–Grass-goldfish, Egg-goldfish, and Wen-goldfish–better reflected the history of domestication.     

Genetic Diversity and Systematic Evolution of Chinese Domestic Ducks Along the Yangtze-Huai River

To investigate the population structure and systematic evolution of the domestic duck in China, we sequenced the 667 bp mitochondrial DNA (mtDNA) D-loop control region of 106 ducks from nine breeds along the Yangtze-Huai River. Of the total analyzed sites, 34 (5.1%) were polymorphic due to transitions, transversions, insertions, and deletions. Nucleotide content was 25.6% A, 33.3% C, 15.2% G, and 25.9% T. In total, 31 haplotypes were identified in the target region; of these, the major haplotype was A7, and nine haplotypes were shared by the tested ducks. The haplotype diversity (Hd) and average nucleotide diversity (Pi) were 0.798% and 0.28%, respectively. Hd was highest in the Jingjiang shelduck, followed by the Youxian and Enshi shelducks, and it was lowest in the Wendeng black duck. Nucleotide diversity (Dxy) among the nine breeds ranged from 0.139 to 0.433%, and the Kimura 2-parameter distances were 0.0013-0.0044. Molecular variance indicated that a very high proportion of the insignificant genetic variance was attributable to variations within breeds. Phylogenetic analysis of 31 haplotypes revealed only one distinct maternal lineage in the tested ducks, and no evidence was found of a contribution of the Anas zonorhyncha group B haplotype to the maternal origin of Chinese domestic duck breeds along the Yangtze-Huai.     

用mtDNA D-环序列探讨蒙古和中国绵羊的起源及遗传多样性

为了在分子水平上探讨绵羊的起源,对中国和蒙古共20个绵羊群体、314只绵羊mtDNA D-环的部分序列进行了测定,结果表明：中国绵羊和蒙古绵羊mtDNA D-环区的部分序列中A、T、G、C含量没有明显的差别;蒙古绵羊的多态位点数（28．85％）略高于中国绵羊（24．22％）;中国绵羊群体的单倍型多样度在青海藏羊、甘肃藏羊、甘肃高山细毛羊、青海细：色羊、甘南藏羊、小尾寒羊和滩羊群体中较高,但在湖羊和岷县黑裘皮羊中较低;蒙古绵羊的单倍型多样度在Bayad和Baidrag群体中最高,但在Gobi—Altai群体中最低。从总体上看,蒙古绵羊的遗传多样性要略高于中国绵羊,例如单倍犁比例的平均值为86．06％（142／185）：78．83％（108／137）,单倍型多样度（Hd）的甲均值为0．976：0．936,核苷酸多样度（Pi（π））的平均值为0．036：0．034,平均核苷酸差异数（k）的平均值为23．50：22．48～217个中国和蒙古绵羊的单倍型序列的系统发生分析表明,中国和蒙古绵羊均有3个母系起源,被定义为A、B和C3类主要的单倍型。其中A类单倍型在所有中国绵羊群体及绝大多数蒙古绵羊群体（9／11）中占优势,平均比例为58．73％;B类单倍型居中,为24．88％;C类单倍型最少,仅为16．59％。进一步从GenBank获得的91个绵羊D-环区的序列与中国和蒙古绵羊D-环区的单倍型的进行网络关系分析,发现欧洲摩弗仑羊（European mouflon,O．musimon）与中国和蒙古绵羊具有较近的亲缘关系,但没有发现塬羊（Argali．O．ammon）、盘羊（0．rignei bochariensis）和东方盘羊（0．ammon nigrimontana）对中国和蒙古绵羊起源有贡献的证据。     

中国圈养梅花鹿的遗传多样性和遗传结构

东北梅花鹿(Cervus nippon hortulorum)的野生种群已濒临灭绝,但其圈养种群遍布全国各地,是我国圈养梅花鹿的主要品种(亚种)。为了探讨圈养梅花鹿种群作为东北梅花鹿野外放归项目资源种群的可行性,测定了来自9个圈养种群45只梅花鹿个体的线粒体DNA控制区的部分序列,以此分析我国圈养梅花鹿种群的遗传多样性和遗传结构。结果表明,我国圈养梅花鹿种群的遗传多样性并不贫乏,种群之间并没有发生显著的遗传分化。因此,东北地区的圈养梅花鹿种群可以作为野外放归项目的资源种群,而野外放归项目的建群者应来源于东北地区的多个圈养种群。     

