我国6个地方绵羊品种微卫星DNA多态性研究

利用聚丙烯酰胺凝胶电泳技术研究了我国蒙古羊、乌珠穆沁羊、哈萨克羊、阿勒泰羊、滩羊和藏绵羊 6个地方绵羊品种 17个微卫星标记的多态性 ,以探讨其遗传多样性、起源分化及群体间的遗传亲缘关系。结果表明微卫星标记不同位点间遗传多样性差异极显著 (P <0 0 1) ,群体间多态信息含量 (PIC)、近交程度 (Fis)和观察杂合度 (Obs .Het)差异不显著 ,但基因多样性 (genediversity)和期望杂合度 (Exp .Het)差异显著 (P <0 0 5 )。所研究的我国 6个地方绵羊品种与欧洲品种具有相似的遗传多样性 ,但具有较高的近交系数。个体和群体的聚类分析结果提示我国地方绵羊品种可能起源于两类祖先。群体间的聚类分析结果还表明 ,蒙古羊与乌珠穆沁羊分化不明显且具有较近的遗传亲缘关系 ,蒙古羊与藏绵羊间分化明显且具有较远的遗传亲缘关系。滩羊、阿勒泰羊以及藏绵羊间也具有较近的遗传亲缘关系。所研究的我国 6个地方绵羊品种的遗传分化 (Fst)与西班牙绵羊品种接近 ,但明显小于欧洲其他绵羊品种     

应用微卫星标记分析23个中国地方马种的遗传多样性

为了调查中国马种的群体遗传分化与遗传结构状况, 本研究应用FAO和ISAG推荐的25对微卫星引物, 结合荧光标记PCR分析技术, 对中国23个马群体和1个英纯血马群体进行了分子遗传学研究。结果表明: 中国地方马群体的遗传多样性比较丰富, 23个中国马群体的等位基因数、多态信息含量和遗传杂合度等都高于英国纯血马。根据群体遗传距离构建的系统进化树, 能够清晰地将英纯血马从中国马中独立出来, 同时可将中国马群体分成不同的支, 基本上与其地理分布格局相符。我们用MVSP软件进行群体遗传分化分析可见, 前三个主成分的三维散点图可以明显地把英纯血马从所有群体中独立出来, 并把中国的马群体分成几个相对独立的支。进一步分析第一、二主成分的二维散点图, 可将中国的马群体分化成南方支系、藏马支系、新疆和青海支系、内蒙古支系及东北支系等5个部分。根据Structure软件分析, 推测中国马群体含有5个潜在的支系, 基本上代表了我国现在主要家马来源的基础遗传支系。这些信息可以为我国现有马种类型的划分与马种资源遗传多样性的保护提供科学依据。     

2个中国藏獒群体遗传多样性及遗传分化的研究

本研究以青海土种犬和藏狮犬为对照,采用RAPD技术对河曲藏獒和青海藏獒群体的遗传多样性及遗传分化进行了分析.研究结果表明,河曲藏獒和青海藏獒群体的多态性位点百分率分别为85.53%和98.16%,平均多态性位点百分率为91.85%.藏獒群体遗传变异分析显示两个藏獒群体的有效等位基因数(Ne)、Nei氏平均预期基因杂合度(H)和Shannon遗传信息指数(I)的平均值分别为1.5354、0.3191和0.4807;且两个藏獒群体93.09%的变异来自群体内,仅6.91%变异来自群体间;两个群体间的基因流为3.3679.研究还发现两个藏獒群体之间的Nei氏标准遗传距离(D)为0.050 5.本研究结果说明藏獒群体内遗传变异丰富,不同地域的藏獒群体之间存在广泛的基因交流,群体之间遗传分化程度很低,这为藏獒品种资源保护与合理开发利用提供了参考.     