黄河上游花斑裸鲤Cytb基因的序列变异和遗传多样性

花斑裸鲤(Gymncypris eckloni)主要分布于黄河上游高原宽符河段深水缓流处或静水湖泊中,在高原淡水生态系统的食物链中具有重要的地位.本文获得了黄河上游仡斑裸鲤5个种群共68个个体线粒体DNA(mtDNA)细胞色素b基因的全序列(1140bp),分析了序列变异和种群遗传多样性.68个序列经比对后,发现30个(2.63%)多态性位点,共定义了18个单倍型.结果显示,花斑裸鲤种群单倍型多样度和核苷酸多样度均低于其它鲤科鱼类,这可能与青藏高原经所经历的地质变迁和古气候环境的改变有关,由此生活在高原水域中的鱼类或多或少经历过瓶颈效应.AMOVA分析结果显示,遗传差异主要发生在种群之内,而不是来自不同地理组群问或组群内种群间.单倍型网络图和系统发育分析均没有显示出单倍型与地理位置的对应关系,提示黄河上游花斑裸鲤自然种群未出现分化,应作为一个整体进行保护.单倍犁歧点分布呈现为单峰以及中性检验Fu's Fs (-15.3400,P＜0.001)和Tajima's D(-0.6254.P=0.3080)结果综合表明,花斑裸鲤可能经历过近期的种群扩张事件.     

黄河上游花斑裸鲤Cyt b基因的序列变异和遗传多样性

花斑裸鲤（Gymncypris eckloni）主要分布于黄河上游高原宽谷河段深水缓流处或静水湖泊中,在高原淡水生态系统的食物链中具有重要的地位。本文获得了黄河上游花斑裸鲤5个种群共68个个体线粒体DNA（mtDNA）细胞色素b基因的全序列（1 140 bp）,分析了序列变异和种群遗传多样性。68个序列经比对后,发现30个（2.63%）多态性位点,共定义了18个单倍型。结果显示,花斑裸鲤种群单倍型多样度和核苷酸多样度均低于其它鲤科鱼类,这可能与青藏高原经所经历的地质变迁和古气候环境的改变有关,由此生活在高原水域中的鱼类或多或少经历过瓶颈效应。AMOVA分析结果显示,遗传差异主要发生在种群之内,而不是来自不同地理组群间或组群内种群间。单倍型网络图和系统发育分析均没有显示出单倍型与地理位置的对应关系,提示黄河上游花斑裸鲤自然种群未出现分化,应作为一个整体进行保护。单倍型歧点分布呈现为单峰以及中性检验Fu’s Fs（&#8722;15.3400, P<0.001）和Tajima’s D（&#8722;0.6254, P =0.3080）结果综合表明,花斑裸鲤可能经历过近期的种群扩张事件。     

Genetic Variations of 13 Indigenous Chinese Goat Breeds Based on Cytochrome b Gene Sequences

Phylogenetic relationships among and genetic variability within 13 Chinese indigenous goat breeds and Boer goat were analyzed using cytochrome b gene sequences. There were 44 variable sites found in a 642 bp sequence, and 46 Cyt b haplotypes were subsequently defined. The phylogeny analysis of haplotypes in combination with goat Cyt b sequences from GenBank shows that Chinese goats are obviously separated from wild goats and might come from Capra aegagrus. Further analysis indicated that indigenous Chinese goats might descend from at least two lineages; most of the individuals analyzed could be classified into lineage A as defined by Luikart, but five other goats were of uncertain lineage. The Tibet plateau is a possible place of origin for Chinese goats. The neighbor-joining tree based on pairwise differences among populations shows that most Tibetan goats, except the Middle Tibet type, cluster closely with North China goats, and then with South China goats. This result confirms that differences in genetic structure exist among goats in different geographic locations. Nucleotide diversity varied among populations. Tibet and North China goats had higher genetic diversity than South China goats. The fixation index (F _st=87.72%) suggested that most of the total genetic variation was due to variation within populations. In addition, the results indicate that Cyt b gene sequence information alone might not be enough for phylogeny analysis among breeds within species, as shown by fewer polymorphic sites and lower bootstrap values on the neighbor-joining tree.     

Origin and Genetic Diversity of Diploid Parthenogenetic Artemia in Eurasia

There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.     

基于线粒体细胞色素b基因分析海南岛褐家鼠种群遗传多样性

褐家鼠(Rattus norvegicus)是海南岛的主要害鼠之一,海南岛是我国南方海上的重要交通口岸,但关于海南岛褐家鼠的种群遗传多样性以及和邻近地区褐家鼠种群间的基因交流情况还缺乏了解。本研究测序分析了来自海南岛、广东、越南等地91只褐家鼠的细胞色素b基因,分析了不同种群中的Cyt b单倍型,种群间的遗传分化程度(F_(st)),构建了全世界60个褐家鼠的Cyt b单倍型之间的系统进化关系。结果发现,海南岛琼中/澄迈和崖城的褐家鼠种群没有共享的Cyt b单倍型,种群间出现了明显的遗传分化(F_(st)=0.453),但这两个群体分别与广东和菲律宾/越南的褐家鼠分享共同的单倍型,表明海南岛褐家鼠与广东和菲律宾/越南褐家鼠近代存在着基因交流。系统进化分析结果表明,多数海南岛和广东褐家鼠的Cyt b单倍型来自共同的单倍型组CⅢ和CⅦ,说明海南岛和广东省的褐家鼠可能由一个或多个共同的祖先种群扩散而来。由于褐家鼠喜欢与人伴生,褐家鼠很可能随着黎族人在新石器时代中期(大约3 000年前)或更早以前,从广西、广东沿海地区迁移至海南。     

中国家鸡的起源探讨

测定了6个家鸡品种30个个体的线粒体D0环区539bp的碱基序列,并与GenBank中的红原鸡、灰原鸡、绿原鸡、黑尾原鸡及鹌鹑的相应序列作比较分析,构建了分析系统树。结果表明,原鸡属4个种间差异较大,其中家鸡与泰国及邻近地区红原鸡关系最近,与印尼红原鸡、黑尾原鸡、灰原鸡、绿原鸡及鹌鹑的关系依次变远。提示中国家鸡可能起源于泰国及邻近地区的红原鸡。结果还显示,该原鸡的两个亚种（G.g.gallus和G.g.spadiceus)间的遗传分化程度显著低于家鸡亚种内的分化程度,这两个亚种似乎可以归为同一亚种。     

Levels and Patterns of Genetic Diversity and Population Structure in Domestic Rabbits

Over thousands of years humans changed the genetic and phenotypic composition of several organisms and in the process transformed wild species into domesticated forms. From this close association, domestic animals emerged as important models in biomedical and fundamental research, in addition to their intrinsic economical and cultural value. The domestic rabbit is no exception but few studies have investigated the impact of domestication on its genetic variability. In order to study patterns of genetic structure in domestic rabbits and to quantify the genetic diversity lost with the domestication process, we genotyped 45 microsatellites for 471 individuals belonging to 16 breeds and 13 wild localities. We found that both the initial domestication and the subsequent process of breed formation, when averaged across breeds, culminated in losses of ~20% of genetic diversity present in the ancestral wild population and domestic rabbits as a whole, respectively. Despite the short time elapsed since breed diversification we uncovered a well-defined structure in domestic rabbits where the F_ST between breeds was 22%. However, we failed to detect deeper levels of structure, probably consequence of a recent and single geographic origin of domestication together with a non-bifurcating process of breed formation, which were often derived from crosses between two or more breeds. Finally, we found evidence for intrabreed stratification that is associated with demographic and selective causes such as formation of strains, colour morphs within the same breed, or country/breeder of origin. These additional layers of population structure within breeds should be taken into account in future mapping studies.     

Origin of Contamination and Genetic Diversity of Escherichia coli in Beef Cattle

The possible origin of beef contamination and genetic diversity of Escherichia coli populations in beef cattle, on carcasses and ground beef, was examined by using random amplification of polymorphic DNA (RAPD) and PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the fliC gene. E. coli was recovered from the feces of 10 beef cattle during pasture grazing and feedlot finishing and from hides, carcasses, and ground beef after slaughter. The 1,403 E. coli isolates (855 fecal, 320 hide, 153 carcass, and 75 ground beef) were grouped into 121 genetic subtypes by using the RAPD method. Some of the genetic subtypes in cattle feces were also recovered from hides, prechilled carcasses, chilled carcasses, and ground beef. E. coli genetic subtypes were shared among cattle at all sample times, but a number of transient types were unique to individual animals. The genetic diversity of the E. coli population changed over time within individual animals grazing on pasture and in the feedlot. Isolates from one animal (59 fecal, 30 hide, 19 carcass, and 12 ground beef) were characterized by the PCR-RFLP analysis of the fliC gene and were grouped into eight genotypes. There was good agreement between the results obtained with the RAPD and PCR-RFLP techniques. In conclusion, the E. coli contaminating meat can originate from cattle feces, and the E. coli population in beef cattle was highly diverse. Also, genetic subtypes can be shared among animals or can be unique to an animal, and they are constantly changing.     