利用分子标记分析遗传多样性时的玉米群体取样策略研究

利用分子标记技术对玉米种质资源进行遗传多样性分析对种质资源的保存和利用具有重要的指导意义。但是,在对地方品种和育种群体这些开放授粉群体进行大规模遗传多样性分析时,取样方法将会严重影响到研究结果和工作效率。本研究用2个育种群体和3个地方品种为试材,利用微卫星(SSR)标记对每个群体100个个体及其组成的不同随机混合样品进行了分子检测。结果表明,不同群体的群体内遗传变异大小存在差异;相同数目的个体随机混合的不同样品间的检测结果基本相同;不同数目的个体混合的样品间存在一定程度的差异,并且与材料本身的遗传变异大小有一定关系。考虑到结果的科学性和工作的可行性,建议在利用分子标记(如SSR)进行地方品种和育种群体的遗传多样性评估时,随机选取30个个体组成混合样(或用15个个体组成2个混合样)来代表1个地方品种或育种群体进行分子鉴定。     

中国地方黄牛的遗传多样性*

中国黄牛起源复杂,我国地方黄牛群体不同品种在毛色、形态外貌、细胞遗传学、血液蛋白座位分析均表现出多样性。计算我国黄牛群体6个毛色座位平均杂合度和6个血液蛋白座位平均杂合度分别为0.3144和0.4873,表明我国地方黄牛群体的遗传多样性非常丰富。计算我国黄牛群体的6个毛色座位和6个血液蛋白座位的基因分化系数分别为0.3404和0.095,表明我国黄牛群体毛色差异中有34.04％是由品种间的差异造成的。血液蛋白的多态性有9.5％是由品种间的差异造成的。我国黄牛群体的遗传多样性主要来自品种内的遗传多样性。保存我国黄牛品种资源多样性不仅要从整个中国黄牛群体上考虑,而且要针对每个品种（或类群）进行保种。     

甘蔗品种资源的表型遗传多样性

为了提高甘蔗品种资源的利用效率, 为甘蔗遗传育种亲本的选择、杂交组合配制及核心种质构建提供理论指导, 我们利用17个质量性状和5个数量性状分析了来自13个国家共20个地区的1,160份甘蔗品种资源的遗传变异、遗传结构和遗传距离等。结果表明: 5个数量性状在不同来源地品种群体之间的变异系数值(CV)变化较大, 说明不同来源地品种群体的数量遗传变异有较大差异, 其中来自海南的品种其群体遗传变异最丰富。质量性状的Shannon-Wiener多样性指数表明, 来自美国的品种群体遗传多样性最高, 其次为中国台湾, 第三为澳大利亚, 说明上述3个地区的甘蔗种质创新比较活跃, 在遗传育种中使用了更多表型性状多样化的亲本。不同来源地品种其群体的遗传分化系数(Gst)和基因流(Nm)显示甘蔗品种群体表型性状的遗传变异主要来自来源地内部, 且不同来源地品种群体之间存在较大的基因交流。遗传距离和UPGMA聚类分析结果表明, 各来源地品种群体之间遗传距离在0.0261–0.2945之间, 其中以福建和广东的品种最为相似, 其次为古巴和美国、广西和云南、澳大利亚和菲律宾、江西和四川、巴西和法国, 说明上述地区在杂交亲本的选择上比较相近。鉴于此, 在遗传育种中应加大利用具有丰富遗传多样性的品种材料并尽量避免选择同一组的品种相互杂交, 同时对于与其他来源地品种群体遗传距离较远的墨西哥品种群体在亲本选配时应给予更多关注。     