Mitochondrial DNA Cleavage Patterns Distinguish Independent Origin of Chinese Domestic Geese and Western Domestic Geese

It has generally been assumed, based on morphology, that Chinese domestic goose breeds were derived from the swan goose (Anser cygnoides) and that European and American breeds were derived from the graylag goose (Anser anser). To test the validity of this assumption, we investigated the mtDNA cleavage patterns of 16 Chinese breeds and 2 European breeds as well as hybrids produced between a Chinese breed and a European breed. After 224 mtDNAs, isolated from the Chinese and European breeds, were digested by 19 restriction endonucleases, variations of the cleavage patterns were observed for four enzymes (EcoRV, HaeII, HincII, and KpnI). All Chinese breeds and their maternal hybrids except the Yili breed showed an identical haplotype, named haplotype I or the Chinese haplotype; the European breeds and the Yili breed showed another haplotype, named haplotype II or the western haplotype. None of the haplotype found in the Chinese type was detectable in the western type and vice versa. The two haplotypes were found to differ from each other at 8.0% of the sites surveyed and with a 0.72% sequence divergence. Using 2% substitution per million years calibrated from the genera Anser and Branta, the two domestic geese haplotypes were estimated to have diverged approximately 360,000 years ago, well outside the 3000-6000 years in domestic history. Our findings provide the first molecular genetic evidence to support the dual origin assumption of domestic geese in the world. Meanwhile, the four mtDNA restriction fragment length polymorphisms can be used as maternal genetic markers to distinguish the two types of domestic geese.     

从细胞色素b基因序列变异分析中国鲇形目鱼类的系统发育

采用PCR技术获得中国鲇形目鱼类11科24属27个代表种类细胞色素b基因1138bp全序列,比较分析了来自北美洲、非洲的部分鲇形目鱼类同一基因序列,并选取脂鲤目、鲤形目和鲱形目鱼类作外类群,采用Bayesian方法和最大简约法(MP)构建分子系统树。结果表明：(1)鲇形目鱼类细胞色素b基因序列中,与脂鲤目、鲤形目以及鲱形目鱼类相比存在3bp的缺失;(2)鲇形目鱼类各科代表种类形成一单系群;(3)两种建树方法均支持铫科、粒鲇科和钝头鮠科形成一单系群;而胡子鲇科、刀鲇科、海鲇科、鮰科、长臀鮠科、鲢科、鲇科、棘脂鲿科、鲿科形成一大的单系群;但鳗鲇科的系统位置两种建树方法没有取得一致结果;而其中长臀鲍科与北美的鮰科形成姐妹群,胡子鲇、鮰科、鲇科、鲿科和鮡科是较明显的单系群。     

绵羊Cytb基因序列多态性及系统进化研究

以8个中国地方绵羊品种和1个外来品种的20个个体为研究对象,通过对Cytb基因的全序列测定,结果表明：绵羊的单倍型多样性为97．1％。所有序列的平均碱基组成为27．1％T,28．5％C,31．4％A及13．0％G,G＋C含量为41．5％,核苷酸多样性为0．602％。在所有序列中共检测到43个变异位点,其中包括40处转换和3处颠换。Fu’S中性检验表明差异不显著（0．10〉P〉0．05）,说明绵羊群体未发生群体扩张事件。NJ、ME及UPGMA聚类结果均表明,我国绵羊可分为3个单倍型组,这提示我国绵羊有3个母系起源。     

分子标记在家畜遗传多样性研究中的应用

家畜遗传多样性是生物多样性的重要组成部分,与人类未来的生存与发展密切相关。中国拥有丰富的地方家畜品种资源,但由于保种不当和盲目引进外来品种进行杂交、资金缺乏等原因,许多品种已濒临灭绝。如何保存利用好我国优良的家畜遗传资源已成为越来越严峻的问题。随着生物学技术的不断发展与完善,许多分子标记技术已经应用于畜禽遗传资源的研究。简要介绍了在家畜遗传多样性研究中应用最广的几种分子标记及其特性,讨论了在家畜遗传多样性的研究中如何选用适当的分子标记。     

国内外甜高粱种质遗传多样性的SSR分析

用24对扩增带型稳定的SSR引物,研究了206份国内外甜高粱种质资源的遗传变异,共检测出220个等位基因,每对引物检测出2～19个等位基因。引物位点的多态信息含量指数(PIC)变幅在0.50～0.87。利用220个多态性标记计算206份甜高粱品种之间的遗传相似系数(GS),范围在0.32～0.96之间。利用SSR标记遗传相似系数矩阵,按UPGMA方法对206份甜高粱品种进行聚类分析,将其分为A、B两大组,B组只包含3个品种,与其他品种遗传关系较远,A组进一步被分成15个类群,农艺性状近似的聚在同一类群。