人工养殖与选育对罗氏沼虾遗传多样性的影响

为探讨人工养殖与选择育种对罗氏沼虾(Macrobrachium rosenbergii)遗传多样性的影响,实验测定了孟加拉野生群体、缅甸野生群体、浙江养殖群体、广西养殖群体及选育群体"南太湖2号"共111只罗氏沼虾核糖体转录间隔区2(Internal transcribed spacer 2,ITS2)基因序列,结果发现58个碱基变异位点,定义56个单倍型。在5个群体中,孟加拉野生群体的遗传多样性最高(平均核苷酸差异数K和核苷酸多态性指数Pi分别为7.186和0.0155),依次为缅甸野生群体、浙江养殖群体、广西养殖群体,选育群体"南太湖2号"遗传多样性最低(K和Pi分别为3.032和0.0065)。5个群体间配对Fst分析表明,养殖群体与野生群体遗传分化显著(P<0.01),选育群体"南太湖2号"不仅与野生群体遗传分化显著,同时还与广西养殖群体产生了显著的遗传分化(P<0.01)。系统树显示,孟加拉野生群体和缅甸野生群体聚为一支,浙江养殖群体、广西养殖群体和选育群体"南太湖2号"则聚为另一支。研究结果表明,人工养殖和选育降低了罗氏沼虾的遗传多样性水平,并导致群体间发生了显著的遗传分化。     

家牦牛线粒体DNA(mtDNA)遗传多样性及其分类

通过分析包括我国10个家牦牛品种(类群)在内共296个样本的mtDNA控制(D-loop)区部分序列的遗传变异,对我国家牦牛的遗传多样性、遗传分化、聚类关系和分类进行了研究.所测序列经比对后,共检测到61个变异位点,定义了77种单倍型.分析显示青海环湖牦牛的单倍型多样性最高,达0.9848±0.0403,而巴州牦牛单倍型多样性最低,为0.8000±0.0825;核苷酸多样性方面,斯布牦牛存在最为丰富的核苷酸序列变异,核苷酸多样性值为0.022582±0.011767,而巴州牦牛仅为0.006856±0.002476,表明我国家牦牛品种(类群)遗传多样性水平存在较大差异.总体上,我国家牦牛单倍型多样性、核苷酸多样性分别为0.9251±0.0095和0.015265±0.007757,呈现出丰富的遗传多样性.聚类分析显示我国家牦牛存在两个聚类簇--斯布牦牛独立为一类;其余9个品种(类群)聚为一类,表明家牦牛品种(类群)间遗传距离与地理分布无明显相关.分子变异分析(AMOVA)显示九龙、嘉黎、斯布牦牛构成的组与其余7个家牦牛品种(类群)构成的组之间存在极显著的遗传分化(?CT=0.05285,P<0.01),且其品种间/组内遗传分化不显著(?SC=0.00648,P>0.05),支持依据遗传分化程度将我国家牦牛划分为两大类型.AMOVA支持的分组在品种(类群)组成上与蔡立的研究结果相符,首次为我国家牦牛划分为横断高山型和青藏高原型两种类型提供了源自分子遗传学的证据.     

用RAPD技术研究9个家猪群体的遗传结构

目的：利用RAPD技术对9个家猪群体的遗传多样性进行分析,方法：采用RAPD技术对13/17罗伯逊易位纯合子猪易位杂合子猪及正常核型猪的三个群体,丹系长白猪群体,加系双肌臀杜洛克猪群体,加系双肌臀大约克猪群体,加系双肌臀长白猪群体及欧洲猪与易位杂合子猪产生的两个杂交后备猪群体的遗传多样性进行分析,并分别计算其共有带率F及遗传距离指数D,采用最小距离法绘制其树状聚类图。结果：19条引物的扩增结果产生多态性,共得到316条清晰稳定的多态型片段,片段长度在200-4000bp之间,由Nei的公式计算获得的遗传距离介于0.016-0.092之间,参照系统进化树可将9个品系划分为3个组群。结论：9个品系之间存在着明显的遗传差异,可作为进一步育种方案设计的依据。     

我国西南地区玉米地方品种遗传多样性的SSR分子标记分析

利用微卫星(SSR)标记技术和DNA混合取样方法,选取均匀覆盖玉米染色体组的42对SSR引物,检测了来自我国西南地区54个玉米地方品种的遗传多样性。在54个玉米地方品种中检测到256个等位基因,每个SSR标记的等位基因数为2～9个,平均6.1个,说明我国西南地区玉米地方品种遗传多样性丰富。根据遗传相似系数矩阵做出的树状图,将54个玉米地方品种大致划分成4类,来源于同一地区的多数玉米地方品种划分在同一类中,表明西南地区玉米地方品种的地理分布与其遗传背景存在内在联系。从54个玉米地方品种中选出11个,每个品种选取15个单株,共165个DNA单株样品,分析玉米地方品种的遗传结构及其品种内的遗传多样性。对于检测玉米地方品种的遗传多样性,DNA单株样品分析优于DNA混合样品分析,42对相同的SSR引物在11个玉米地方品种中检测到330个等位基因,平均等位基因数A=7.86,有效等位基因数Ae=3.90,平均期望杂合度He=0.69,实际观察杂合度H0=0.37。据遗传结构分析结果,固定指数(F)为0.25～0.79,表明玉米地方品种是典型的混合繁育系统;由于杂合体不足,玉米地方品种群体间及群体内的遗传结构均偏离了Hardy-Weinberg平衡;杂合性基因多样度比率(Fst)平均为0.07,表明品种间和品种内的遗传变异分别占总遗传变异的7%和93%。玉米地方品种内遗传多样性及品种间遗传距离分析结果表明,在我国西南地区,分布在四川的玉米地方品种具有最丰富的遗传变异。经综合分析推测,我国西南地区玉米地方品种最早引进到四川种植,由此向毗邻地区传播扩散。     

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H_E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.     

Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics

The horse was essential to past human societies but became a recreational animal during the twentieth century as the world became increasingly mechanized. As the author reviews here, recent studies of ancient genomes have revisited the understanding of horse domestication, from the very early stages to the most modern developments. They have uncovered several extinct lineages roaming the far ends of Eurasia some 4000 years ago. They have shown that the domestic horse has been significantly reshaped during the last millennium and experienced a sharp decline in genetic diversity within the last two centuries. At a time when no truly wild horses exist any longer, this calls for enhanced conservation in all endangered populations. These include the Przewalski's horse native to Mongolia, and the many local breeds side-lined by the modern agenda, but yet representing the living heritage of over five millennia of horse breeding.     

Genetic analysis of the Venezuelan Criollo horse

Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger of losing variation unless there is a large drop in population size.     

Farm‐by‐farm analysis of microsatellite,mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems – microsatellites, SNPs and mtDNA – were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (H_e = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm‐based practices and farm‐based breeding stocks can aid in the design of a sustainable breeding program for minority breeds.     

Phylogeography and Origin of Sheep Breeds in Northern China

With the establishment of modern sheep production systems in China, various forms of hybridization with Western breeds and between native breeds have been utilized for genetic improvement. At the same time, the progressive destruction or deterioration of sheep habitat has accompanied urbanization in China. Together these factors have accelerated the loss of genetic diversity, or even resulted in the extinction of some indigenous breeds. It is therefore important that efficient strategies for surveillance, evaluation, conservation and utilization of available genetic resources are developed for this species. In this study, a total of 30 microsatellite markers were used to assess genetic diversity for 12 native breeds and one Western sheep breed in Northern China. The high polymorphism information contents at the 30 markers, varying from averages of 0.519 to 0.666 for the 13 breeds, imply the retention of natural variation from source populations in the domestic breeds from different geographic regions in China. Analysis of genetic differentiation revealed substantial divergence among these breeds. Neutrality tests indicated that more than one third of the 30 loci were in departure from neutrality, implying that some evolutionary forces (e.g. selection and migration) had acted on these populations. Phylogenetic and phylogeographic analyses displayed a remarkable degree of consistency between geographic origins, breeding histories and the pattern of genetic differentiation.     

Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers

We compared the genetic diversity and distance among six German draught horse breeds to wild (Przewalski's Horse), primitive (Icelandic Horse, Sorraia Horse, Exmoor Pony) or riding horse breeds (Hanoverian Warmblood, Arabian) by means of genotypic information from 30 microsatellite loci. The draught horse breeds included the South German Coldblood, Rhenish German Draught Horse, Mecklenburg Coldblood, Saxon Thuringa Coldblood, Black Forest Horse and Schleswig Draught Horse. Despite large differences in population sizes, the average observed heterozygosity (H(o)) differed little among the heavy horse breeds (0.64-0.71), but was considerably lower than in the Hanoverian Warmblood or Icelandic Horse population. The mean number of alleles (N(A)) decreased more markedly with declining population sizes of German draught horse breeds (5.2-6.3) but did not reach the values of Hanoverian Warmblood (N(A) = 6.7). The coefficient of differentiation among the heavy horse breeds showed 11.6% of the diversity between the heavy horse breeds, as opposed to 21.2% between the other horse populations. The differentiation test revealed highly significant genetic differences among all draught horse breeds except the Mecklenburg and Saxon Thuringa Coldbloods. The Schleswig Draught Horse was the most distinct draught horse breed. In conclusion, the study demonstrated a clear distinction among the German draught horse breeds and even among breeds with a very short history of divergence like Rhenish German Draught Horse and its East German subpopulations Mecklenburg and Saxon Thuringa Coldblood.     

High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia

The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvac?k Pony, Malakan Horse, H?n?s Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia’s role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.     

Marker-assisted conservation of European cattle breeds: An evaluation

Two methods have been developed for the assessment of conservation priorities on the basis of molecular markers. According to the Weitzman approach, contributions to genetic diversity are derived from genetic distances between populations. Alternatively, diversity within and across populations is optimized by minimizing marker-estimated kinships. We have applied, for the first time, both methods to a comprehensive data set of 69 European cattle breeds, including all cosmopolitan breeds and several local breeds, for which genotypes of 30 microsatellite markers in 25–50 animals per breed have been obtained. Both methods were used to calculate the gain in diversity if a breed was added to a set of nine non-endangered breeds. Weitzman-derived diversities were confounded by genetic drift in isolated populations, which dominates the genetic distances but does not necessarily increase the conservation value of a breed. Marker-estimated kinships across populations were less disturbed by genetic drift than the Weitzman diversities and assigned high conservation values to Mediterranean breeds, which indeed have genetic histories that differ from the non-endangered breeds. Prospects and limitations of marker-assisted decisions on conservation priorities are discussed.     

Molecular Analysis Using Mitochondrial DNA and Microsatellites to Infer the Formation Process of Japanese Native Horse Populations

To assess the genetic diversity of Japanese native horse populations, we examined seven such populations using mitochondrial DNA (mtDNA) and microsatellite analyses. Four reference populations of Mongolian horses and European breeds were employed as other equids. In the mtDNA analysis, the control region (D-loop) of 411 bp was sequenced, and 12 haplotypes with 33 variable sites were identified in the Japanese native horses. The phylogenetic tree constructed by haplogrouping and using worldwide geographic references indicated that the haplotypes of the Japanese native horses were derived from six equid clusters. Compared with the foreign populations, the Japanese native populations showed lower within-population diversity and higher between-population differentiation. Microsatellite analysis, using 27 markers, found an average number of alleles per locus of 9.6 in 318 native and foreign horses. In most native populations, the within-population diversity was lower than that observed in foreign populations. The genetic distance matrix based on allelic frequency indicated that several native populations had notably high between-population differentiation. The molecular coancestry-based genetic distance matrix revealed that the European populations were differentiated from the Japanese and Mongolian populations, and no clear groups could be identified among the Japanese native horse populations. The genetic distance matrices had few correlations with the geographic distribution of the Japanese native populations. Based on the results of both mtDNA and microsatellite analyses, it could be speculated that each native population was formed by the founder populations derived from Mongolian horses. The genetic construction of each population appears to have been derived from independent breeding in each local area since the time of population fission, and this was accompanied by drastic genetic drift in recent times. This information will help to elucidate the ancestry of Japanese native horses. An erratum to this article can be found at     

European domestic horses originated in two holocene refugia

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.